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  • 1.
    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.

  • 2.
    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.

  • 3.
    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.

  • 4.
    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’.

  • 5.
    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.

  • 6.
    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.

  • 7.
    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.

  • 8.
    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.

  • 9.
    Koehler, Birgit
    et al.
    Uppsala University.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Tranvik, Lars J.
    Uppsala University.
    Apparent quantum yield of photochemical dissolvedorganic carbon mineralization in lakes2016In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 61, no 6, p. 2207-2221Article in journal (Refereed)
    Abstract [en]

    Up to one tenth of the carbon dioxide (CO2) emissions from inland waters worldwide are directly inducedby the photochemical mineralization of dissolved organic matter (DOM). The photochemical production ofdissolved inorganic carbon (DIC) per photon absorbed by chromophoric DOM (CDOM) decreases exponentiallywith increasing irradiance wavelength, and is commonly described by an “apparent quantum yield”(AQY) spectrum. Although an essential model parameter to simulate photochemical mineralization the AQYremains poorly constrained. Here, the AQY of photochemical DIC production for 25 lakes located in boreal,polar, temperate, and tropical areas, including four saline lagoons, was measured. The wavelength-integratedAQY (300–500 nm; mol DIC mol CDOM-absorbed photons21) ranged from 0.05 in an Antarctic lake to 0.61in a humic boreal lake, averaging 0.2460.03 SE. AQY was positively linearly correlated with the absorptioncoefficient at 420 nm (a420) as a proxy for CDOM content (R2 of 0.64 at 300 nm and 0.26 at 400 nm), withspecific UV absorption coefficients as a proxy for DOM aromaticity (R2 of 0.56 at 300 nm and 0.38 at400 nm), and with the humification index (R2 of 0.41 at 300 nm and 0.42 at 400 nm). Hence, a considerablefraction of the AQY variability was explained by water optical properties in inland waters. The correlation ofAQY with a420 opens up the possibility to improve large-scale model estimates of sunlight-induced CO2 emissionsfrom inland waters based on water color information derived by satellite remote sensing.

  • 10.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University, Sweden.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish University of Agricultural Sciences, Sweden.
    Bertilsson, Stefan
    Uppsala University, Sweden;Swedish University of Agricultural Sciences, Sweden.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, p. 1-6, article id e01470-19Article in journal (Refereed)
    Abstract [en]

    Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H-2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omits studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

  • 11.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    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. Univ Copenhagen, Denmark.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling2018In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 94, no 8, article id fiy121Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.

  • 12.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Canizales, Sebastian
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Palwai, Viraja R.
    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.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Sleutels, Tom
    Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2308Article in journal (Refereed)
    Abstract [en]

    Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the 'cyanate' degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.

  • 13.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish University of Agricultural Sciences.
    Palma, Daniela
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    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.
    A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, article id 2945Article in journal (Refereed)
    Abstract [en]

    Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbemineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-likepopulation had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylylsulfate released electrons and the extracellular electrontransfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganicsulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

  • 14.
    Roman, Pawel
    et al.
    Wageningen Univ, Netherlands;Wetsus, Netherlands.
    Klok, Johannes B. M.
    Wetsus, Netherlands;Paqell, Netherlands.
    Sousa, João A. B.
    Wageningen Univ, Netherlands;Wetsus, Netherlands.
    Broman, Elias
    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.
    Zessen, Erik Van
    Paques BV, Netherlands.
    Bijmans, Martijn F. M.
    Wetsus, Netherlands.
    Sorokin, Dimitry Y.
    Russian Acad Sci, Russia;Delft Univ Technol, Netherlands.
    Janssen, Albert J. H.
    Wageningen Univ, Netherlands;Shell Technol Ctr Bangalore, India.
    Selection and Application of Sulfide Oxidizing Microorganisms Able to Withstand Thiols in Gas Biodesulfurization Systems2016In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 50, no 23, p. 12808-12815Article in journal (Refereed)
    Abstract [en]

    After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H2S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family). The sulfide-oxidizing potential of the acclimatized population was investigated under elevated thiol loading rates (4.5–9.1 mM d–1), consisting of a mix of methanethiol, ethanethiol, and propanethiol. With this biomass, it was possible to achieve a stable bioreactor operation at which 80% of the supplied H2S (61 mM d–1) was biologically oxidized to elemental sulfur. The remainder was chemically produced thiosulfate. Moreover, we found that a conventionally applied method for controlling the oxygen supply to the bioreactor, that is, by maintaining a redox potential set-point value, appeared to be ineffective in the presence of thiols.

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