| 1. |
- Bertilsson, Stefan, et al.
(författare)
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Non-cyanobacterial diazotrophs dominate nitrogen-fixing communities in permafrost thaw ponds
- 2020
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 65, s. S180-S193
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Tidskriftsartikel (refereegranskat)abstract
- There is a growing concern about the implications of accelerated thawing of permafrost for regional biogeochemical cycling of carbon and other bioreactive elements. One such element of concern is nitrogen, and in this study, we investigated the diversity and biogeography of potential diazotrophs within a series of thaw ponds representing different ontogenetic stages in pond development. Using metagenomic sequence data from subarctic thaw ponds, we identified an array of nitrogenase genes across the ponds. The iron-only nitrogenase gene (anfH) was positively correlated with sulfate, while there was no correlation with methane despite previous findings that organisms carrying anfH can simultaneously participate in nitrogen fixation and methanogenesis. Sulfate is known to inhibit microbial uptake of molybdate, an element essential for the activity of the nifH (molybdenum-iron) nitrogenase and this may explain the high potential for nitrogen fixation utilizing anfH in sulfate-rich ponds. NifH was particularly abundant in the hypolimnion of the deeper and older ponds, with Deltaproteobacteria and Chlorobi as the putative dominant diazotrophs. In the epilimnetic waters, nifH composition was more variable, with various Gammaproteobacteria as abundant representatives, while cyanobacterial diazotrophs were scarce. Interestingly, nifH gene abundance was significantly positively correlated with in situ methane concentration. Based on genome-resolved metagenomics, we hypothesize that diazotrophs and methanogens engage in syntrophic interactions in anoxic waters, possibly via propionate oxidation or (in Geobacter) by interspecies electron transfer. Our results also suggest that nitrogen fixers may supply bioreactive nitrogen compounds to the thaw pond communities, thereby enhancing growth and activity of methanogens.
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| 2. |
- Bravo, Andrea G., et al.
(författare)
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Methanogens and iron-reducing bacteria : the overlooked members of mercury-methylating microbial communities in boreal lakes
- 2018
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 84:23
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCE: Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.
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| 3. |
- Bravo, Andrea Garcia, et al.
(författare)
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Methanogens and Iron-Reducing Bacteria : the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes
- 2018
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 84:23
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Tidskriftsartikel (refereegranskat)abstract
- Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the di- versity of these mercury-methylating microbial communities remains largely unex- plored. Previous studies have implicated sulfate-reducing bacteria as the main mer- cury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments us- ing high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abun- dant members of the mercury-methylating communities. In fact, incubation experi- ments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These re- sults suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.
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| 4. |
- Buck, Moritz, et al.
(författare)
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16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds
- 2022
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 88, s. 25-30
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Tidskriftsartikel (refereegranskat)abstract
- A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5 %) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: Ca. Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of Ca. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.
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| 5. |
- Buck, Moritz, et al.
(författare)
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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds
- 2021
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.
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| 6. |
- Fernandez-Vidal, Leyden, et al.
(författare)
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Diazotroph genomes and their seasonal dynamics in a stratified humic bog lake
- 2020
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Ingår i: Frontiers in Microbiology. - : FRONTIERS MEDIA SA. - 1664-302X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Aquatic N-fixation is generally associated with the growth and mass development ofCyanobacteriain nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data andnifgene clusters analysis. Groups with diazotrophic operons were functionally divergent and includedCholorobi,Geobacter,Desulfobacterales,Methylococcales, andAcidobacteria. In addition tonifH(a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within theChlorobipopulation, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence ofrnfgenes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) inMethylococcalesandDesulfobacteralessuggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.
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| 7. |
- Fernandez-Vidal, Leyden
(författare)
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Non-cyanobacterial nitrogen fixation insights in humic freshwater lakes and ponds
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The biological basis of nitrogen fixation beyond the canonical role of Cyanobacteria is not well understood in freshwater ecosystems. To address this gap in knowledge, the main objective of this thesis is to study non-cyanobacterial nitrogen fixation in freshwater lakes and ponds.Microbial communities and diazotrophic potential were characterized by direct metagenome sequencing from seasonally stratified lakes and permafrost thaw ponds, both of which are systems featuring strong redox gradients. To quantify the nitrogen fixation process, we also adopted and applied a 15N tracer method to estimate realized diazotrophic activity in five of the studied lakes. Chemical characteristics were also measured concomitantly to link diazotroph distribution patterns to chemical features and metabolic traits in the studied freshwaters.Exploring a 3-year metagenomic time series of a humic lake (Trout Bog), widespread and stable occurrence of nifH genes were detected. This marker gene for nitrogen fixation appeared with accessory genes, validating the marker. The diazotrophic community was diverse and dynamic with contributions from Geobacter, Desulfobacterales, Methylococcales, Acidobacteria, Verrucomicrobia and Chlorobi. Accordingly, nitrogen fixation may be fueled by a variety of metabolic processes (heterotrophic sulfate/iron reducers, methylotrophs and photolithotrophs) in oxygen depleted dark waters. Interestingly the photolithotrophic Chlorobi also carried a Fe-only nitrogenase (anfH) recently implicated in alternative methane production. Overall, we demonstrated widespread potential for nitrogen fixation within hypolimnia in stratified humic lakes, and analyses of depth profiles also confirmed the presence of active diazotrophic communities in boreal lakes. These active nitrogen fixing communities were characterized by overall higher bacterial abundances, cellular aggregation and increased phosphorus availability as compared to communities where nitrogen fixation was not detected.Expanding our work to include recently formed freshwater ecosystems, we characterized microbial communities in arctic thaw ponds at different ontogenetic stages. We also investigated the possible role of anfH in methane production, but the abundance of this gene was not correlated with high methane concentration in the water column. NifH was detected in all systems, and interestingly the hypolimnetic waters in the more established systems emerged as suitable niche for diazotrophs with nifH abundances positively correlated to elevated methane concentrations. Based on this observation, we propose that nitrogen-fixing microorganisms may be important partners in complex syntrophic networks established between bacteria and archaeal methanogens. In conclusion, the results presented across the different types of terrestrially influenced freshwater systems revealed widespread potential for nitrogen fixation within hypolimnia of humic lakes and permafrost thaw ponds. Furthermore, nitrogen fixation was confirmed at and below the redoxcline in five Finnish humic lakes. This implies that we need to look beyond phototrophic cyanobacteria to more fully understand the role of nitrogen fixation and overall nitrogen cycling in freshwater ecosystems.
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| 8. |
- Garcia, Sarahi L., et al.
(författare)
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Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations
- 2021
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Ingår i: mSystems. - : American Society for Microbiology. - 2379-5077. ; 6:3
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.
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| 9. |
- Grubisic, Lorena M, et al.
(författare)
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Bacterial and phytoplankton succession during a freshwater diatom bloom
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic bacterial communities experience rapid turnover as they have fast reproductive rates and are highly susceptible to predation and other mortality factors. Short-lived changes in the environment, such as the spring phytoplankton bloom which alter both resource supply and food web interactions can therefore cause rapid shifts in bacterioplankton community composition and function. Information about the temporal dynamics of such successional changes is still limited and has for the most part been obtained in studies of experimental enclosures with limited ability to extrapolate findings to complex natural ecosystems. To address this gap in knowledge, we followed bacterial community shifts at high temporal resolution during the onset and decline of a spring diatom bloom in a dimictic temperate lake. Water was collected from shortly before ice-off until the onset of summer stratification. Bacterioplankton community composition was assessed using 16S rRNA amplicon sequencing while parallel samples were collected for chemical analyses and microscopy-based phytoplankton community composition. In agreement with previous work, Proteobacteria, Actinobacteria and Bacterioidetes were the dominant bacterial phyla throughout the study period. Under the ice proteobacterial LD12 (Fonsibacter) and betI were dominant tribes. At ice-off there was a rapid initiation of the phytoplankton spring bloom and concurrently an immediate positive response in bacterial abundances which lasted throughout the bloom. Tribes Flavo-A3 is and acI-A6 responded positively to the bloom and at the maximum bloom intensity, acI-A6 was very abundant while LD12 were scarce. Immediately after the phytoplankton bloom, the bacterial community went into a more stable phase without major changes in bacterial community composition except that LD12 and bacI-A1 (FukuN47) became more abundant. Focusing on abundant bacterial freshwater bacterial groups, we observed diverse responses in the bacterioplankton community to the environmental shifts caused by the annually recurring diatom blooms. These diverse responses likely reflect contrasting pelagic lifestyles and traits, including variable abilities to profit from the organic substrates released from the phytoplankton. Our work puts the spotlight on a dynamic but so far poorly studied phase in the annual cycle of seasonally freezing lakes and calls for more work on the biotic interactions that control the initiation and demise of spring phytoplankton blooms.
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| 10. |
- Hellman, Maria, et al.
(författare)
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Substrate type determines microbial activity and community composition in bioreactors for nitrate removal by denitrification at low temperature
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 755
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Tidskriftsartikel (refereegranskat)abstract
- High levels of nitrogen originating from blasting operations, for example at mining sites or quarries, risk contaminating water bodies through leaching from waste rock dumps. Woodchip bioreactors can be a simple and cost-effective way of reducing nitrate concentrations in the leachate. In this study we investigated how bottle sedge, barley straw, and pine woodchips used as electron donors for denitrification influenced microbial community composition and nitrate removal in lab-scale bioreactors during 270 days. The reactors were operated to ensure that nitrate was never limiting and to achieve similar nitrate removal (%). Distinct bacterial communities developed due to the different substrates, as determined by sequencing of the 16S rRNAgene. Sedge and straw reactors shared more taxa with each other than with woodchips and throughout the experimental period, sedge and straw were more diverse than woodchips. Cellulose degrading bacteria like Fibrobacteres and Verrucomicrobia were detected in the substrates after 100-150 days of operation. Nitrate removal rates were highest in the sedge and straw reactors. After initial fluctuations, these reactors removed 5.1-6.3 g N m(-3) water day(-1), which was 3.3-4.4 times more than in the woodchip reactors. This corresponded to 48%, 42%, and 44% nitrate removal for the sedge, straw, and woodchip reactors respectively. The functional communities were characterized by quantitative PCR and denitrification was the major nitrate removing process based on genetic potential and water chemistry, although sedge and straw developed a capacity for ammonification. Gene ratios suggested that denitrification was initially incomplete and terminating with nitrous oxide. An increase in abundances of nitrous oxide reducing capacity in all substrate types towards the end increased the potential for less emissions of the greenhouse gas nitrous oxide. (C) 2020 The Author(s). Published by Elsevier B.V.
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