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  • 1.
    Abreu, Clare I.
    et al.
    MIT, USA;Stanford Univ, USA.
    Dal Bello, Martina
    MIT, USA.
    Bunse, Carina
    University of Gothenburg, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gore, Jeff
    MIT, USA.
    Warmer temperatures favor slower-growing bacteria in natural marine communities2023Inngår i: Science Advances, E-ISSN 2375-2548, Vol. 9, nr 19, artikkel-id 26eade8352Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slowgrowing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperaturedependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.

  • 2.
    Aguilera, Anabella
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Alegria Zufia, Javier
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Bas Conn, Laura
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gurlit, Leandra
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Śliwińska‐Wilczewska, Sylwia
    Mount Allison University, Canada;University of Gdansk, Poland.
    Budzałek, Gracjana
    University of Gdansk, Poland.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Halmstad University, Sweden.
    Farnelid, Hanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria2023Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 25, nr 9, s. 1674-1695Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcBandcpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light(10–190 μmol  photons  m-2s-1), and salinity (2–14  PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

  • 3.
    Akram, Neelam
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Palovaara, Joakim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsberg, Jeremy
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Milton, Debra L.
    Luo, Haiwei
    Gonzalez, Jose M.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND42013Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 15, nr 5, s. 1400-1415Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.

  • 4. Allers, E
    et al.
    Gomez-Consarnau, Laura
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Simek, K
    Gasol, JM
    Pernthaler, J
    Population dynamics of Alteromonas and Roseobacter in marine mesocosms after substrate and nutrient manipulations2007Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 9, s. 2417-2429Artikkel i tidsskrift (Fagfellevurdert)
  • 5.
    Alneberg, Johannes
    et al.
    KTH Royal instute of technology, Sweden.
    Bennke, Christin
    Leibniz Inst Balt Sea Res, Germany.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Germany;Sorbonne Univ, France.
    Bunse, Carina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Carl von Ossietzky Univ Oldenburg, Germany;Alfred Wegener Institut, Germany.
    Quince, Christopher
    Univ Warwick, UK.
    Ininbergs, Karolina
    Stockholm University, Sweden;Karolinska Institutet, Sweden.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Ekman, Martin
    Stockholm University, Sweden.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res, Germany.
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res, Germany.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Andersson, Anders F.
    KTH Royal instute of technology, Sweden.
    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes2020Inngår i: Communications Biology, E-ISSN 2399-3642, Vol. 3, nr 1, s. 1-10, artikkel-id 119Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

  • 6.
    Alneberg, Johannes
    et al.
    KTH Royal Institute of Technology, Sweden.
    Karlsson, Christofer M. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Divne, Anna-Maria
    Uppsala University, Sweden.
    Bergin, Claudia
    Uppsala University, Sweden.
    Homa, Felix
    Uppsala University, Sweden.
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Lund University, Sweden.
    Hugerth, Luisa W.
    KTH Royal Institute of Technology, Sweden;Karolinska Institutet, Sweden.
    Ettema, Thijs J. G.
    Uppsala University, Sweden.
    Bertilsson, Stefan
    Uppsala University, Sweden.
    Andersson, Anders F.
    KTH Royal Institute of Technology, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes2018Inngår i: Microbiome, E-ISSN 2049-2618, Vol. 6, artikkel-id 173Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

  • 7.
    Alneberg, Johannes
    et al.
    KTH Royal Institute of Technology, Sweden.
    Sundh, John
    Stockholm University, Sweden.
    Bennke, Christin
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Beier, Sara
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Hugerth, Luisa W.
    KTH Royal Institute of Technology, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Kisand, Veljo
    Univ Tartu, Estonia.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Andersson, Anders F.
    KTH Royal Institute of Technology, Sweden.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018Inngår i: Scientific Data, E-ISSN 2052-4463, Vol. 5, artikkel-id 180146Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

  • 8. Alonso-Saez, L
    et al.
    Aristegui, J
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Gomez-Consarnau, Laura
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Gonzalez, JM
    Vaque, D
    Agusti, S
    Gasol, JM
    Bacterial assemblage structure and carbon metabolism along a productivity gradient in the NE Atlantic Ocean2007Inngår i: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 46, s. 43-53Artikkel i tidsskrift (Fagfellevurdert)
  • 9. Alonso-Saez, L
    et al.
    Balagué, V
    Sanchez, ESO
    Gonzalez, JM
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Massana, R
    Pernthaler, J
    Pedros-Alio, C
    Gasol, JM
    Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH2007Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 60, s. 98-112Artikkel i tidsskrift (Fagfellevurdert)
  • 10. Alonso-Saez, L.
    et al.
    Vazquez-Dominguez, E.
    Cardelus, C.
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Sala, M. M.
    Lekunberri, I.
    Balague, V.
    Vila-Costa, M.
    Unrein, F.
    Massana, R.
    Simo, R.
    Gasol, J. M.
    Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system2008Inngår i: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 11, nr 3, s. 397-409Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu(-1) h(-1)) as compared to summer (around 150 pM Leu(-1) h(-1)). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu(-1), with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 mu g C l(-1) d(-1)) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.

  • 11. Alonso-Saez, Laura
    et al.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Pernthaler, Jakob
    Gasol, Josep M.
    Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence?2010Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 12, nr 11, s. 2988-2997Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25–73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups (Gamma-, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast-growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs.

  • 12.
    Aparicio, Fran L.
    et al.
    CSIC, Spain.
    Nieto-Cid, Mar
    CSIC, Spain.
    Borrull, Encarna
    CSIC, Spain.
    Calvo, Eva
    CSIC, Spain.
    Pelejero, Carles
    CSIC, Spain;CREA, Spain.
    Montserrat Sala, Maria
    CSIC, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gasol, Josep M.
    CSIC, Spain.
    Marrase, Celia
    CSIC, Spain.
    Eutrophication and acidification: Do they induce changes in the dissolved organic matter dynamics in the coastal Mediterranean Sea?2016Inngår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 563, s. 179-189Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Two mesocosms experiments were conducted in winter 2010 and summer 2011 to examine how increased pCO(2) and/or nutrient concentrations potentially perturbate dissolved organic matter dynamics in natural microbial assemblages. The fluorescence signals of protein-and humic-like compounds were used as a proxy for labile and non-labile material, respectively, while the evolution of bacterial populations, chlorophyll a (Chl a) and dissolved organic carbon (DOC) concentrations were used as a proxy for biological activity. For both seasons, the presence of elevated pCO(2) did not cause any significant change in the DOC dynamics (p-value < 0.05). The conditions that showed the greatest changes in prokaryote abundances and Chl a content were those amended with nutrients, regardless of the change in pH. The temporal evolution of fluorophores and optical indices revealed that the degree of humification of the organic molecules and their molecular weight changed significantly in the nutrient-amended treatment. The generation of protein-like compounds was paired to increases in the prokaryote abundance, being higher in the nutrient-amended tanks than in the control. Different patterns in the magnitude and direction of the generation of humic-like molecules suggested that these changes depended on initial microbial populations and the availability of extra nutrient inputs. Based on our results, it is expected that in the future projected coastal scenarios the eutrophication processes will favor the transformations of labile and recalcitrant carbon regardless of changes in pCO(2). (c) 2016 The Authors. Published by Elsevier B.V.

  • 13.
    Arahal, David R.
    et al.
    Univ Valencia, Spain.
    Lucena, Teresa
    Univ Valencia, Spain.
    Carmen Macian, M.
    Univ Valencia, Spain.
    Ruvira, Maria A.
    Univ Valencia, Spain.
    Gonzalez, Jose M.
    Univ La Laguna, Spain.
    Lekumberri, Itziar
    Univ Girona, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pujalte, Maria J.
    Univ Valencia, Spain.
    Marinomonas blandensis sp nova, a novel marine gammaproteobacterium2016Inngår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 66, s. 5544-5549Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121(T), was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7% sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121(T) was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5% (w/v) marine salts and tolerates up to 7% (w/v) salts. Its major cellular fatty acids in order of abundance are C-16:1 omega 7c/C-16:1 omega 6c,C-18:1 omega 7c(1), C-16:0 and C-10:0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (O8) and the polar lipids phosphatidylglycerol and phosphatidylethanolannine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121(T) (=CECT 7076(T)=LMG 29722(T)).

  • 14. Arahal, DR
    et al.
    Lekunberri, I
    Gonzalez, JM
    Pascual, J
    Pujalte, MJ
    Pedros-Alio, C
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium2007Inngår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 57, s. 1000-1006Artikkel i tidsskrift (Fagfellevurdert)
  • 15.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). University of Otago, New Zealand.
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea2016Inngår i: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 13, nr 9, s. 2815-2821Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Extracellular enzymatic activities (EEA) are a crucial step on the degradation of organic matter. Dissolved (cell-free) extracellular enzymes in seawater can make up a significant contribution of the bulk EEA. However, the factors controlling the proportion of dissolved EEA in the marine environment remain unknown. Here we studied the seasonal changes in the proportion of dissolved relative to total EEA (of alkaline phosphatase [APase], β-glucosidase, [BGase], and leucine aminopeptidase, [LAPase]), in the Baltic Sea for 18 months. The proportio n of dissolved EEA ranged between 37-100%, 0-100%, 34-100% for APase, BGase and LAPase, respectively. A consistent seasonal pattern in the proportion of dissolved EEA was found among all the studied enzymes, with values up to 100% during winter and <40% du ring summer. A significant negative relation was found between the 21proportion of dissolved EEA and temperature, indicating that temperature might be a critical factor controlling the proportion of dissolved relative to total EEA in marine environments. Our results suggest a strong decoupling of hydrolysis rates from mi crobial dynamics in cold waters. This implies that under cold conditions, cell-free enzymes can contribute to substrate availability at large distances from the producing cell, increasing the dissociation between the hydrolysis of organic compounds and the actual microbes producing the enzymes. This also indicates that global warming could come to affect the hydrolysis of organic matter by reducing the hydrolytic activity of cell-free enzymes.

  • 16.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Lindh, Markus V.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Parparov, Arkadi
    Israel Oceanographic and Limnological Research.
    Berman, Tom
    Israel Oceanographic and Limnological Research.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Prokaryotic community structure and respiration during long-term incubations2012Inngår i: MicrobiologyOpen, E-ISSN 2045-8827, Vol. 1, nr 2, s. 214-224Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite the importance of incubation assays for studies inmicrobial ecology that frequentlyrequire long confinement times, few reports are available in which changesin the assemblage structure of aquatic prokaryotes were monitored during longtermincubations.We measured rates of dissolved organic carbon degradation andmicrobial respiration by consumption of dissolved oxygen (DO) in four experimentswith Lake Kinneret near-surface water and, concomitantly, we analyzed thevariability in prokaryotic community structure during long-term dark bottle incubations.During the first 24 h, therewere only minor changes in bacterial communitycomposition. Thereafter there were marked changes in the prokaryotic communitystructure during the incubations. In contrast, oxygen consumption rates (a proxyfor both respiration and dissolved organic carbon degradation rates) remained stablefor up to 10–23 days. This study is one of the first to examine closely the phylogeneticchanges that occur in the microbial community of untreated freshwaterduring long-term (days) incubations in dark, sealed containers. Novel informationon the diversity of the main bacterial phylotypes that may be involved in dissolvedorganic matter degradation in lake Kinneret is also provided. Our results suggestthat, under certain ecological settings, constant community metabolic rates can bemaintained as a result of shifts in community composition.

    Fulltekst (pdf)
    fulltext
  • 17.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Univ Otago, New Zealand.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Palovaara, Joakim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lekunberri, Itziar
    Univ Vienna, Austria;Inst Catala Recerca Aigua, Spain.
    Reinthaler, Thomas
    Univ Vienna, Austria.
    Herndl, Gerhard J.
    Univ Vienna, Austria;Univ Utrecht, Netherlands.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic2016Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, artikkel-id 1670Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.

  • 18.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). University of Otago, New Zealand.
    Palovaara, Joakim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Wageningen University, The Netherlands.
    Unrein, Fernando
    Institut de Ciències del Mar CSIC, Spain.
    Catala, Philippe
    Pierre-and-Marie-Curie University, France.
    Hornak, Karel
    Biology Centre of the Academy of Sciences of the Czech Republic, Czech Republic.
    Simek, Karel
    Biology Centre of the Academy of Sciences of the Czech Republic, Czech Republic.
    Vaque, Dolors
    Institut de Ciències del Mar CSIC, Spain.
    Massana, Ramon
    Institut de Ciències del Mar CSIC, Spain.
    Gasol, Josep M.
    Institut de Ciències del Mar CSIC, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions2016Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 3, s. 568-581Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 x 10(6) cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 x 10(4) cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (similar to 3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 x 10(6) bacteria per ml per day) and bacterial production (from 3 to 379 mu g per Cl per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.

  • 19.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Univ Otago, New Zealand.
    Palovaara, Joakim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Vila-Costa, Maria
    Univ Barcelona, Spain.
    Salazar, Guillem
    CSIC, Spain.
    Calvo, Eva
    CSIC, Spain.
    Pelejero, Carles
    CSIC, Spain ; Inst Catalana Recerca & Estudis Avancats, Spain.
    Marrase, Celia
    CSIC, Spain.
    Gasol, Josep M.
    CSIC, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site2015Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, nr 6, artikkel-id UNSP fiv058Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow.

  • 20.
    Baltar, Federico
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Reinthaler, Thomas
    University of Vienna, Austria.
    Herndl, Gerhard J.
    University of Vienna, Austria;Royal Netherlands Institute for Sea Research (NIOZ), The Netherlands.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Major Effect of Hydrogen Peroxide on Bacterioplankton Metabolism in the Northeast Atlantic2013Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 8, nr 4, artikkel-id e61051Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reactive oxygen species such as hydrogen peroxide have the potential to alter metabolic rates of marine prokaryotes, ultimately impacting the cycling and bioavailability of nutrients and carbon. We studied the influence of H2O2 on prokaryotic heterotrophic production (PHP) and extracellular enzymatic activities (i.e., beta-glucosidase [BGase], leucine aminopeptidase [LAPase] and alkaline phosphatase [APase]) in the subtropical Atlantic. With increasing concentrations of H2O2 in the range of 100-1000 nM, LAPase, APase and BGase were reduced by up to 11, 23 and 62%, respectively, in the different water layers. Incubation experiments with subsurface waters revealed a strong inhibition of all measured enzymatic activities upon H2O2 amendments in the range of 10-500 nM after 24 h. H2O2 additions also reduced prokaryotic heterotrophic production by 36-100% compared to the rapid increases in production rates occurring in the unamended controls. Our results indicate that oxidative stress caused by H2O2 affects prokaryotic growth and hydrolysis of specific components of the organic matter pool. Thus, we suggest that oxidative stress may have important consequences on marine carbon and energy fluxes.

  • 21. Beja, Oded
    et al.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Spudich, John L.
    Proteorhodopsins: widespread microbial light-driven proton pumps2013Inngår i: Encyclopedia of Biodiversity / [ed] Levin S.A., Waltham, MA: Academic Press, 2013, 2:nd edition, vol. 2, s. 280-285Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Proteorhodopsins (PRs) are membrane-embedded, retinal-containing proteins that function as light-driven proton pumps. Since their discovery in 2000 in uncultured marine bacteria, PRs have been detected in numerous bacteria, archaea, and microbial eukarya. PRs have now been detected in diverse habitats, including marine, brackish, and freshwater environments; leaf surfaces; and soil crusts. Their widespread distribution and relatively simple single-molecule design suggests them as the earliest light-energy transducing proteins to have evolved. Currently, PRs represent the simplest biological means to convert light energy into chemical energy.

  • 22.
    Berner, Christoffer
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Bertos-Fortis, Mireia
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea2018Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, artikkel-id 1562Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Frequencies and biomass of Baltic Sea cyanobacterial blooms are expected to be higher in future climate conditions, but also of longer duration as a result of increased sea surface temperature. Concurrently, climate predictions indicate a reduced salinity in the Baltic Sea. These climate-driven changes are expected to alter not solely the phytoplankton community but also the role of microbial communities for nutrient remineralization. Here, we present the response of summer plankton communities (filamentous cyanobacteria, picocyanobacteria, and heterotrophic bacteria) to the interplay of increasing temperature (from 16 to 18 degrees C and 20 degrees C) and reduced salinity (from salinity 6.9 to 5.9) in the Baltic Proper (NW Gotland Sea) using a microcosm approach. Warmer temperatures led to an earlier peak of cyanobacterial biomass, while yields were reduced. These conditions caused a decrease of nitrogen-fixers (Dolichospermum sp.) biomass, while non nitrogen-fixers (Pseudanabaena sp.) increased. Salinity reduction did not affect cyanobacterial growth nor community composition. Among heterotrophic bacteria, Actinobacteria showed preference for high temperature, while Gammaproteobacteria thrived at in situ temperature. Heterotrophic bacteria community changed drastically at lower salinity and resembled communities at high temperature. Picocyanobacteria and heterotrophic bacterial biomass had a pronounced increase associated with the decay of filamentous cyanobacteria. This suggests that shifts in community composition of heterotrophic bacteria are influenced both directly by abiotic factors (temperature and salinity) and potentially indirectly by cyanobacteria. Our findings suggest that at warmer temperature, lower yield of photosynthetic cyanobacteria combined with lower proportion of nitrogen-fixers in the community could result in lower carbon export to the marine food web with consequences for the decomposer community of heterotrophic bacteria.

  • 23.
    Bertos-Fortis, Mireia
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Farnelid, Hanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Andersson, Agneta
    Umeå University.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors2016Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, artikkel-id 625Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a 2-year monthly time series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An "epidemic population structure" (dominance of a single cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this cluster simultaneously occurred with opportunistic clusters/OTUs, e.g., Nodulana spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formed a consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocyanobacteria and the bloom of filamentous/colonial clusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic Sea predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.

  • 24.
    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
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Bergman, Birgitta
    Stockholm University.
    Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters2016Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, nr 12, s. 4442-4455Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 25.
    Broman, Elias
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Stockholm University, Sweden.
    Asmala, Eero
    Univ Helsinki, Finland.
    Carstensen, Jacob
    Aarhus Univ, Denmark.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Dopson, Mark
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter2019Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 10, s. 1-15, artikkel-id 2579Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 26.
    Broman, Elias
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Sachpazidou, Varvara
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Dopson, Mark
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism2017Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 8, artikkel-id 2453Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 27.
    Broman, Elias
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Sjöstedt, Johanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Lund university;Tech Univ Denmark, Denmark.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Dopson, Mark
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism2017Inngår i: Microbiome, E-ISSN 2049-2618, Vol. 5, artikkel-id 96Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 28.
    Bunse, Carina
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Bertos-Fortis, Mireia
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    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
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom2016Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, artikkel-id 517Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 29.
    Bunse, Carina
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Carl von Ossietzky Univ Oldenburg, Germany.
    Israelsson, Stina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Baltar, Federico
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Univ Vienna, Austria.
    Bertos-Fortis, Mireia
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Fridolfsson, Emil
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindehoff, Elin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Swedish Meteorological and Hydrological Institute, Sweden.
    Martínez-García, Sandra
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Univ Vigo, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities2019Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, artikkel-id 3296Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 30.
    Bunse, Carina
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Karlsson, Christofer M. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Akram, Neelam
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Vila-Costa, Maria
    Centre d’Estudis Avançats de Blanes-CSIC, Spain.
    Palovaara, Joakim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Svensson, Lovisa
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Holmfeldt, Karin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    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
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gasol, Josep
    Institut de Ciències del Mar—CSIC, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Response of marine bacterioplankton pH homeostasis gene expression to elevated CO22016Inngår i: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 6, nr 5, s. 483-487Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 31.
    Bunse, Carina
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Lund University.
    Sjöstedt, Johanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Israelsson, Stina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Martínez-García, Sandra
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Universidade de Vigo, Spain.
    Baltar, Federico
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). University of Otago, New Zealand.
    Muthusamy, Sarala Devi
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pontiller, Benjamin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Karlsson, Christofer M. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Seasonality and co-occurrences of free-living Baltic Sea bacterioplanktonManuskript (preprint) (Annet vitenskapelig)
  • 32.
    Bunse, Carina
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Marine bacterioplankton seasonal succession dynamics2017Inngår i: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 25, nr 6, s. 495-505Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 33.
    Capo, Eric
    et al.
    Umeå University, Sweden;Swedish university of agricultural sciences, Sweden.
    Bravo, Andrea G.
    Inst Ciencies Mar ICM CSIC, Spain.
    Soerensen, Anne L.
    Swedish Museum of Natural History, Sweden.
    Bertilsson, Stefan
    Swedish university of agricultural sciences, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Feng, Caiyan
    Umeå University, Sweden.
    Andersson, Anders F.
    KTH Royal institute of technology, Sweden.
    Buck, Moritz
    Swedish university of agricultural sciences, Sweden.
    Bjorn, Erik
    Umeå University, Sweden.
    Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea2020Inngår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, s. 1-11, artikkel-id 574080Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (thehgcABgene cluster). We determined the relative abundance of thehgcABgenes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water column. ThehgcABgenes were predominantly detected in anoxic water, but somehgcABgenes were also detected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities ofhgcABgenes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversity of the microorganisms with the potential to mediate MeHg production in the Baltic Sea and pinpoint the important ecological niches for these microorganisms within the marine water column.

  • 34.
    Capo, Eric
    et al.
    Umeå University, Sweden;SLU Uppsala, Sweden.
    Broman, Elias
    Stockholm University, Sweden.
    Bonaglia, Stefano
    Stockholm University, Sweden;University of Gothenburg, Sweden.
    Bravo, Andrea G.
    CSIC, Spain.
    Bertilsson, Stefan
    Swedish University of agricultural sciences, Sweden.
    Soerensen, Anne L.
    Swedish Museum of Natural History, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Buck, Moritz
    Swedish University of Agricultural Sciences, Sweden.
    Hall, Per O. J.
    University of Gothenburg, Sweden.
    Nascimento, Francisco J. A.
    Stockholm University, Sweden.
    Björn, Erik
    Umeå University, Sweden.
    Oxygen-deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments2022Inngår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 67, nr 1, s. 135-146Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (Hg-II) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand.

    Fulltekst (pdf)
    fulltext
  • 35.
    Capo, Eric
    et al.
    Umeå University, Sweden;Swedish University of Agricultural Sciences, Sweden.
    Feng, Caiyan
    Umeå University, Sweden.
    Bravo, Andrea G.
    CSIC, Spain.
    Bertilsson, Stefan
    Swedish University of Agricultural Sciences, Sweden.
    Soerensen, Anne L.
    Swedish Museum of Natural History, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Buck, Moritz
    Swedish University of Agricultural Sciences, Sweden.
    Karlsson, Camilla
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Hawkes, Jeffrey
    Uppsala University, Sweden.
    Björn, Erik
    Umeå University, Sweden.
    Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters2022Inngår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 56, nr 18, s. 13119-13130Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (Hg-II) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not know nif the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved Hg-II-sulfide species were strong predictors of both the Hg-II methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc(+) microorganisms by reconstructing their genomes from metagenomes (i.e., hgc(+) MAGs), which highlighted the versatility of putative Hg-II methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the Hg-II methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficientzones.

    Fulltekst (pdf)
    fulltext
  • 36.
    Capo, Eric
    et al.
    CSIC, Spain;Swedish University of Agricultural Sciences, Sweden.
    Peterson, Benjamin D.
    Univ Wisconsin, USA.
    Kim, Minjae
    Colorado State Univ, USA.
    Jones, Daniel S.
    New Mexico Inst Min & Technol, USA;Natl Cave & Karst Res Inst, USA.
    Acinas, Silvia G.
    CSIC, Spain.
    Amyot, Marc
    Univ Montreal, Canada.
    Bertilsson, Stefan
    Swedish University of Agricultural Sciences, Sweden.
    Bjoern, Erik
    Umeå University, Sweden.
    Buck, Moritz
    Swedish University of Agricultural Sciences, Sweden.
    Cosio, Claudia
    Univ Reims, France.
    Elias, Dwayne A.
    Elias Consulting LLC, USA.
    Gilmour, Cynthia
    Smithsonian Environm Res Ctr, USA.
    Goni-Urriza, Marisol
    Univ Pau & Pays Adour, France.
    Gu, Baohua
    Oak Ridge Natl Lab, USA.
    Lin, Heyu
    Univ Melbourne, Australia.
    Liu, Yu-Rong
    Huazhong Agr Univ, China.
    McMahon, Katherine
    Univ Wisconsin, USA.
    Moreau, John W.
    Univ Glasgow, UK.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Podar, Mircea
    Oak Ridge Natl Lab, USA.
    Puente-Sanchez, Fernando
    Swedish University of Agricultural Sciences, Sweden.
    Sanchez, Pablo
    CSIC, Spain.
    Storck, Veronika
    Univ Montreal, Canada.
    Tada, Yuya
    Natl Inst Minamata Dis, Japan.
    Vigneron, Adrien
    Univ Pau & Pays Adour, France.
    Walsh, David A.
    Concordia Univ, Canada.
    Vandewalle-Capo, Marine
    Swedish University of Agricultural Sciences, Sweden.
    Bravo, Andrea G.
    CSIC, Spain.
    Gionfriddo, Caitlin M.
    Smithsonian Environm Res Ctr, USA.
    A consensus protocol for the recovery of mercury methylation genes from metagenomes2023Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 23, nr 1, s. 190-204Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

    Fulltekst (pdf)
    fulltext
  • 37.
    Cerro-Galvez, Elena
    et al.
    CSIC - IDAEA, Spain.
    Casal, Paulo
    CSIC - IDAEA, Spain.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pina, Benjamin
    CSIC - IDAEA, Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Dachs, Jordi
    CSIC - IDAEA, Spain.
    Vila-Costa, Maria
    CSIC - IDAEA, Spain.
    Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters2019Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, nr 4, s. 1466-1481Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-angstrom lesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

  • 38.
    Churakova, Yelena
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Aguilera, Anabella
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Charalampous, Evangelia
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Conley, Daniel J.
    Lund University, Sweden.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Farnelid, Hanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle2023Inngår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 15, nr 4, s. 282-290Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2-3 mu m), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 mu M). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell(-1). Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.

  • 39.
    Delgadillo-Nuno, Erick
    et al.
    Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Spain.
    Teira, Eva
    Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Spain.
    Pontiller, Benjamin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). GEOMAR Helmholtz Ctr Ocean Res Kiel, Germany.
    Lundin, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Joglar, Vanessa
    Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Spain.
    Pedros-Alio, Carlos
    Ctr Nacl Biotecnol CNB CSIC, Spain.
    Fernandez, Emilio
    Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Spain.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Martinez-Garcia, Sandra
    Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Spain.
    Coastal upwelling systems as dynamic mosaics of bacterioplankton functional specialization2024Inngår i: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 10, artikkel-id 1259783Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world ' s oceans.

  • 40.
    Dupont, Chris L.
    et al.
    J. Craig Venter Institute, USA.
    Larsson, John
    Stockholm University.
    Yooseph, Shibu
    J. Craig Venter Institute, USA.
    Ininbergs, Karolina
    Stockholm University.
    Goll, Johannes
    J. Craig Venter Institute, USA.
    Asplund-Samuelsson, Johannes
    Stockholm University.
    McCrow, John P.
    J. Craig Venter Institute, USA.
    Celepli, Narin
    Stockholm University.
    Allen, Lisa Zeigler
    J. Craig Venter Institute, USA.
    Ekman, Martin
    Stockholm University.
    Lucas, Andrew J.
    Hagström, Åke
    University of Gothenburg.
    Thiagarajan, Mathangi
    Brindefalk, Bjorn
    Richter, Alexander R.
    Andersson, Anders F.
    Tenney, Aaron
    Lundin, Daniel
    KTH Royal Institute of Technology.
    Tovchigrechko, Andrey
    Nylander, Johan A. A.
    Brami, Daniel
    Badger, Jonathan H.
    Allen, Andrew E.
    Rusch, Douglas B.
    Hoffman, Jeff
    Norrby, Erling
    Friedman, Robert
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Venter, J. Craig
    Bergman, Birgitta
    Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition2014Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 9, nr 2, artikkel-id e89549Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

    Fulltekst (pdf)
    fulltext
  • 41.
    Fahlgren, Camilla
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gómez-Consarnau, Laura
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Zabori, Julia
    Stockholm University.
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Krejci, Radovan
    Stockholm University.
    Mårtensson, E. Monica
    Stockholm University;Uppsala University.
    Nilsson, Douglas
    Stockholm University.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols2015Inngår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 7, nr 3, s. 460-470Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Biogenic aerosols critically control atmospheric processes. However, although bacteria constitute major portions of living matter in seawater, bacterial aerosolization from oceanic surface layers remains poorly understood. We analysed bacterial diversity in seawater and experimentally generated aerosols from three Kongsfjorden sites, Svalbard. Construction of 16S rRNA gene clone libraries from paired seawater and aerosol samples resulted in 1294 sequences clustering into 149 bacterial and 34 phytoplankton operational taxonomic units (OTUs). Bacterial communities in aerosols differed greatly from correspondingseawater communities in three out of four experiments. Dominant populations of both seawater and aerosols were Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria. Across the entire dataset, most OTUs from seawater could also be found in aerosols; in each experiment, however, several OTUs were either selectively enriched in aerosols or little aerosolized. Notably, a SAR11 clade OTU was consistently abundant in the seawater, but was recorded insignificantly lower proportions in aerosols. A strikingly high proportion of colony-forming bacteria were pigmented in aerosols compared with seawater, suggesting that selection during aerosolization contributes to explaining elevated proportions of pigmented bacteria frequently observed in atmospheric samples. Our findings imply that atmospheric processes could be considerably influenced by spatiotemporal variations in the aerosolization efficiency of different marine bacteria.

  • 42. Fernandez-Gomez, Beatriz
    et al.
    Richter, Michael
    Schueler, Margarete
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Acinas, Silvia G.
    Gonzalez, Jose M.
    Pedros-Alio, Carlos
    Ecology of marine Bacteroidetes: a comparative genomics approach2013Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, nr 5, s. 1026-1037Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface. The ISME Journal (2013) 7, 1026-1037; doi:10.1038/ismej.2012.169; published online 10 January 2013

  • 43.
    Figueroa, Daniela
    et al.
    Umeå University, Sweden.
    Capo, Eric
    Umeå University, Sweden.
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Swedish Meteorological and Hydrological Institute, Sweden.
    Rowe, Owen F.
    Baltic Marine Environm Protect Commiss HELCOM, Finland.
    Paczkowska, Joanna
    Umeå University, Sweden.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Linnéuniversitetet, Kunskapsmiljöer Linné, Vatten.
    Andersson, Agneta
    Umeå University, Sweden.
    Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea)2021Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 23, nr 8, s. 4200-4213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting similar to 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.

  • 44.
    Forss, Jörgen
    et al.
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för byggd miljö och energiteknik (BET).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Welander, Ulrika
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för byggd miljö och energiteknik (BET).
    Microbial biotreatment of actual textile wastewater in a continuous sequential rice husk biofilter and the microbial community involved2017Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 12, nr 1, artikkel-id e0170562Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments.

  • 45.
    Forss, Jörgen
    et al.
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för bygg- och energiteknik (BE).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Lindh, Markus V.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Welander, Ulrika
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för bygg- och energiteknik (BE).
    Microbial diversity in a continuous system based on rice husks for biodegradation of the azo dyes Reactive Red 2 and Reactive Black 52013Inngår i: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 130, s. 681-688Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the present study the degradation of two common azo dyes used in dye houses today, Reactive Black 5 and Reactive Red 2 was evaluated in biofilters. In two experiments, bioreactors performed over 80% decolorization at a hydraulic retention time of only 28.4 h with little production of metabolites. Molecular analyses showed a diverse and dynamic bacterial community composition in the bioreactors, including members of the Bacteroidetes, Acinetobacter (Gammaproteobacteria) and Clostridium (Firmicutes) that possess the capacity to reduce azo dyes. Collectively, the results indicate that the development of mixed bacterial communities from natural biomaterials contributes to an efficient and robust degradation performance in bioreactors even at high concentration of dyes.

  • 46.
    Fridolfsson, Emil
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Bunse, Carina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). University of Gothenburg, Sweden.
    Lindehoff, Elin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Farnelid, Hanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pontiller, Benjamin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany.
    Bergström, Kristofer
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Pinhassi, Jarone
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Legrand, Catherine
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). Halmstad University, Sweden.
    Hylander, Samuel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper2023Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, nr 1, artikkel-id 11865Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models. 

    Fulltekst (pdf)
    fulltext
  • 47. Gasol, J. M.
    et al.
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Alonso-Saez, L.
    Ducklow, H.
    Herndl, G. J.
    Koblizek, M.
    Labrenz, M.
    Luo, Y.
    Moran, X. A. G.
    Reinthaler, T.
    Simon, M.
    Towards a better understanding of the microbial carbon flux in the sea2008Inngår i: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 53, s. 21-38Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.

  • 48. Gasol, J.M.
    et al.
    Doval, M D
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Calderon-Paz, J I
    Guixa-Boixareu, N
    VaquZ, D
    Pedros-Alio, C
    Diel variations in bacterial heterotrophic activity and growth in the northwestern Mediterranean1998Inngår i: Marine Ecology Progress Series, Vol. 164, s. 107-124Artikkel i tidsskrift (Fagfellevurdert)
  • 49.
    Gomez-Consarnau, Laura
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Gonzalez, J M
    Coll-Llado, Montserrat
    Gourdon, Pontus
    Pascher, Torbjörn
    Neutze, Richard
    Pedros-Alio, C
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Light stimulates growth of proteorhodopsin-containing marine Flavobacteria2007Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 445, s. 210-213Artikkel i tidsskrift (Fagfellevurdert)
  • 50. Gomila, Marga
    et al.
    Pinhassi, Jarone
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Falsen, Enevold
    Moore, Edward
    Lalucat, Jorge
    Kinneretia asaccharophila, gen. nov., sp. nov., isolated from fresh water, a novel member of the Rubrivivax-branch of the family Comamonadaceae2010Inngår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 60, s. 809-814Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A strictly aerobic, Gram-negative bacterium, strain KIN192(T), isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA-DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192(T) (=CCUG 53117(T) =CECT 7319(T)).

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