Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake

Reboul, Guillaume; Moreira, David; Annenkova, Nataliia V.; Bertolino, Paola; Vershinin, K. E.; López‐García, Purificación

doi:10.1038/s41396-021-01011-y

Cited by 7 publications

(3 citation statements)

References 21 publications

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“…We also included in this analysis metagenomes of freshwater sediments and microbial mats from previous and ongoing studies in our laboratory (Table S8). DNA from Lake Baikal sediment samples collected in July 2017 was purified using the Power Soil DNA purification kit (Qiagen, Germany) [47]. DNA from microbial mat samples collected from the Salada de Chiprana (Spain, December 2013), lakes Bezymyannoe and Reid (Antarctica, January 2017) and several hot springs around Lake Baikal (Southern Siberia, July 2017), fixed in situ in ethanol as previously described [48], was purified using the Power Biofilm DNA purification kit (Qiagen, Germany).…”

Section: Dna Purification Of Sediment and Microbial Mats Sequencing A...mentioning

confidence: 99%

Metagenome-derived virus-microbe ratios across ecosystems

et al. 2023

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It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa–200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2–4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

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Section: Dna Purification Of Sediment and Microbial Mats Sequencing A...mentioning

confidence: 99%

Metagenome-derived virus-microbe ratios across ecosystems

et al. 2023

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“…We also included in this analysis metagenomes of freshwater sediments and microbial mats from previous and ongoing studies in our laboratory (Extended Data Fig 2, Supplementary Table 8). DNA from Lake Baikal sediment samples collected in July 2017 was purified using the Power Soil™ DNA purification kit (Qiagen, Germany) 67 . DNA from microbial mat samples collected from the Salada de Chiprana (Spain, December 2013), lakes Bezymyannoe and Reid (Antarctica, January 2017) and several hot springs around Lake Baikal (Southern Siberia, July 2017), fixed in situ in ethanol as previously described 36 , was purified using the Power Biofilm™ DNA purification kit (Qiagen, Germany).…”

Section: Methodsmentioning

confidence: 99%

Metagenome-derived virus-microbe ratios across ecosystems

López‐García

Gutiérrez-Preciado

Krupovìč³

et al. 2021

Preprint

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It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on fluorescently-labelled viral-like particles (VLPs) counts. However, these exclude cell-infecting lytic and lysogenic viruses and potentially include many false positives, e.g. DNA-containing membrane vesicles, gene-transfer agents or inert particles. Here, we develop a metagenome-based VMR estimate (mVRM) accounting for all viral stages (virion-lytic-lysogenic) using normalised counts of viral DNA-polymerases and cellular universal single-copy genes as proxies for individuals. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 um size range) in freshwater, seawater and 6-14-32% salt solar-saltern ponds. Viruses outnumbered cells in non-blooming freshwater and marine plankton by around twofold. However, mVMR in 133 uniformly-analysed metagenomes from diverse ecosystems showed that free-living cells largely exceeded viruses and epibiont DPANN archaea and/or CPR bacteria in compact environments (sediments, soils, microbial mats, host-associated microbiomes). Along the Piggyback-the-winner model lines, lysogenic genes significantly correlated with cell, but not necessarily biotope, density. While viruses likely are the most diverse biological entities on Earth, our results suggest that cells are the most abundant and that cellular parasites may exert population-size control in some high-density ecosystems.

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“…The analysis of the OTUs obtained using the UP-ARSE clustering method have been widely used for highthroughput sequencing analysis (Gad et al, 2022;Xu et al, 2022;Zhang et al, 2022;Reboul et al, 2021;Sun et al, 2022). Some of the diversity indices in our study were more comparable to previous research using 97 % sequence similarity OTUs (Chen et al, 2022;Wang et al, 2021;Y.…”

Section: Polymerase Chain Reaction (Pcr) and Illumina Miseqmentioning

confidence: 99%

Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)

Zhang

Zeng

et al. 2022

Biogeosciences

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Abstract. The diversity, co-occurrence patterns, and assembly processes of microbial eukaryotes (0.2–20 µm) in Antarctic freshwater lakes are not well understood, despite their wide distribution and ecological importance. This study used Illumina high-throughput sequencing to investigate the microbial eukaryotic communities of five freshwater lakes on the Fildes Peninsula over three summer seasons. A total of 28 phyla were detected, with phytoplankton occupying the highest percentage of sequences (accounting for up to 98 %). The dominant taxa consisted of Chrysophyta, Chlorophyta, and Cryptophyta. The species richness (113–268) and Shannon index (1.70–3.50) varied among the lakes, with higher values recorded in Lake Chang Hu and Lake Kitec and the lowest value obtained for Lake Yue Ya. There were significant differences between the microbial eukaryotic communities of the lakes, with spatial and temporal heterogeneity in the relative abundance of the dominant taxa (P<0.05). Environmental variables explained about 39 % of the variation in community structures, with water temperature and phosphate identified as the driving factors (P<0.05). Network analysis revealed comprehensive co-occurrence relationships (positive correlation 82 % vs. negative correlation 18 %). The neutral community model revealed that neutral processes explained more than 55 % of the community variation. Stochastic processes (e.g. homogenizing dispersal and undominated processes) predominated in community assembly over the deterministic processes. These findings demonstrate the diversity of the microbial eukaryotic communities in the freshwater lakes of the Fildes Peninsula and have important implications for understanding the community assembly in these ecosystems.

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Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake

Cited by 7 publications

References 21 publications

Metagenome-derived virus-microbe ratios across ecosystems

Metagenome-derived virus-microbe ratios across ecosystems

Metagenome-derived virus-microbe ratios across ecosystems

Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)

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