Diversity and Dynamics of Bacterial Communities in Freshwater Lakes

Bertilsson, Stefan; Mehrshad, Maliheh

doi:10.1016/b978-0-12-819166-8.00124-9

Cited by 3 publications

(3 citation statements)

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“…Over a third (349) belonged to novel genera, substantially expanding the known genomic diversity of lake bacteria. We recovered a surprising diversity of MAGs assigned to Bacteroidota, a group that plays a major role in organic particle attachment and degradation in marine settings (Fernández-Gómez et al ., 2013) but is much less studied in freshwater systems (Bertilsson & Mehrshad, 2022). A third of the Bacteroidota MAGs (80 of 275) represented new genera ( Table S2 ), representing a rich genomic resource for future targeted research on understudied freshwater Bacteroidota ecology and metabolism, including potential symbiotic associations within the guts of zooplankton and other freshwater animals.…”

Section: Resultsmentioning

confidence: 99%

“…Freshwater bacterial communities are a diverse component of lake ecosystems, and are central to biogeochemical cycles and the regulation of water quality (Newton et al ., 2011; Bertilsson & Mehrshad, 2022). Collectively, Earth’s millions of lakes exhibit an immense environmental heterogeneity, reflecting a range of influences from global climate to regional variation in the terrestrial landscapes in which lakes are situated (Kratz, MacIntyre & Webster, 2005).…”

Section: Introductionmentioning

confidence: 99%

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A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

Garner

Kraemer

Onana

et al. 2022

Preprint

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Lakes are highly heterogenous ecosystems inhabited by a rich microbiome whose genomic diversity remains poorly defined compared to other major biomes. Here, we present a continental-scale study of metagenomes collected across one of the most lake-rich landscapes on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 bacterial genomospecies spanning a broad phylogenetic and metabolic diversity. Lake trophic state was a significant determinant of taxonomic and functional turnover of MAG assemblages. We detected a role for resource availability, particularly carbohydrate diversity, in driving biogeographic patterns. Coupling the MAG catalogue with geomatics information on watershed characteristics revealed an influence of soil properties and human land use on MAG assemblages. Agriculture and human population density were particularly influential on MAG functional turnover, signifying a detectable human footprint in lake bacterial communities. Overall, the Canadian lake MAG catalogue greatly expands the freshwater microbial genomic landscape, bringing us closer to an integrative view of bacterial genome diversity across Earth's biomes.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A genome catalogue of lake bacteria across watershed land use gradients at a continental scale

Garner

Kraemer

Onana

et al. 2022

Preprint

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“…Lake sediments as microbial niches and prokaryotic DNA repositories Microorganisms are abundant and diverse in inland waters (Newton et al, 2011;Magnabosco et al, 2018;Bertilsson and Mehrshad, 2021), where they contribute significantly to global element fluxes through regulation of biogeochemical cycles. The distribution, density, and composition of microbial communities in aquatic sediments arise from multiple environmental processes that interactively create microbial niches.…”

Section: Introductionmentioning

confidence: 99%

Chapter 4. Bacterial and archaeal DNA from lake sediments

Vuillemin,

Coolen,

Kallmeyer

et al. 2023

Preprint

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General microbial patterns of biogeography can be established based on sedimentary DNA (sedDNA) retrieved from diverse inland aquatic ecosystems, provided that certain variable environmental factors are taken into consideration in order to trace the admixture of prokaryotic sedDNA preserved in lacustrine sediments from source to sink. These include several watershed characteristics, such as climate and mineralogy in the catchment and degree of urbanization, which in turn determine the lake regime, productivity and geochemistry of the water body, redox conditions at the sediment-water interface, sedimentation rates and organic matter content over time.Records of environmental conditions through the preservation of prokaryotic sedDNA will partially be obscured by the presence of a subsurface biosphere that remains active during burial. Sediment colonization and selective growth of specific sub-populations of the resident microbiomes are inherent to the substrates available in lacustrine deposits. Microbial guilds reflective of respiration types and organic matter decomposition usually go hand-in-hand with the geochemical gradient that develops in the sedimentary column during early diagenetic processes, but may also prevail in specific stratigraphic intervals. Thus, the correct attribution of prokaryotic sedDNA sources to an environmental context is essential for resolving past and modern ecosystem functioning. Because the succession of microbial taxa pre-adapted to gradual depletion of electron donors and acceptors is relatively well known, sources of sedDNA inherent to resident microbial communities can be discriminated and provide evidence of diagenetic processes during burial. In contrast, ancient sources of sedDNA that persist in microbially active sediments are exposed to a constant turnover, leading to preferential preservation of dormant stages over free sedDNA.Bacteria and archaea are tremendously diverse, and therefore there is the need to rigorously assign their metabolic functions and assess their degree of activity along sediment archives. Beyond taxonomic surveys and geochemical profiling of the subsurface biosphere, novel procedures are being customized to sort, target, sequence and assemble sedDNA fragments of interest to unravel specific biogeochemical interactions in lacustrine ecosystems pertaining past and actual ecological changes at the local and global scale.

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