Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds

Buck, Moritz; Garcia, Sarahi L.; Vidal, Laurent; Martin, Gaëtan; Rodriguez, Glorimar; Saarenheimo, Jatta; Zopfi, Jakob; Bertilsson, Stefan; Peura, Sari

doi:10.1101/2020.11.12.379446

Cited by 6 publications

(21 citation statements)

References 26 publications

(42 reference statements)

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“…In addition, Methylobacter in boreal lake sediments have genetic potential for denitrification, as indicated by our functional annotation analysis (Prokka, version 1.14.5, Seemann 2014) finding genes coding for dissimilatory nitrate and nitrite reduction in two MAGs representing genus Methylobacter in sediments of Lake Alinen Mustajärvi (NCBI accession no. GCA_903932065.1 and GCA_903870475.1; MAGs constructed/published by Buck et al 2020).…”

Section: Resultsmentioning

confidence: 99%

Anaerobic oxidation of methane in sediments of a nitrate-rich, oligo-mesotrophic boreal lake

Rissanen

Jilbert

Simojoki

et al. 2021

Preprint

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The importance of nitrate in promoting anaerobic oxidation of methane (AOM) in the sediments of boreal lakes is currently unknown. Here we investigated the extent to which sediment AOM is linked to nitrate reduction in a nitrate-rich, oligo-mesotrophic, boreal lake (Lake Paajarvi, Finland). AOM potential of sediment slurries, collected from three profundal stations of the study lake, was measured at varying nitrate concentrations using 13C-labelling. This was coupled with analysis of vertical profiles of the sediment and porewater geochemistry and the microbial communities (16S rRNA gene and shotgun metagenomic sequencing). Sediment AOM potential was enhanced by nitrate at a shallow station with high contents of labile phytoplankton-derived organic matter (Station 1), but not at the other two stations. AOM was also much higher at Station 1 (2.0-6.8 nmol C cm-3 d-1) than at the other stations (0-0.3 nmol C cm-3 d-1). Accordingly, methanotrophic archaea (Candidatus Methanoperedens sp.) and bacteria (Methylococcales) had the highest relative abundance at Station 1. Furthermore, geochemical profiles indicated that AOM was potentially coupled with reduction of nitrate, iron, or sulfate at all stations. We conclude that AOM linked to nitrate reduction takes place in boreal lake sediments. However, our data cannot resolve whether nitrate affects the process directly, via enhancing nitrate reduction-mediated AOM, or indirectly, via enhancing AOM mediated by reduction of other electron acceptors.

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Section: Resultsmentioning

confidence: 99%

Anaerobic oxidation of methane in sediments of a nitrate-rich, oligo-mesotrophic boreal lake

Rissanen

Jilbert

Simojoki

et al. 2021

Preprint

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“…Genome collection. Assembling and binning the 265 metagenomes resulted in ;12,000 metagenome-assembled genomes (MAGs) from water bodies spanning five different countries (29). Of these, 454 belonged to the class Chlorobia and were used in this study.…”

Section: Methodsmentioning

confidence: 99%

“…Amplified DNA was mixed thoroughly by pipetting up and down. After screening for bacterial 16S rRNA genes, DNA from confirmed Chlorobia members was sequenced on an Illumina HiSeqX v2.5 PE at 2 Â 150 bp (29). mOTU analysis.…”

Section: Methodsmentioning

confidence: 99%

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

et al. 2021

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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. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

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“…For shotgun metagenomic analysis of the Lovojärvi samples, the library preparation and sequencing (Illumina NovaSeq) were performed as previously described (Buck et al . 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…Trimming of the raw data, assembly of the quality-controlled reads, as well as binning of the assembled contigs into metagenomic bins, are explained in detail in Buck et al . ( 2020 ). In addition, Kaiju was used for taxonomic classification of the trimmed reads against the NCBI nr-database (Menzel, Ng and Krogh 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

Rissanen

Saarela

Jäntti

et al. 2020

FEMS Microbiology Ecology

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The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived, especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in clusters of orthologous groups (COG) categories L (replication, recombination and repair) and S (function unknown) were relatively high in metagenome-assembled genomes representing Methylococcales clearly thriving below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. By contrast, genes in COG category N (cell motility) were relatively high in metagenome-assembled genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.

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Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds

Cited by 6 publications

References 26 publications

Anaerobic oxidation of methane in sediments of a nitrate-rich, oligo-mesotrophic boreal lake

Anaerobic oxidation of methane in sediments of a nitrate-rich, oligo-mesotrophic boreal lake

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

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