The aftermath of a trophic cascade: Increased anoxia following species invasion of a eutrophic lake

Rohwer, Robin R; Ladwig, Robert; Dugan, Hilary A.; Hanson, Paul C.; Walsh, Jake R.; Zanden, M. Jake Vander

doi:10.1101/2023.01.27.525925

Cited by 4 publications

(3 citation statements)

References 61 publications

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Section: Introductionmentioning

confidence: 99%

“…Trophic cascades can emerge when introduced invasive species eliminate a trophic level, allowing a di↵erent taxon to become overabundant [15]. Ongoing microscopic count observations in Lake Mendota confirmed an increase in diatoms (class Bacillariophyta) and chlorophytes (phylum Chlorophyta) and a decrease in cryptophytes (phylum Cryptophyta), but lacked taxonomic resolution or the inclusion of heterotrophic protists that cannot be easily captured by net tows or visually identified [27].To explore protistan ecology and interactions in Lake Mendota, we analyzed the diversity, structure, and composition of the lake's protistan community over the course of 20 years. We have extracted 16S and 18S rRNA gene sequences and quantified the abundance of these sequences in the underlying raw read data.…”

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confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

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

Krinos,

Bowers,

Rohwer

et al. 2024

Preprint

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“…Lake Mendota (Madison, Wisconsin, USA) is a eutrophic freshwater lake that has a longterm continuous monitoring program focused on microbial communities in the upper mixed layer 15,16 and some studies of the microbial community in the anoxic hypolimnion (deep waters) 6 . Prior work shows that the microbial community in hypolimnion is different compared to the epilimnion, and has distinct biogeochemical functions 6,17 .…”

Section: Introductionmentioning

confidence: 99%

Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

Tran

Bachand

Peterson

et al. 2023

Preprint

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Microbial biogeochemical cycling relies on alternative electron acceptors when oxygen is unavailable, yet the role of viruses (bacteriophages) in these processes is understudied. We investigated how seasonal anoxia impacts viral and microbial biogeochemical cycling, by using paired total metagenomes, viromes, and metatranscriptomes, that were collected weekly. Stratification and anoxia drove microbial community composition, but dataset origin impacted the interpretation of viral community structure, activity, and function. Importantly, taxa abundance did not correlate with activity for both microbes and viruses. We identified virus-host linkages for 116 phages across 55 distinct hosts, many of which expressed genes for aerobic methane oxidation, nitrogen fixation, denitrification, and sulfate reduction. Overall, this work demonstrates the breadth and dynamics of virus-host interactions in mediating biogeochemistry. Additionally, we propose that viral community detection, functional potential, and activity are sensitive to pre-sequencing decisions, which must be kept in mind when interpreting genomic data in a biologically meaningful way.

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Bacterial ecology and evolution converge on seasonal and decadal scales

Rohwer,

Kirkpatrick,

Garcia

et al. 2024

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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 abundantNanopelagicaceaefamily 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.

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The aftermath of a trophic cascade: Increased anoxia following species invasion of a eutrophic lake

Cited by 4 publications

References 61 publications

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

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

Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

Bacterial ecology and evolution converge on seasonal and decadal scales

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