Bacterial ecology and evolution converge on seasonal and decadal scales

Rohwer, Robin R; Kirkpatrick, Mark; Garcia, Sarahi L; Kellom, Matthew; McMahon, Katherine D; Baker, Brett J.

doi:10.1101/2024.02.06.579087

Cited by 3 publications

References 71 publications

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A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets

Rohwer

McMahon

2022

Preprint

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Lakes are focal points of biogeochemical cycling on the terrestrial landscape, and microbial communities are the machines driving these processes. However, our view into how freshwater microbial communities function is obscured by high short-term variability. We provide a long-term, two-decade time series (years 2000 - 2019) of a freshwater microbial community characterized with 16S rRNA gene amplicon sequencing. We provide raw sequencing data from 1,023 total sequenced samples and controls, as well as references to paired publicly available environmental data. Moreover, processed, curated, and formatted microbial data are also available for easy download as an R package, along with well-documented functions for subsetting the data by samples and taxa. This processed dataset includes 970 total replicates from 496 samples. The "limony" dataset and its paired environmental data is a complete and ready-to-use resource for ecologists, modellers, educators, data scientists, and others from diverse fields.

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A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets

Rohwer

McMahon

2022

Preprint

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Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Krinos,

Bowers,

Rohwer

et al. 2024

Preprint

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Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last twenty years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community, and to hypothesize about their interactions with bacteria. Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Further, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g. ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes, and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

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Nature should be the model for microbial sciences

Baker,

Hyde,

Leão

2024

J Bacteriol

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Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10 28 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota ( Nitrosopumilus maritimus ), SAR11 ( Pelagibacter ubique ), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera , Aliivibrio , and Rhizobium , should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.

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Bacterial ecology and evolution converge on seasonal and decadal scales

Cited by 3 publications

References 71 publications

A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets

A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Nature should be the model for microbial sciences

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