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  • 151.
    Bonsdorff, Erik
    et al.
    Åbo Akademi University, Finland.
    Andersson, AgnetaUmeå University.Elmgren, RagnarStockholm University.Bidleman, TerryUmeå University.Blenckner, ThorstenStockholm University.Gorokhova, ElenaStockholm University.Legrand, CatherineLinnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.Wikner, JohanUmeå University.
    Special Issue: Baltic Sea ecosystem-based management under climate change2015Collection (editor) (Refereed)
  • 152.
    Borg, Olivia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Diversity of Avian Coronaviruses in Mallards Anas platyrhynchos, Ottenby, Sweden2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Coronavirus are single-stranded plus-strand RNA viruses that cause several respiratory and neurological diseases in a wide range of animals and humans. There are 4 main groups of Coronaviruses: alpha, beta, gamma and deltacoronavirus, where gamma and deltacoronaviruses have been found in wild birds. This study evaluated the epidemiology and phylogeny of coronavirus in Swedish waterfowl in order to increase the existing knowledge of these viruses in nature. The RNA-dependent RNA polymerase gene of 36 different samples from Mallards collected from Ottenby Bird Observatory, Sweden (56°12’58”N 16°24’40”E) in 2011 were sequenced. These sequences were characterized and compared to other gammacoronaviruses using a phylogenetic approach. Analysis revealed that there is diversity of sequences from the samples as there was evidence of at least 4 groups of RNA-dependent RNA-polymerase sequences. A difference of sequences over time was also detected which might suggest virus turnover due to host herd immunity. However, the results doesn´t demonstrate a clear pattern of reinfection with the same or different RNA-dependent RNA sequences within individuals over time. This study has contributed 1/3 of all gammacoronavirus sequences, and demonstrates the need in finding a method to complete genome sequence these viruses. Comparative genomic studies are important to determine the diversity of virus gene lineages and viral phenotypes, and also to be able to understand the relations behind interclass jumping, which is important to predict and avoid pandemics that coronavirus might cause.

  • 153.
    Borgström, Maja
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    De tre dimensionerna av hållbar utveckling -en kvalitativ studie av hur de tre dimensionerna av hållbar utveckling förekommer i elevernas uppfattningar av begreppet2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med denna studie är att ta reda på hur de tre dimensionerna av hållbar utveckling förekommer i elevernas uppfattningar av begreppet, samt vilka aspekter av dimensionerna som kan kopplas till elevernas uppfattningar. Studiens frågeställningar har undersökts med hjälp av kvalitativa intervjuer. Empiri har samlats in under fyra intervjuer av semistrukturerad karaktär med totalt tolv deltagande elever där resultatet sedan analyserats och kategoriserats för att förtydliga elevernas uppfattningar. Resultatet visar att samtliga dimensioner förekommer i elevernas uppfattningar, men att den ekologiska dimensionen är den dimension som eleverna tydligast kopplar till hållbar utveckling. De elevuppfattningar som förekommer i studiens resultat synliggör vilka dimensioner som bör belysas ytterligare för att elever ska ges möjligheten att skapa en korrekt uppfattning av begreppet och därmed kunna agera för att en hållbar utveckling ska vara möjlig.

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  • 154.
    Boström, Ullalena
    et al.
    Swedish University of Agricultural Sciences, Department of Crop Production Ecology.
    Andersson, Lars
    Swedish University of Agricultural Sciences, Department of Crop Production Ecology.
    Forkman, Johannes
    Swedish University of Agricultural Sciences, Department of Crop Production Ecology.
    Hakman, Inger
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Liew, Josefine
    Swedish University of Agricultural Sciences, Department of Crop Production Ecology.
    Magnuski, Ewa
    Swedish University of Agricultural Sciences, Department of Crop Production Ecology.
    Seasonal variation in sprouting capacity from intact rhizome systems of three perennial weeds.2013In: Weed research (Print), ISSN 0043-1737, E-ISSN 1365-3180, Vol. 53, no 5, p. 387-398Article in journal (Refereed)
    Abstract [en]

    The three rhizomatous perennials Elytrigia repens, Equisetum arvense and Tussilago farfara are all problematic in Scandinavian agriculture, due to their low susceptibility to soil cultivation. While repeated soil tillage is a fundamental part of the integrated control of these species, it is highly energy consuming and inefficient during periods when little sprout regrowth occurs. Substituting cultivation with mowing will reduce the environmental impact and labour costs, but its efficiency will still depend on the capacity of plants to sprout. Therefore, we studied the seasonal pattern in emergence and rhizome biomass allocation from July to April in six populations for each of the species. Plants were grown outdoors in pots buried in soil and exhumed at regular intervals in a two-year experiment. In all three species, biomass allocation to rhizomes continued until late in the autumn. Emergence was severely impaired in E.arvense and T.farfara in September-October, while in E.repens, there was no such reduction in the number of emerged shoots. However, in the latter species, the shoot/rhizome ratio decreased and remained low until the plants had been exposed to a period of low temperatures. The increase in shoot/rhizome ratio for E.repens coincided with the resumed capacity to emerge for E.arvense and T.farfara. These results imply that there is no need to repeat a defoliation of E.arvense and T.farfara, if carried out in September-October. However, removal of the aerial plant parts early in the autumn is important to interrupt the upload of storage compounds to the rhizome systems of all species.

  • 155.
    Braga, R.
    et al.
    Pontifícia Universidade Católica do Rio Grande do Sul, Brazil.
    Iglesias, Rodrigo S.
    Pontifícia Universidade Católica do Rio Grande do Sul, Brazil.
    Romio, Christiane
    Aarhus University, Denmark.
    Praeg, Daniel
    Pontifícia Universidade Católica do Rio Grande do Sul, Brazil;Géoazur, France.
    Miller, Dennis
    PETROBRAS, Brazil.
    Viana, Adriano
    PETROBRAS, Brazil.
    Ketzer, João Marcelo
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Modelling methane hydrate stability changes and gas release due to seasonal oscillations in bottom water temperatures on the Rio Grande cone, offshore southern Brazil2020In: Marine and Petroleum Geology, ISSN 0264-8172, E-ISSN 1873-4073, Vol. 112, p. 1-15, article id 104071Article in journal (Refereed)
    Abstract [en]

    The stability of methane hydrates on continental margins worldwide is sensitive to changes in temperature and pressure conditions. It has been shown how gradual increases in bottom water temperatures due to ocean warming over post-glacial timescales can destabilize shallow oceanic hydrate deposits, causing their dissociation and gas release into the ocean. However, bottom water temperatures (BWT) may also vary significantly over much shorter timescales, including due to seasonal temperature oscillations of the ocean bottom currents. In this study, we investigate how a shallow methane hydrate deposit responds to seasonal BWT oscillations with an amplitude of up to 1.5 °C. We use the TOUGH + HYDRATE code to model changes in the methane hydrate stability zone (MHSZ) using data from the Rio Grande Cone, in the South Atlantic Ocean off the Brazilian coast. In all the cases studied, BWT oscillations resulted in significant gaseous methane fluxes into the ocean for up to 10 years, followed by a short period of small fluxes of gaseous methane into the ocean, until they stopped completely. On the other hand, aqueous methane was released into the ocean during the 100 years simulated, for all the cases studied. During the temperature oscillations, the MHSZ recedes continuously both horizontally and, in a smaller scale, vertically, until a permanent and a seasonal region in MHSZ are defined. Sensitivity tests were carried out for parameters of porosity, thermal conductivity and initial hydrate saturation, which were shown to play an important role on the volume of methane released into the ocean and on the time interval in which such release occurs. Overall, the results indicate that in a system with no gas recharge from the bottom, seasonal temperature oscillations alone cannot account for long-term gas release into the ocean.

  • 156.
    Bragée, P.
    et al.
    Lund University.
    Mazier, F.
    Jean Jaures University, France.
    Nielsen, Anne Birgitte
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Rosén, P.
    Umeå University.
    Fredh, D.
    Lund University.
    Broström, A.
    Lund University.
    Granéli, W.
    Lund University.
    Hammarlund, D.
    Lund University.
    Historical TOC concentration minima during peak sulfur deposition in two Swedish lakes2015In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 12, no 2, p. 307-322Article in journal (Refereed)
    Abstract [en]

    Decadal-scale variations in total organic carbon (TOC) concentration in lake water since AD1200 in two small lakes in southern Sweden were reconstructed based on visible-near-infrared spectroscopy (VNIRS) of their recent sediment successions. In order to assess the impacts of local land-use changes, regional variations in sulfur, and nitrogen deposition and climate variations on the inferred changes in TOC concentration, the same sediment records were subjected to multi-proxy palaeolimnological analyses. Changes in lake-water pH were inferred from diatom analysis, whereas pollen-based land-use reconstructions (Landscape Reconstruction Algorithm) together with geochemical records provided information on catchment-scale environmental changes, and comparisons were made with available records of climate and population density. Our long-term reconstructions reveal that inferred lake-water TOC concentrations were generally high prior to AD1900, with additional variability coupled mainly to changes in forest cover and agricultural land-use intensity. The last century showed significant changes, and unusually low TOC concentrations were inferred at AD1930-1990, followed by a recent increase, largely consistent with monitoring data. Variations in sulfur emissions, with an increase in the early 1900s to a peak around AD1980 and a subsequent decrease, were identified as an important driver of these dynamics at both sites, while processes related to the introduction of modern forestry and recent increases in precipitation and temperature may have contributed, but the effects differed between the sites. The increase in lake-water TOC concentration from around AD1980 may therefore reflect a recovery process. Given that the effects of sulfur deposition now subside and that the recovery of lake-water TOC concentrations has reached pre-industrial levels, other forcing mechanisms related to land management and climate change may become the main drivers of TOC concentration changes in boreal lake waters in the future.

  • 157.
    Brandmaier, Stefan
    et al.
    German Research Center for Environmental Health, Germany.
    Peijnenburg, Willie
    National Institute for Public Health and the Environment - RIVM, The Netherlands ; Leiden University, The Netherlands.
    Durjava, Mojca K.
    National Institute of Health Environment and Food, Slovenia.
    Kolar, Boris
    National Institute of Health Environment and Food, Slovenia.
    Gramatica, Paola
    University of Insubria, Italy.
    Papa, Ester
    University of Insubria, Italy.
    Bhhatarai, Barun
    University of Insubria, Italy.
    Kovarich, Simona
    University of Insubria, Italy.
    Cassani, Stefano
    University of Insubria, Italy.
    Roy, Partha Pratim
    University of Insubria, Italy.
    Rahmberg, Magnus
    IVL Swedish Environmental Research Institute.
    Öberg, Tomas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jeliazkova, Nina
    Golsteijn, Laura
    Comber, Mike
    Charochkina, Larisa
    Novotarskyi, Sergii
    Sushko, Iurii
    Abdelaziz, Ahmed
    D’Onofrio, Elisa
    Kunwar, Prakash
    Ruggiu, Fiorella
    Tetko, Igor V.
    The QSPR-THESAURUS: The Online Platform of the CADASTER Project2014In: ATLA (Alternatives to Laboratory Animals), ISSN 0261-1929, Vol. 42, no 1, p. 13-24Article in journal (Refereed)
    Abstract [en]

    The aim of the CADASTER project (CAse Studies on the Development and Application of in Silico Techniques for Environmental Hazard and Risk Assessment) was to exemplify REACH-related hazard assessments for four classes of chemical compound, namely, polybrominated diphenylethers, per and polyfluorinated compounds, (benzo)triazoles, and musks and fragrances. The QSPR-THESAURUS website (http: / /qspr-thesaurus.eu) was established as the project's online platform to upload, store, apply, and also create, models within the project. We overview the main features of the website, such as model upload, experimental design and hazard assessment to support risk assessment, and integration with other web tools, all of which are essential parts of the QSPR-THESAURUS.

  • 158.
    Brindefalk, Bjorn
    et al.
    Stockholm University.
    Ekman, Martin
    Stockholm University.
    Ininbergs, Karolina
    Stockholm University.
    Dupont, Christopher L.
    J Craig Venter Inst, USA.
    Yooseph, Shibu
    J Craig Venter Inst, USA.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bergman, Birgitta
    Stockholm University.
    Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed)
    Abstract [en]

    Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.

  • 159. Brojer, Caroline
    et al.
    Jarhult, Josef D.
    Muradrasoli, Shaman
    Soderstrom, Hanna
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gavier-Widen, Dolores
    Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir2013In: Journal of Wildlife Diseases, ISSN 0090-3558, E-ISSN 1943-3700, Vol. 49, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    Low-pathogenic avian influenza (LPAI) viruses in wild birds are important as they can constitute the basis for the development of highly pathogenic avian influenza viruses or form part of human-adapted strains with pandemic potential. However, the pathogenesis of LPAI viruses is not well characterized in dabbling ducks, one of the natural reservoirs of LPAI viruses. Between 21 September 2009 and 21 December 2009, we used real-time reverse transcriptase polymerase chain reaction (q-PCR), histopathology, and immunohistochemistry (IHC) to study Mallards (Anas platyrhynchos) infected with an influenza A/H1N1 virus isolated from a wild Mallard in Sweden. The ducks were either inoculated intraesophageally ("artificial infection") or infected by virus shed by other ducks in the experiment ("contact infection"). The ducks were subjected to three low concentrations (80 ng/L, 1 mu g/L, and 80 mu g/L) of the active metabolite of oseltamivir (Tamiflu (R)), oseltamivir carboxylate (OC), which resulted in the development of the viral resistance mutation H274Y at 1 and 80 mu g/L. The LPAI virus infection was localized to the intestinal tract and cloacal bursa except in one Mallard. The exception was a duck euthanized 1 day postinoculation, whose infection was located solely in the lung, possibly due to intratracheal deposition of virus. The intestinal infection was characterized by occasional degenerating cells in the lamina propria and presence of viral antigen as detected by IHC, as well as positive q-PCR performed on samples from feces and intestinal contents. Histopathologic changes, IHC positivity, and viral shedding all indicated that the infection peaked early, around 2 days postinfection. Furthermore, more viral antigen and viral RNA were detected with IHC and q-PCR in the proximal parts early in the infection. There was no obvious difference in the course of the infection in artificial versus contact infection, when the level of OC was increased from 80 ng/L to 1 mu g/L (based on IHC and q-PCR), when the level of OC was increased to 80 mu/L, or when the resistance mutation H274Y developed (based on q-PCR).

  • 160.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ecology and evolution of coastal Baltic Sea 'dead zone' sediments2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since industrialization and the release of agricultural fertilizers began, coastal and open waters of the Baltic Sea have been loaded with nutrients. This has increased the growth of algal blooms and because a portion of the algal organic matter sinks to the sea floor, hypoxia has increased. In conjunction to this, natural stratification of the water column makes the bottom zones especially prone to oxygen depletion due to microbes using oxygen and organic matter to grow. Hypoxia (<2 mg/L O2) and anoxia (no oxygen) are deadly for many organisms and only specialists (typically some microorganisms) are able to survive. Due to the harsh conditions these bottom zones are commonly referred to as 'dead zones'. The focus of this thesis was to look closer at the microbial community changes upon degradation of algal organic matter and the effect of oxygenating coastal Baltic Sea 'dead zone' sediments on chemistry fluxes, phyto- and zooplankton, the microbial community structure, and microbial metabolic responses. Results from field sampling and incubation experiments showed that degradation of algal biomass in nutrient rich oxic sediment was partly related to the growth of archaea; that oxygenation of anoxic sediments decreased stored organic matter plus triggered hatching of zooplankton eggs increasing the benthic-pelagic coupling; and resting diatoms buried in hypoxic/anoxic sediment were alive and triggered to germinate by light rather than oxygen. Changes in the microbial community structures to oxygen shifts were dependent on the historical exposure to oxygen and that microbial generalists adapted to episodic oxygenation were favored during oxygen shifts. Facultative anaerobic sulfur/sulfide oxidizing bacterial genera were favored upon oxygenation of hypoxic/anoxic sediment plus sulfur cycling and nitrogen fixation genes were abundant. Finally, it was discovered that oxygenation regulates metabolic processes involved in the sulfur and methane cycles, especially by metabolic processes that results in a decrease of toxic hydrogen sulfide as well as the potent greenhouse gas methane. This thesis has explored how 'dead zones' change and develop during oxygen shifts and that re-oxygenation of ‘dead zones’ could bring favorable conditions in the sediment surface for reestablishment of new micro- and macroorganism communities.

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  • 161.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Abbtesaim, Jawad
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Copenhagen, Denmark.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sundkvist, Jan-Eric
    Boliden Mineral AB.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor2017In: Biodegradation, ISSN 0923-9820, E-ISSN 1572-9729, Vol. 28, no 4, p. 287-301Article in journal (Refereed)
    Abstract [en]

    Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH < 3) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8 °C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.

  • 162.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University, Sweden.
    Asmala, Eero
    Univ Helsinki, Finland.
    Carstensen, Jacob
    Aarhus Univ, Denmark.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-15, article id 2579Article in journal (Refereed)
    Abstract [en]

    Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

  • 163.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Brüsin, Martin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hylander, Samuel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Oxygenation of anoxic sediments triggers hatching of zooplankton eggs2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1817, article id 20152025Article in journal (Refereed)
    Abstract [en]

    Many coastal marine systems have extensive areas with anoxic sediments and it is not well known how these conditions affect the benthic-pelagic coupling. Zooplankton lay their eggs in the pelagic zone, and some sink and lie dormant in the sediment, before hatched zooplankton return to the water column. In this study, we investigated how oxygenation of long-term anoxic sediments affects the hatching frequency of dormant zooplankton eggs. Anoxic sediments from the brackish Baltic Sea were sampled and incubated for 26 days with constant aeration whereby, the sediment surface and the overlying water were turned oxic. Newly hatched rotifers and copepod nauplii (juveniles) were observed after 5 and 8 days, respectively. Approximately 1.5 × 105 nauplii per m-2 emerged from sediment turned oxic compared to 0.02 × 105 m-2 from controls maintained anoxic. This study demonstrated that re-oxygenation of anoxic sediments activated a large pool of buried zooplankton eggs, strengthening the benthic-pelagic coupling of the system. Modelling of the studied anoxic zone suggested that a substantial part of the pelagic copepod population can derive from hatching of dormant eggs. We suggest that this process should be included in future studies to understand population dynamics and carbon flows in marine pelagic systems.

  • 164.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Li, Lingni
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Fredrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Eutrophication induced early stage hypoxic ‘dead zone’ sediment releases nitrate and stimulates growth of archaeaManuscript (preprint) (Other academic)
    Abstract [en]

    In the Baltic Sea, two annual algal blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water column, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen, referred to as ‘dead zones’). These zones prevent the establishment of benthic communities and result in fish mortality. The aim of the study was to determine how the sediment chemistry and microbial community composition changed due to phytoplankton biomass degradation by adding cyanobacterial or diatom biomass to sediment cores from an all-year round oxic coastal Baltic Sea bay. After biomass addition, some typical anaerobic microbial processes were observed such as a decrease in NO2-+NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2-+NO3- was observed in the water phase in all incubations (including controls without addition of phytoplankton biomass). The combination of NO2-+NO3- diffusion from the sediment plus nitrification of the available NH4+ could not account for this increase. Potential nitrogen sources that could at least partially explain this discrepancy included microbial nitrogen fixation and cycling of nitrogen compounds from deeper layers of the sediment. Based on 16S rRNA gene sequences, the addition of diatom biomass caused minor changes in the relative abundance of microbial community members while cyanobacterial biomass caused a large increase in ferrous iron-oxidizing archaea. Considering that OTUs sharing lineages with acidophilic microorganisms were present, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling in oxic sediments and early microbial community changes in the sediment surface due to sinking phytoplankton before major hypoxia events occur. The release of nitrate into the water could potentially enhance algal blooms and facilitate the development of ‘dead zones’.

  • 165.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Li, Lingni
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Fredrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure2019In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 2, p. 288-303Article in journal (Refereed)
    Abstract [en]

    Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2 + NO3 in the sediment surface (0–1 cm) and iron in the underlying layer (1–2 cm). In addition, an increase in NO2 + NO3 was observed in the overlying benthic water in all amended and control incubations. The combination of NO2 + NO3 diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

  • 166.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sachpazidou, Varvara
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hylander, Samuel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1864, article id 20171617Article in journal (Refereed)
    Abstract [en]

    An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.

  • 167.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sachpazidou, Varvara
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 2453Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.

  • 168.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund university;Tech Univ Denmark, Denmark.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism2017In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, article id 96Article in journal (Refereed)
    Abstract [en]

    Background

    A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as ‘dead zones’. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.

    Results

    Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.

    Conclusions

    These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.

  • 169.
    Brussaard, Corina P. D.
    et al.
    NIOZ Royal Netherlands Institute of Sea Research, Netherlands;University of Utrecht, Netherlands.
    Bidle, Kay D.
    Rutgers University, USA.
    Pedrós-Alió, Carlos
    Institut de Ciències del Mar (CSIC), Spain.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    The interactive microbial ocean2017In: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, article id 16255Article in journal (Refereed)
    Abstract [en]

    Marine microorganisms inhabit diverse environments and interact over different spatial and temporal scales. To fully understand how these interactions shape genome structures, cellular responses, lifestyles, community ecology and biogeochemical cycles, integration of diverse approaches and data is essential.

  • 170.
    Bröms, Elena
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Orsaker till Vattenaloes (Stratiotes aloides L.) omfattande utbredning i Limsjön, Leksand, Dalarna2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This study concerns the distribution and ecology of the water plant water soldiers in the lake Limsjön located in the municipality of Leksand, Dalarna. Limsjön is part of Österdal river system located in the eastern part of the municipality. The area consists of a wetland and comprises about 95 hectares, of which 25 hectares are made up of the lake. It is an important bird lake, Natura-2000 and a recreation area. Since 2006, the lake is overgrowing due to the establishment of the floating aquatic macrophyte water soldiers (Stratiotes aloides L.). Stratiotes aloides L. has developed a dense vegetation mat with about 80 000 000 individuals (2017), which is currently occupying about 20 hectares of the wetland. If the spread continues, birds, aquatic organisms and indigenous vegetation of the area be threatened. This invasion, among other things, causes depletion of the very rare wreath algae Nitella syncarpa. In addition, phosphorus (P) stored in the wetland sediment will be released and flow into the Österdal river. The study indicates that the hydro-chemical conditions prevailing in Limsjön are extremely favorable for this species. Limsjön is an overgrowing, shallow, well heated, nutrient-rich lake with a slow water flow, clear slope in the catchment area and a long residence time. All these factors together with the admission of the drainage of surface water contributes to Limsjöns eutrophication and consequently the increase of the number of individuals of Stratiotes aloides L.

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  • 171.
    Brüsin, Martin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, P. Andreas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hylander, Samuel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Individual changes in zooplankton pigmentation in relation to ultraviolet radiation and predator cues2016In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 61, no 4, p. 1337-1344Article in journal (Refereed)
    Abstract [en]

    Copepods are common crustaceans in aquatic systems and one of the most important producers of carotenoidastaxanthin pigments, which can enhance the animals’ resistance against potentially damaging ultraviolet radiation (UVR), but at the same time, increases the risk of fish predation. Previous studies have demonstrated that copepods have different pigmentation levels matching the current threat level in terms of UVR and fish occurrence. However, these other studies have quantified population-levels changes in pigmentation, making it difficult to disentangle the role of individual phenotypic colour changes from that of selection.We quantified carotenoid-based pigmentation with colorimetric methods, which enabled us to track changes within individual copepods. Two species of copepods, Diaptomus castor and Eudiaptomus gracilis, were exposed to high and low UVR and fish cues in a factorial design. L*a*b* colour values (CIE; CommissionInternational de l’Eclairage) were extracted from digital photographs of each copepod and used as proxies for carotenoid concentration. Our results showed that individual copepods significantly changed their pigmentation in response to both UVR and fish cues within a period of 2 weeks. However, the responses differed between sexes and between adults and juveniles. UVR effects were present in all life-stages whereas fish effects were only detected in juveniles, with largest responses in D. castor. This confirms that carotenoid pigmentation is a phenotypically plastic trait, and highlights that strategies for trading off risks of UVR and predation differ between males and females as well as between life-stages.

  • 172.
    Buck, Brenda J.
    et al.
    Univ Nevada, USA.
    Londono, Sandra C.
    Arizona State Univ, USA.
    McLaurin, Brett T.
    Bloomsburg Univ Penn, USA.
    Metcalf, Rodney
    Univ Nevada, USA.
    Mouri, Hassina
    Univ Johannesburg, South Africa.
    Selinus, Olle
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shelembe, Refilwe
    Univ Johannesburg, South Africa.
    The emerging field of medical geology in brief: some examples2016In: Environmental Earth Sciences, ISSN 1866-6280, E-ISSN 1866-6299, Vol. 75, no 6, article id 449Article in journal (Refereed)
    Abstract [en]

    Emerging medical problems present medical practitioners with many difficult challenges. Emergent disciplines may offer the medical community new opportunities to address a range of these diseases. One such emerging discipline is medical geology, a science that is dealing with the influence of natural environmental factors on the geographical distribution of health in humans and animals. It involves the study of the processes and causes of diseases and also the use research findings to present solutions to health problems.

  • 173.
    Buetti-Dinh, Antoine
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Dethlefsen, Olga
    Stockholm University.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes2016In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 162, no 8, p. 1422-1434Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic microorganisms (optimum growth pH of ≤3) maintain a near neutral cytoplasmic pH via several homeostatic mechanisms, including an inside positive membrane potential created by potassium ions. Transcriptomic responses to pH stress in the thermoacidophilic archaeon, Sulfolobus acidocaldarius were investigated by growing cells without added sodium and/or potassium ions at both optimal and sub-optimal pH. Culturing the cells in the absence of added sodium or potassium ions resulted in a reduced growth rate compared to full-salt conditions as well as 43 and 75 significantly different RNA transcript ratios, respectively. Differentially expressed RNA transcripts during growth in the absence of added sodium ions included genes coding for permeases, a sodium/proline transporter and electron transport proteins. In contrast, culturing without added potassium ions resulted in higher RNA transcripts for similar genes as a lack of sodium ions plus genes related to spermidine that has a general role in response to stress and a decarboxylase that potentially consumes protons. The greatest RNA transcript response occurred when S. acidocaldarius cells were grown in the absence of potassium and/or sodium at a sub-optimal pH. These adaptations included those listed above plus osmoregulated glucans and mechanosensitive channels that have previously been shown to respond to osmotic stress. In addition, data analyses revealed two co-expressed IclR family transcriptional regulator genes with a previously unknown role in the S. acidocaldarius pH stress response. Our study provides additional evidence towards the importance of potassium in acidophile growth at acidic pH.

  • 174.
    Buetti-Dinh, Antoine
    et al.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Galli, Vanni
    University of Applied Sciences of Southern Switzerland, Switzerland.
    Bellenberg, Sören
    Universität Duisburg-Essen, Germany.
    Ilie, Olga
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Boretska, Mariia
    Universität Duisburg-Essen, Germany.
    Pivkin, Igor V.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Sand, Wolfgang
    Universität Duisburg-Essen, Germany;Donghua University, People's Republic of China;Mining Academy and Technical University Freiberg, Germany.
    Vera, Mario
    Pontificia Universidad Católica de Chile, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition2019In: Biotechnology Reports, ISSN 0156-1383, E-ISSN 2215-017X, Vol. 22, p. 1-5, article id e00321Article in journal (Refereed)
    Abstract [en]

    Background: Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases. Methods: The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles. Results: A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts. Conclusions: Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods. © 2019 The Author

  • 175.
    Buetti-Dinh, Antoine
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    El Hajjami, Mohamed
    QNLM, China.
    Delogu, Francesco
    Norwegian University of Life Sciences, Norway.
    Ilie, Olga
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Bellenberg, Sören
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Poetsch, Ansgar
    Ruhr University Bochum, Germany;QNLM, China;Ocean University of China, China.
    Sand, Wolfgang
    University Duisburg-Essen, Germany;Donghua University, China;3Mining Academy and Technical University Freiberg, Germany.
    Vera, Mario
    Pontificia Universidad Católica de Chile, Chile.
    Pivkin, Igor V.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations2020In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 21, no 1, p. 1-15, article id 23Article in journal (Refereed)
    Abstract [en]

    Background: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. Methods: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. Results: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. Conclusions: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.

  • 176.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bacterioplankton community associated with the Baltic Sea spring bloom2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Marine microbial communities are highly dynamic, respond to environmental drivers and change on spatial and temporal scales. In the Baltic Sea, recent surveys show that the salinity gradient structures bacterioplankton community composition. Yet, these surveys were conducted during summer when environmental conditions were relatively stable. The spring bloom is initiated by near-zero temperatures, depletes inorganic nutrients and is the major source of organic matter in the system. In this study, bacterioplankton dynamics, phytoplankton and environmental parameters were monitored during the transition of the spring bloom on transects across the Baltic Proper, from Finland to Germany. Using next generation amplicon sequencing of the 16S rRNA gene, we studied the bacterial community composition during the general transition of the plankton community from new to regenerated production. We show that on short temporal scales, the microbial community composition varies across large spatial scales. Gammaproteobacteria and Betaproteobacteria were highly abundant in the open Baltic Proper, and were strongly correlated to phosphate availability during early stages of the spring bloom. During the mature bloom stage, the bacterioplankton communities was highly similar along the entire transect, dominated by Bacteroidetes, Actinobacteria and Alphaproteobacteria. Compared to other surveys we found that salinity is not solely driving the Baltic Sea bacterioplankton community composition during spring bloom conditions. Thus, changes in nutrient availability, timing and transition of the bloom can act as selective forces, structuring microbial communities.

  • 177.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bacterioplankton in the light of seasonality and environmental drivers2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacterioplankton are keystone organisms in marine ecosystems. They are important for element cycles, by transforming dissolved organic carbon and other nutrients. Bacterioplankton community composition and productivity rates change in surface waters over spatial and temporal scales. Yet, many underlying biological processes determining when, why and how bacterioplankton react to changes in environmental conditions are poorly understood. Here, I used experiments with model bacteria and natural assemblages as well as field studies to determine molecular, physiological and ecological responses allowing marine bacteria to adapt to their environment.

    Experiments with the flavobacterium Dokdonia sp. MED134 aimed to determine how the metabolism of bacteria is influenced by light and different organic matter. Under light exposure, Dokdonia sp. MED134 expressed proteorhodopsin and adjusted its metabolism to use resources more efficiently when growing with lower-quality organic matter. Similar expression patterns were found in oceanic datasets, implying a global importance of photoheterotrophic metabolisms for the ecology of bacterioplankton.

    Further, I investigated how the composition and physiology of bacterial assemblages are affected by elevated CO2 concentrations and inorganic nutrients. In a large-scale experiment, bacterioplankton could keep productivity and community structure unaltered by adapting the gene expression under CO2 stress. To maintain pH homeostasis, bacteria induced higher expression of genes related to respiration, membrane transport and light acquisition under low-nutrient conditions. Under high-nutrient conditions with phytoplankton blooms, such regulatory mechanisms were not necessary. These findings indicate that open ocean systems are more vulnerable to ocean acidification than coastal waters.

    Lastly, I used field studies to resolve how bacterioplankton is influenced by environmental changes, and how this leads to seasonal succession of marine bacteria. Using high frequency sampling over three years, we uncovered notable variability both between and within years in several biological features that rapidly changed over short time scales. These included potential phytoplankton-bacteria linkages, substrate uptake rates, and shifts in bacterial community structure. Thus, high resolution time series can provide important insights into the mechanisms controlling microbial communities.

    Overall, this thesis highlights the advantages of combining molecular and traditional oceanographic methodological approaches to study ecosystems at high resolution for improving our understanding of the physiology and ecology of microbial communities and, ultimately, how they influence biogeochemical processes.

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  • 178.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sassenhagen, Ingrid
    Lund University.
    Sildever, Sirje
    Tallinn University of Technology, Estonia.
    Sjöqvist, Conny
    Marine Research Centre, Finland;Åbo Akademi University, Finland.
    Godhe, Anna
    University of Gothenburg.
    Gross, Susanna
    University of Gothenburg.
    Kremp, Anke
    Marine Research Centre, Finland.
    Lips, Inga
    Tallinn University of Technology, Estonia.
    Lundholm, Nina
    University of Copenhagen, Denmark.
    Rengefors, Karin
    Lund University.
    Sefbom, Josefin
    University of Gothenburg.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 517Article in journal (Refereed)
    Abstract [en]

    In temperate systems, phytoplankton spring blooms deplete inorganic nutrients and are major sources of organic matter for the microbial loop. In response to phytoplankton exudates and environmental factors, heterotrophic microbial communities are highly dynamic and change their abundance and composition both on spatial and temporal scales. Yet, most of our understanding about these processes comes from laboratory model organism studies, mesocosm experiments or single temporal transects. Spatial -temporal studies examining interactions of phytoplankton blooms and bacterioplankton community composition and function, though being highly informative, are scarce. In this study, pelagic microbial community dynamics (bacteria and phytoplankton) and environmental variables were monitored during a spring bloom across the Baltic Proper (two cruises between North Germany to Gulf of Finland). To test to what extent bacterioplankton community composition relates to the spring bloom, we used next generation amplicon sequencing of the 16S rRNA gene, phytoplankton diversity analysis based on microscopy counts and population genotyping of the dominating diatom Skeletonema rnarinoi. Several phytoplankton bloom related and environmental variables were identified to influence bacterial community composition. Members of Bacteroidetes and Alphaproteobacteria dominated the bacterial community composition but the bacterial groups showed no apparent correlation with direct bloom related variables. The less abundant bacterial phyla Actinobacteria, Planctomycetes, and Verrucomicrobia, on the other hand, were strongly associated with phytoplankton biomass, diatom:dinoflagellate ratio, and colored dissolved organic matter (cDOM). Many bacterial operational taxonomic units (OTUs) showed high niche specificities. For example, particular Bacteroidetes OTUs were associated with two distinct genetic clusters of S. marinoi. Our study revealed the complexity of interactions of bacterial taxa with inter- and intraspecific genetic variation in phytoplankton. Overall, our findings imply that biotic and abiotic factors during spring bloom influence bacterial community dynamics in a hierarchical manner.

  • 179.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Carl von Ossietzky Univ Oldenburg, Germany.
    Israelsson, Stina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Vienna, Austria.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridolfsson, Emil
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish Meteorological & Hydrological Institute.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Vigo, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 3296Article in journal (Refereed)
    Abstract [en]

    Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.

  • 180.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vila-Costa, Maria
    Centre d’Estudis Avançats de Blanes-CSIC, Spain.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Lovisa
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    González, José M.
    University of La Laguna, Spain.
    Calvo, Eva
    Institut de Ciències del Mar—CSIC, Spain.
    Pelejero, Carles
    Institut de Ciències del Mar—CSIC, Spain.
    Marrasé, Cèlia
    Institut de Ciències del Mar—CSIC, Spain.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gasol, Josep
    Institut de Ciències del Mar—CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Response of marine bacterioplankton pH homeostasis gene expression to elevated CO22016In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 6, no 5, p. 483-487Article in journal (Refereed)
    Abstract [en]

    Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes1; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled2, 3, 4, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l−1); however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l−1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

  • 181.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Israelsson, Stina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universidade de Vigo, Spain.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Muthusamy, Sarala Devi
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pontiller, Benjamin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Seasonality and co-occurrences of free-living Baltic Sea bacterioplanktonManuscript (preprint) (Other academic)
  • 182.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Marine bacterioplankton seasonal succession dynamics2017In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 25, no 6, p. 495-505Article in journal (Refereed)
    Abstract [en]

    Bacterioplankton (bacteria and archaea) are indispensable regulators of global element cycles owing to their unique ability to decompose and remineralize dissolved organic matter. These microorganisms in surface waters worldwide exhibit pronounced seasonal succession patterns, governed by physicochemical factors (e.g., light, climate, and nutrient loading) that are determined by latitude and distance to shore. Moreover, we emphasize that the effects of large-scale factors are modulated regionally, and over shorter timespans (days to weeks), by biological interactions including molecule exchanges, viral lysis, and grazing. Thus the interplay and scaling between factors ultimately determine the success of particular bacterial populations. Spatiotemporal surveys of bacterioplankton community composition provide the necessary frame for interpreting how the distinct metabolisms encoded in the genomes of different bacteria regulate biogeochemical cycles.

  • 183.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ferrans, Laura
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Krumins, Janis
    University of Latvia, Latvia.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klavins, Maris
    University of Latvia, Latvia.
    Fluorescence Spectroscopy – Applied Tool for Organic Matter Analysis2019In: Goldschmidt Abstracts, 2019, 2019Conference paper (Refereed)
    Abstract [en]

    Large applied projects in various sub-fields of environmental science studied and analyzed properties of organic matter. The “Life-Sure” is as continuation of started work for cost effective bottom sediments treatment where organic matter play important role of sorption of urban contaminants; “CONTRA” - beach wrack studies for advanced value-based bioeconomy development. Another project on Jurassic clay is interesting in discourse on Pleistocene glaciers glaciodynamics. Material from field was tested by 3D fluorescence excitation-emission matrix (EEM) providing “fingerprints” for a single compound or a mixture of fluorescent components. Thus humic macromolecules might be well seen nevertheless structural units have variable effects on the wavelength as well as intensity of fluorescence. It decreases with increasing molecular size of the humic macromolecule. For applied environmental projects this is well non-destructive tool to quantify the decomposition degree of organic matter requiring negligible amount of sample. This important method is valid for both organic matter and humic substances analytics. Chemical nature of humic substances can be correlated to structural information, e.g., functional groups, poly-condensation, aromaticity, dynamic properties related to intermolecular interactions. Acquired data from EEM provided significant input for scientific knowledge and innovation along with other analytical tools. 

  • 184.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Estonia university of life sciences, Estonia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vincevica-Gaile, Zane
    University of Latvia, Latvia.
    Kriipsalu, Mait
    Estonia university of life sciences, Estonia;University of Latvia, Latvia.
    Klavins, Maris
    University of Latvia, Latvia.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Setyobudi, Roy Hendroko
    university of Muhammadiyah Malang, Indonesia.
    Bikše, Jānis
    University of Latvia, Latvia.
    Rud, Vasiliy
    Russian Agricultural Academy, Russia.
    Tamm, Toomas
    Estonia university of life sciences, Estonia.
    Environmental Quality of Groundwater in Contaminated Areas—Challenges in Eastern Baltic Region2020In: Water Resources Quality and Management in Baltic Sea Countries / [ed] Abdelazim M. Negm, Martina Zelenáková & Katarzyna Kubiak-Wójcicka, Switzerland: Springer, 2020, p. 59-84Chapter in book (Refereed)
    Abstract [en]

    The lack of water in the future will force society to find more sophisticated solutions for treatment and improvement of groundwater wherever it comes from. Contamination of soil and groundwater is a legacy of modern society, prevention of contaminants spread and secondary water reuse options shall be considered. The aim of the book chapter is to give oversight view on problems and challenges linked to groundwater quality in Eastern Baltic region whilst through case studies explaining the practical problems with groundwater monitoring, remediation and overall environmental quality analysis. The reader will get introduced with case studies in industry levels as credibility of scientific fundamentals is higher when practical solutions are shown. Eastern Baltic countries experience cover contamination problems that are mainly of historic origin due to former Soviet military and industrial policy implementation through decades. Short summaries for each case study are given and main conclusions provided in form of recommendations at the very end of the chapter.

  • 185.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kriipsalu, Mait
    Estonian Univ Life Sci, Estonia.
    Vincevica-Gaile, Zane
    Univ Latvia, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Celma, Gunita
    Univ Latvia, Latvia.
    Ozola, Ruta
    Univ Latvia, Latvia.
    Rozina, Laine
    Univ Latvia, Latvia.
    Rudovica, Vita
    Univ Latvia, Latvia.
    Hogland, Marika
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Viksna, Arturs
    Univ Latvia, Latvia.
    Pehme, Kaur-Mikk
    Estonian Univ Life Sci, Estonia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klavins, Maris
    Univ Latvia, Latvia.
    On the way to 'zero waste' management: Recovery potential of elements, including rare earth elements, from fine fraction of waste2018In: Journal of Cleaner Production, ISSN 0959-6526, E-ISSN 1879-1786, Vol. 186, p. 81-90Article in journal (Refereed)
    Abstract [en]

    Existing schemes of solid waste handling have been improved implementing advanced systems for recovery and reuse of various materials. Nowadays, the 'zero waste' concept is becoming more topical through the reduction of disposed waste. Recovery of metals, nutrients and other materials that can be returned to the material cycles still remain as a challenge for future. Landfill mining (LFM) is one of the approaches that can deal with former dumpsites, and derived materials may become important for circular economy within the concept 'beyond the zero waste'. Perspectives of material recovery can include recycling of critical industrial metals, including rare earth elements (REEs). The LFM projects performed in the Baltic Region along with a conventional source separation of iron-scrap, plastics etc. have shown that the potential of fine-grained fractions (including clay and colloidal matter) of excavated waste have considerably large amounts of potentially valuable metals and distinct REEs. In this paper analytical screening studies are discussed extending the understanding of element content in fine fraction of waste derived from excavated, separated and screened waste in a perspective of circular economy. Technological feasibility was evaluated by using modified sequential extraction technique where easy extractable amount of metals can be estimated. Results revealed that considerable concentrations of Mn (418-823 mg/kg), Ni (41-84 mg/kg), Co (10.7-19.3 mg/kg) and Cd (1.0-3.0 mg/kg) were detected in fine fraction (<10 mm) of waste sampled from Hogbytorp landfill, while Cr (49-518 mg/kg) and Pb (30-264 mg/kg) were found in fine fraction (<10 mm) of waste from Torma landfill revealing wide heterogeneity of tested samples. Waste should become a utilizable resource closing the loop of anthropogenic material cycle as the hidden potential of valuable materials in dumps is considerable. (C) 2018 Elsevier Ltd. All rights reserved.

  • 186.
    Burlakovs, Juris
    et al.
    University of Latvia, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Orupold, Kaja
    Estonian University of Life Sciences, Estonia.
    Bhatnagar, Amit
    University of Eastern Finland, Finland.
    Gaile-Vincevica, Zane
    University of Latvia, Latvia.
    Rudovica, Vita
    University of Latvia, Latvia.
    Kriipsalu, Mait
    Estonian University of Life Sciences, Estonia.
    Hogland, Marika
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Stapkevica, Mara
    University of Latvia, Latvia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klavins, Maris
    University of Latvia, Latvia.
    Field-portable X-ray fluorescence spectrometry as rapid measurement tool for landfill mining operations: comparison of field data vs. laboratory analysis2015In: International Journal of Environmental Analytical Chemistry, ISSN 0306-7319, E-ISSN 1029-0397, Vol. 95, no 7, p. 609-617Article in journal (Refereed)
    Abstract [en]

    Landfill mining applied in reclamation at the territories of old dump sites and landfills is a known approach tended to global economic and environmental benefits as recovery of metals and energy is an important challenge. The aim of this study was to analyse the concentration of several metallic elements (Ca, Cu, Cr, Fe, K, Mn, Pb, Zn) in the fine fraction of waste derived in the landfill and to compare the results of measurements obtained by field-portable equipment with the data gained by advanced analytical tools. Atomic absorption spectrometry (AAS) and inductively coupled plasma mass spectrometry (ICP-MS) were used for the quantitative detection of metallic elements at the laboratory; whereas field-portable X-ray fluorescence spectrometry (FPXRF) was applied for rapid sample characterisation in the field (on-site). Wet digestion of samples (fine fraction of waste at landfill) was done prior analytical procedures at the laboratory conditions, but FPXRF analysis was performed using raw solid samples of waste fine fraction derived in the Kudjape Landfill in Estonia. Although the use of AAS and ICP-MS for the measurements of metals achieves more precise results, it was concluded that precision and accuracy of the measurements obtained by FPXRF is acceptable for fast approximate evaluation of quantities of metallic elements in fine fraction samples excavated from the waste at landfills. Precision and accuracy of the results provided by express method is acceptable for quick analysis or screening of the concentration of major and trace metallic elements in field projects; however, data correction can be applied by calculating moisture and organic matter content dependent on sample matrix as well as special attention must be paid on sample selection and homogenisation and number of analysed samples.

  • 187.
    Burlakovs, Juris
    et al.
    University of Latvia, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vincevica-Gaile, Zane
    University of Latvia, Latvia.
    Rudovica, Vita
    University of Latvia, Latvia.
    Orupold, Kaja
    Estonian University of Life Sciences, Estonia.
    Stapkevica, Mara
    University of Latvia, Latvia.
    Bhatnagar, Amit
    University of Eastern Finland, Finland.
    Kriipsalu, Mait
    Estonian University of Life Sciences, Estonia.
    Hogland, Marika
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klavins, Maris
    University of Latvia, Latvia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Mobility of Metals and Valorization of Sorted Fine Fraction of Waste After Landfill Excavation2016In: Waste and Biomass Valorization, ISSN 1877-2641, E-ISSN 1877-265X, Vol. 7, no 3, p. 593-602Article in journal (Refereed)
    Abstract [en]

    Reclamation of landfills and dumpsites requiresdetailed technical and economic evaluation of actual and potential pollution at the site, including detection of the main contaminants, their concentration, chemical stability and mobility in the environment. Contamination with metallic elements and metalloids is among the most important problems that limits recultivation of landfills and dumpsites and reuse of landfilled materials. This study was implemented at the Kudjape Municipal Landfill, located on Saaremaa Island in Estonia. The Kudjape Landfill is apartly closed landfill recultivated by covering it with a layer of a fine fraction of landfill material after the landfill mining operations. The fine fraction was derived at the site by sorting the landfill material (i.e., disposed waste) using mechanical screening, manual sorting and sieving. Obtained relatively homogeneous material, consisting of particles smaller than 10 mm, was defined as a fine fractionof waste. Samples from the fine fraction at different depth were collected and analyzed. Metal mobility was assessed after the sequential extraction. Results revealed that such elements as Zn, Mn, Mg are found in various fractions; Fe,Cd, Cr—mainly in residual fraction; Cu, Pb, Ni, Ba, Co and Rb mostly in fractions of residuals and reduced compounds,but they are presented in larger proportion of acid and water soluble fractions. Slight interconnection ofdetected parameters and sampling depth was revealed. Sequential extraction of elements in the fine fraction suggested the valorization of waste and confirmed that such landfill material can be successfully used as a landfill covering layer under the specific engineering circumstances.

  • 188.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Krievans, Maris
    University of Latvia, Latvia.
    Seglins, V.
    Berzins, K.
    Stiebrins, O.
    Dobele impact structure in latvia: Review of archived reports for future2018In: International Multidisciplinary Scientific GeoConference Surveying Geology and Mining Ecology Management, SGEM, International Multidisciplinary Scientific GeoConference & EXPO SGEM , 2018, no 1.1, p. 75-81Conference paper (Refereed)
    Abstract [en]

    Latvia is a State near Baltic Sea formerly included in Soviet Union that hardly classified all types of cartographical and geological information making it not available for scientific evaluation. Geological mapping data, deep boreholes with cores available from various depth up to crystalline basement (>1km), intersections and seismic data from 60-ties indicate the existence of an enigmatic structure similar to structural forms called astroblemes; it is located south of the town of Dobele in Latvia N56°35’ E23°15’. The structure at the beginning was suspected as kimberlitic pipe; however, gravimetric and magnetometer data did not approve these suspicions. The impact crater formed in between Late Triassic and Early Quaternary time; the age is not known precisely and one of versions of evolution of structure is possible explosion of a meteorite 2-5 km high above the land. Hydrogeological and geochemical data is contradictory to structural evidence therefore, a new survey including modern geophysical methods is highly recommended. The aim of this paper is reviewing of archived classified data from expedition reports of geological mapping events never published before and emphasize the need to recover hidden data about the formation of Dobele impact structure according to available research data and recommend future research approaches to shed light on unclear questions. The field geological mapping expedition was in charge during whole study of Dobele structure. The most devoted person to find the answers of development of the Dobele structure was Mr. Atis Murnieks, who left this world in summer 2017. © SGEM2018.

  • 189.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Latvia, Latvia.
    Kriipsalu, M.
    Estonian University of Life Sciences, Estonia.
    Arina, D.
    Latvia University of Agriculture, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shmarin, S.
    Kyiv National University, Ukraine.
    Denafas, G.
    Kaunas University of Technology, Lithuania.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Former dump sites and the landfill mining perspectives in baltic countries and Sweden: The status2013In: SGEM2013 Conference Proceedings, 2013, p. 485-492Conference paper (Refereed)
    Abstract [en]

    Landfills are considered as places where the life cycle of products ends thus meaning that resources and materials, which before were valuables, become useless and are disposed forever in places away from the sight. Landfills that were not closed appropriately are of primary importance as the EU legislation demands closure of noncompliant landfills, re-cultivation followed by soil and groundwater remediation. Waste dumps in former times were created without any environmental planning and it causes problems. Planned actions to reduce and prevent impacts to the environment and get extracted valuables from dump sites are proposed in a new approach known as "landfill mining" (LFM). The number of dumpsites which are still not appropriately closed according to the EU Directives has diminished, but not completely. Landfills that are located close to the Baltic Sea and Black Seas could be good candidates for LFM. This research topic has had evolved in many aspects with the interest increase on material recovery, refuse derived fuels (RDF) production, greenhouse gas and leachate emission diminishing. Real-time applied LFM in last decade in Sweden has started and Estonian scientists and entrepreneurs took over the initiative - the project in Saaremaa Island is an example of closing the life cycle of dumpsites by following a more sustainable approach. The rise of raw material and energy costs promotes the process of LFM to be economically feasible, but this approach must be adjusted in regulations (permittingprohibiting schemes, environmental impact assessment, staff safety, monitoring).

  • 190.
    Burlakovs, Juris
    et al.
    University of Latvia, Latvia.
    Kriipsalu, Mait
    Estonian University of Life Sciences, Estonia.
    Arina, Dace
    Institute of Physical Energetics, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ozola, Ruta
    University of Latvia, Latvia.
    Denafas, Gintaras
    Kaunas University of Technology, Lithuania.
    Hogland, Marika
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Mykhaylenko, Valeriy
    Taras Shevchenko National University of Kyiv, Ukraine.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Orupold, Kaja
    Estonian University of Life Sciences, Estonia.
    Turkadze, Tsitsino
    A. Tsereteli State University, Georgia.
    Daugelaite, Valdone
    Kaunas University of Technology, Lithuania.
    Bucinskas, Algimantas
    Kaunas University of Technology, Lithuania.
    Rudovica, Vita
    University of Latvia, Latvia.
    Horttanainen, Mika
    Lappeenranta University of Technology, Finland.
    Klavins, Maris
    University of Latvia, Latvia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Metals and rare Earth’s elements in landfills: case studies2016In: 3rd Int. Symposium on Enhanced Landfill Mining, Lisboa, 8-10/2/2016, 2016Conference paper (Refereed)
    Abstract [en]

    Landfills are considered as places where the life cycle of products ends and materialshave been “disposed forever”. The landfill mining (LFM) approach can deal with formerdumpsites and this material may become important for circular economy perspectiveswithin the concept “Beyond the zero waste”. Potential material recovery should includeperspectives of recycling of critical industrial metals where rare Earth elements (REEs)are playing more and more important role. Real-time applied LFM projects in the BalticRegion have shown the potential of fine-grained fractions (including clay and colloidalmatter) of excavated waste as storage of considerably large amounts of valuable metalsand REEs. Analytical screening studies have extended a bit further the understanding offine fraction contents of excavated, separated and screened waste in a circular economyperspective. The Swedish Institute and Latvian Research Program “Res Prod” supportedthe research.

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  • 191.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Latvia, Latvia.
    Kriipsalu, Mait
    Estonian Univ Life Sci, Estonia.
    Klavins, Maris
    Univ Latvia, Latvia.
    Bhatnagar, Amit
    Univ Eastern Finland, Finland.
    Vincevica-Gaile, Zane
    Univ Latvia, Latvia.
    Stenis, Jan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Mykhaylenko, Valeriy
    Taras Shevchenko Natl Univ Kyiv, Ukraine.
    Denafas, Gintaras
    Fac Chem Technol, Lithuania.
    Turkadze, Tsitsino
    Akaki Tsereteli State Univ, Republic of Georgia.
    Hogland, Marika
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Rudovica, Vita
    Univ Latvia, Latvia.
    Kaczala, Fabio
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Rosendal, Rene Moller
    Danish Waste Solut ApS, Denmark.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Paradigms on landfill mining: From dump site scavenging to ecosystem services revitalization2017In: Resources, Conservation and Recycling, ISSN 0921-3449, E-ISSN 1879-0658, Vol. 123, p. 73-84Article in journal (Refereed)
    Abstract [en]

    For the next century to come, one of the biggest challenges is to provide the mankind with relevant and sufficient resources. Recovery of secondary resources plays a significant role. Industrial processes developed to regain minerals for commodity production in a circular economy become ever more important in the European Union and worldwide. Landfill mining (LFM) constitutes an important technological toolset of processes that regain resources and redistribute them with an accompanying reduction of hazardous influence of environmental contamination and other threats for human health hidden in former dump sites and landfills. This review paper is devoted to LFM problems, historical development and driving paradigms of LFM from 'classical hunting for valuables' to 'perspective in ecosystem revitalization'. The main goal is to provide a description of historical experience and link it to more advanced concept of a circular economy. The challenge is to adapt the existing knowledge to make decisions in accordance with both, economic feasibility and ecosystems revitalization aspects. (C) 2016 Elsevier B.V. All rights reserved.

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  • 192.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kriipsalu, Mait
    Estonian Univ Life Sci, Estonia.
    Porshnov, Dmitry
    Univ Latvia, Latvia.
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ozols, Viesturs
    Univ Latvia, Latvia.
    Pehme, Kaur-Mikk
    Estonian Univ Life Sci, Estonia.
    Rudovica, Vita
    Univ Latvia, Latvia.
    Grinfelde, Inga
    Latvia Univ Life Sci & Technol, Latvia.
    Pilecka, Jovita
    Latvia Univ Life Sci & Technol, Latvia.
    Vincevica-Gaile, Zane
    Univ Latvia, Latvia.
    Turkadze, Tsitsino
    Akaki Tsereteli State Univ, Georgia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klavins, Maris
    Univ Latvia, Latvia.
    Gateway of Landfilled Plastic Waste Towards Circular Economy in Europe2019In: Separations, E-ISSN 2297-8739, Vol. 6, no 2, p. 1-8, article id 25Article in journal (Refereed)
    Abstract [en]

    For decades, significant work has been conducted regarding plastic waste by dealing with rejected materials in waste masses through their accumulation, sorting and recycling. Important political and technical challenges are involved, especially with respect to landfilled waste. Plastic is popular and, notwithstanding decrease policies, it will remain a material widely used in most economic sectors. However, questions of plastic waste recycling in the contemporary world cannot be solved without knowing the material, which can be achieved by careful sampling, analysis and quantification. Plastic is heterogeneous, but usually all plastic waste is jointly handled for recycling and incineration. Separation before processing waste through the analytical approach must be applied. Modern landfill mining and site clean-up projects in contemporary waste management systems require comprehensive material studies ranging from the macro-characterization of waste masses to a more detailed analysis of hazardous constituents and properties from an energy calorific standpoint-where, among other methods, thermogravimetric research coupled with life cycle assessment (LCA) and economic assessment is highly welcomed.

  • 193.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pehme, Kaur-Mikk
    Estonian Univ Life Sci, Estonia.
    Anne, O.
    Kriipsalu, Mait
    Estonian Univ Life Sci, Estonia.
    Hogland, William
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Remarks on novel case studies for integrated pollution prevention in the baltic sea region2018In: International Multidisciplinary Scientific GeoConference Surveying Geology and Mining Ecology Management, SGEM, International Multidisciplinary Scientific GeoConference & EXPO SGEM , 2018, no 3.2, p. 1167-1174Conference paper (Refereed)
    Abstract [en]

    The Baltic Sea is suffering from extended surplus of phosphorus, nitrogen and other pollutants. It causes diminishing biodiversity and increased eutrophication (mainly due to nitrogen and phosphorous in various substances). The common effort in the region is environmental standpoint in sustainable circular economy. Oil pollutants, heavy metals, organic substances are being released to the Baltic Sea and consequences for maritime environment are serious. However, Baltic Sea Region is one of the most innovative regions in the world considering environmental technology development. The interregional potential is about to solve the above mentioned challenges there were developed the project “Reviving Baltic Resilience (RBR)”. By using prior experiences in other EU projects as well as continuously working and acquiring new data and knowledge, our aim is to test at proactive methods/technologies for preventing pollution reaching the maritime environment and entering biological chains. The paper focuses on three novel case studies: 1) pollution prevention through phytoremediation at landfill close to the sea; 2) studies on sludge deposits with focus on recovery potential; 3) prevention of release of pollutants from sediments in bays and lagoons. This project was supported by Interreg South Baltic program “Reviving Baltic Resilience” (RBR) and Swedish Institute “PECEC”. © SGEM 2018.

  • 194.
    Burlakovs, Juris
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Purmalis, Oskars
    Krievāns, Māris
    Jani, Yahya
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ground-penetrating Radar (GPR) Geoenvironmental Screening in Lakes of Latvia - Challenges and Outcomes2016Conference paper (Refereed)
    Abstract [en]

    Geophysical studies in mapping and geoenvironmental applications for screening purposes are widely applied in Latvia. Ground-penetrating radar (GPR) as the one method from geophysical toolbox is a non-invasive and non-destructive way where pulsed electromagnetic signal is recorded as scattering from subsurface objects. Aim of two described screening studies was to analyse potential advantages of GPR use for mapping bottom sediments and topography in two lakes and pinpoint challenges to overcome during works. Both lakes are relatively deep and of sub-glacial origin that became lakes after the ice retreat from Baltic region. Characterization of bottom sediments as well as full core description of upper limnic layers for comparison with GPR signals were performed. Major results show that GPR, coring and laboratory analysis can be used simultaneously, however, ground penetration radar sometimes fails to recognize full picture needed for geoenvironmental application needs. Proper treatment of data nevertheless diminish the necessity of dense coring in lakes when budgets are strict.

  • 195.
    Camargo, Samia M.
    et al.
    Universidade Estadual Paulista, Brazil ; Universidade Federal de São Paulo, Brazil.
    Coelho, Rui
    Instituto Português do Mar e da Atmosfera, Portugal ; Universidade Algarve, Portugal.
    Chapman, Demian
    Stony Brook University, USA.
    Howey-Jordan, Lucy
    Microwave Telemetry, Inc., USA.
    Brooks, Edward J.
    Cape Eleuthera Institute, Bahamas.
    Fernando, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. The Manta Trust, UK ; Blue Resources, Sri Lanka.
    Mendes, Natalia J.
    Universidade Estadual Paulista, Brazil.
    Hazin, Fabio H. V.
    Universidade Federal Rural de Pernambuco, Brazil.
    Oliveira, Claudio
    Universidade Estadual Paulista, Brazil.
    Santos, Miguel N.
    Instituto Português do Mar e da Atmosfera, Portugal.
    Foresti, Fausto
    Universidade Estadual Paulista, Brazil.
    Mendonca, Fernando F.
    Universidade Federal de São Paulo, Brazil.
    Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, article id e0155623Article in journal (Refereed)
    Abstract [en]

    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (pi) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (phi(ST) = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  • 196.
    Cao, Xianyong
    et al.
    Helmholtz Ctr Polar & Marine Res, Germany;Chinese Acad Sci, Peoples Republic of China.
    Tian, Fang
    Helmholtz Ctr Polar & Marine Res, Germany.
    Li, Furong
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gaillard, Marie-José
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Rudaya, Natalia
    Helmholtz Ctr Polar & Marine Res, Germany;Russian Acad Sci, Russia;Univ Potsdam, Germany.
    Xu, Qinghai
    Hebei Normal Univ, Peoples Republic of China.
    Herzschuh, Ulrike
    Helmholtz Ctr Polar & Marine Res, Germany;Univ Potsdam, Germany.
    Pollen-based quantitative land-cover reconstruction for northern Asia covering the last 40 ka cal BP2019In: Climate of the Past, ISSN 1814-9324, E-ISSN 1814-9332, Vol. 15, no 4, p. 1503-1536Article in journal (Refereed)
    Abstract [en]

    We collected the available relative pollen productivity estimates (PPEs) for 27 major pollen taxa from Eurasia and applied them to estimate plant abundances during the last 40 ka cal BP (calibrated thousand years before present) using pollen counts from 203 fossil pollen records in northern Asia (north of 40 degrees N). These pollen records were organized into 42 site groups and regional mean plant abundances calculated using the REVEALS (Regional Estimates of Vegetation Abundance from Large Sites) model. Time-series clustering, constrained hierarchical clustering, and detrended canonical correspondence analysis were performed to investigate the regional pattern, time, and strength of vegetation changes, respectively. Reconstructed regional plant functional type (PFT) components for each site group are generally consistent with modern vegetation in that vegetation changes within the regions are characterized by minor changes in the abundance of PFTs rather than by an increase in new PFTs, particularly during the Holocene. We argue that pollen-based REVEALS estimates of plant abundances should be a more reliable reflection of the vegetation as pollen may overestimate the turnover, particularly when a high pollen producer invades areas dominated by low pollen producers. Comparisons with vegetation-independent climate records show that climate change is the primary factor driving land-cover changes at broad spatial and temporal scales. Vegetation changes in certain regions or periods, however, could not be explained by direct climate change, e.g. inland Siberia, where a sharp increase in evergreen conifer tree abundance occurred at ca. 7-8 ka cal BP despite an unchanging climate, potentially reflecting their response to complex climate-permafrost-fire-vegetation interactions and thus a possible long-term lagged climate response.

  • 197.
    Carlbrand, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    The bacterium Candidatus Neoehrlichia mikurensis in ticks from humans2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The bacterium Candidatus Neoehrlichia mikurensis (CNM) is a novel human pathogen that was first discovered on the island of Mikura, Japan, in 2004. In the year 2007 a man in Sweden who had received chemotherapy due to chronic lymphocytic leukemia suffered from a severe infection. After analyzing blood samples from the man it was determined that the infection was due to CNM. This was the first documented human case of CNM infection. Unlike many other bacteria, CNM is not yet possible to cultivate and therefore is hard to detect. Methods used to detect the bacterium are screening for specific gene fragments by PCR and further phylogenetic studies where the DNA-sequences are compared to known documented sequences. Due to the difficulties with detection it is not known if CNM been among us for a long time or if it is just starting to establish. In this study DNA from ticks biting humans was analyzed for the presence of CNM. Ticks were handed in from bitten people to health care centers in Southern Sweden and Åland as part of a large science-project called the STING-study. Out of 836 ticks screened, 68 (8%) were positive for CNM. Looking at the distribution of the ticks in different life stages it was clear that none of the ticks positive for CNM were larvae. This indicates that the bacterium only transmits through blood-meals and that no transovarial transmission occurs. 

  • 198.
    Carlsson, Bo
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Meir, Michaela
    Aventa AS, Norway.
    Rekstad, John
    Aventa AS, Norway.
    Preiss, Dieter
    AEE-INTEC, Austria.
    Ramschak, Thomas
    AEE-INTEC, Austria.
    Replacing traditional materials with polymeric materials in solar thermosiphon systems: Case study on pros and cons based on a total cost accounting approach2016In: Solar Energy, ISSN 0038-092X, E-ISSN 1471-1257, Vol. 125, p. 294-306Article in journal (Refereed)
    Abstract [en]

    The pros and cons of replacing traditional materials with polymeric materials in solar thermosiphon systems were analysed by adopting a total cost accounting approach.

    In terms of climatic and environmental performance, polymeric materials reveal better key figures than traditional ones like metals. In terms of present value total cost of energy, taking into account functional capability, end user investment cost, O&M cost, reliability and climatic cost, the results suggest that this may also be true when comparing a polymeric based thermosiphon system with a high efficient thermosiphon system of conventional materials for DHW production in the southern Europe regions. When present values for total energy cost are assessed for the total DHW systems including both the solar heating system and the auxiliary electric heating system, the difference in energy cost between the polymeric and the traditional systems is markedly reduced.

    The main reason for the difference in results can be related to the difference in thermal performance between the two systems. It can be concluded that the choice of auxiliary heating source is of utmost importance for the economical competiveness of systems and that electric heating may not be the best choice.

  • 199.
    Carlsson, Bo
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Persson, Helena
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Meir, Michaela
    Aventa AS, Norway.
    Rekstad, John
    University of Oslo, Norway.
    A total cost perspective on use of polymeric materials in solar collectors - Importance of environmental performance on suitability2014In: Applied Energy, ISSN 0306-2619, E-ISSN 1872-9118, Vol. 125, p. 10-20Article in journal (Refereed)
    Abstract [en]

    To assess the suitability of solar collector systems in which polymeric materials are used versus those in which more traditional materials are used, a case study was undertaken. In this case study a solar heating system with polymeric solar collectors was compared with two equivalent but more traditional solar heating systems: one with flat plate solar collectors and one with evacuated tube solar collectors. To make the comparison, a total cost accounting approach was adopted. The life cycle assessment (LCA) results clearly indicated that the polymeric solar collector system is the best as regards climatic and environmental performance when they are expressed in terms of the IPPC 100 a indicator and the Ecoindicator99, H/A indicator, respectively. In terms of climatic and environmental costs per amount of solar heat collected, the differences between the three kinds of collector systems were small when compared with existing energy prices. With the present tax rates, it seems unlikely that the differences in environmental and climatic costs will have any significant influence on which system is the most favoured, from a total cost point of view. In the choice between a renewable heat source and a heat source based on the use of a fossil fuel, the conclusion was that for climatic performance to be an important economic factor, the tax or trade rate of carbon dioxide emissions must be increased significantly, given the initial EU carbon dioxide emission trade rate. The rate would need to be at least of the same order of magnitude as the general carbon dioxide emission tax rate used in Sweden. If environmental costs took into account not only the greenhouse effect but also other mechanisms for damaging the environment as, for example, the environmental impact factor Ecoindicator99 does, the viability of solar heating versus that of a natural gas heating system would be much higher.

  • 200.
    Carlsson, Sara
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hållbar dagvattenhantering - En fallstudie i Nyköping2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In urban areas stormwater have become a problem due to limited infiltration. Impermeable surfaces such as asphalt covers and buildings cause changes in the flow of water and content of contaminating products, which normally are not processed by sewage treatment works. Instead, the stormwater often drained off to an adjacent watercourse which end in a lake or the sea, in order to limit inundation of streets and cellars in houses. Using vegetated recipients, such as wetlands, tree plantations, grass and herbcovered surfaces is anefficient and economical way to manage stormwaterinflow, which also improves the infiltration and the biodiversity in the area. Green ceilings reduce the formation of stormwater, especially designed ditches are efficient storage at extreme rainfalls and slow down the drainage

     

    In this study, a few different natural retaining and equalisation methods are evaluated and  proposed for the design of an industrial area in Nyköping municipality which is planned to be a residential area. Challenges for the introduction of various natural water systems are that they need land space and relate to the existing buildings and at the same time get a sufficient drainage. Much of the report is based on the requirement in the area of Södermanland county, but also presents expected precipitation rates for the entire country that are essential for optimal water treatment

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