Brett Baker
Professor of microbial ecology and evolution at Univ of Texas Austin.
Beyond methane, new frontiers in anaerobic microbial hydrocarbon utilizing pathwaysenviromicro-journals.onlinelibrary.wiley.com Microbial Biotechnology is an open access applied microbiology journal publishing significant advances in microbial processes applied to biotechnology.
Bacterial ecology and evolution converge on seasonal and decadal scaleswww.biorxiv.org Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum. ### Competing Interest Statement The authors have declared no competing interest.
A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolutionwww.biorxiv.org Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, including psbA for photosynthesis, pmoC for methane oxidation, and katG for hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both top-down and bottom-up interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earth's microbiomes and ecosystems. ### Competing Interest Statement The authors have declared no competing interest.
A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution https://www.biorxiv.org/content/10.1101/2024.02.06.579183v1 www.biorxiv.org Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sul...microbiomejournal.biomedcentral.com Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse ...
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sul...microbiomejournal.biomedcentral.com Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse ...
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Asgard archaea defense systems and their roles in the origin of immunity in eukaryoteswww.biorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffoldwww.biorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution