The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Bolduc, Benjamin; Hodgkins, S. B.; Varner, R. K.; Crill, PM; McCalley, CK; Chanton, JP; Tyson, Gene W.; Riley, William J.; Palace, M. W.; Duhaime, Melissa B.; Hough, Moira; Saleska, S. R.; Sullivan, MB; Rich, VI; Frolking, S. E.; Li, C; Brodie, Edmund D.; Anderson, Darya; Axen, Heather J.; Bennett, Kathryn Ann; Dominguez, S; Ernakovich, Jessica G.; Fahnestock, F; Garnello, AJ; Jansen, Joachim; Jones, Robert M.; Eh, Kim; Logan, T. A.; Marcus, T. S.; McCabe, Samantha; McClure, Amelia; Mondav, Rhiannon; Perry, Anja; Raab, Nicole; Solheim, K; Tansey, Patrick; Trubl, Gareth; Wik, M.; Wilson, Rachel M.; Boyd, Joel A.; Burke, S. A.; Ky, Chang; Cooper, William T.; Cory, Alexandra B.; Cronin, Dylan; Crossen, K. B.; Deng, Jia; Dorrepaal, Ellen; Emerson, Joanne B.; Evans, Paul N.; Hoelzle, Robert D.; Huettel, Bruno; Hurwitz, Bonnie; Karaöz, Ulaş; Kolengowski, J; Li, F; Martı́nez, Miguel Ángel; Morales, Irasema Castillo; Nguyen, Don D.; Perryman, C. R.; Singleton, Caitlin M.; Tfaily, Malak M.; VerBerkmoes, Nathan C.; Vining,; Wehr, Richard; Winters, Kristi; Woodcroft, Ben J.; Zane, Grant M.; Zayed, Ahmed A.; Braswell, Rob; Campbell, Eleanor E. B.; DelGreco, J. L.; Fisk, J.; Herrick, C.; Lamit, LJ; Shorter, J. H.; Sullivan, F.; Torbick, Nathan; Ziniti, B

doi:10.7717/peerj.9467

Cited by 7 publications

(4 citation statements)

References 79 publications

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“…Recent estimates show substantial winter C loss [ 9 ], which may be greater than the average growing season C uptake [ 10 ]. While the winter months include large air temperature fluctuations and extreme temperature minimums [ 11 ], the temperatures found in much of the soil profile of permafrost or seasonally frozen bogs can remain stable and just below the freezing point (−1 to −5°C) [ 5 , 12 , 13 ]. Bacteria have been shown to remain active below the freezing point in soils with both catabolic and anabolic activities observed [ 14 – 16 ].…”

Section: Introductionmentioning

confidence: 99%

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

et al. 2021

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Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

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Section: Introductionmentioning

confidence: 99%

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

et al. 2021

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“…The combination of these qualities has attracted researchers globally and allowed unique long-term experiments to be conducted that provide historical data spanning more than a century. For more than a decade, the IsoGenie project, now the EMERGE Biology Integration Institute, has leveraged the historical data to advance a systems-level understanding of permafrost thaw with matched amplicon, meta-omic, process measurements, and biogeochemical characterization of thaw stages (comprehensive review in Bolduc et al 2020). We expanded these sampling efforts by collecting 20 peatland samples spanning three stages author/funder.…”

Section: Resultsmentioning

confidence: 99%

Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

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Roux

Borton

et al. 2023

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Climate change is disproportionately warming northern peatlands, which may release large carbon stores via increased microbial activity. While there are many unknowns about such microbial responses, virus roles are especially poorly characterized with studies to date largely restricted to bycatch from bulk metagenomes. Here, we used optimized viral particle purification techniques on 20 samples along a highly contextualized peatland permafrost thaw gradient, extracted and sequenced viral particle DNA using two library kits to capture single-stranded (ssDNA) and double-stranded (dsDNA) virus genomes (40 total viromes), and explored their diversity and potential ecosystem impacts. Both kits recovered similar dsDNA virus numbers, but only one also captured thousands of ssDNA viruses. Combining these data, we explored population-level ecology using genomic representation from 9,560 viral operational taxonomic units (vOTUs); nearly a 4-fold expansion from permafrost-associated soils, and 97% of which were novel when compared against large datasets from soils, oceans, and the human gut. In silico predictions identified putative hosts for 44% (4,149 dsDNA + 17 ssDNA) of the identified vOTUs spanning 2 eukaryotic, 12 archaeal, and 30 bacterial phyla. The recovered vOTUs encoded 1,684 putative auxiliary metabolic genes (AMGs) and other metabolic genes carried by ~10% of detected vOTUs, of which 46% were related to carbon processing and 644 were novel. These AMGs grouped into five functional categories and 11 subcategories, and nearly half (47%) of the AMGs were involved in carbon utilization. Of these, 112 vOTUs encoded 123 glycoside hydrolases spanning 15 types involved in the degradation of polysaccharides (e.g., cellulose) to monosaccharides (e.g., galactose), or further monosaccharide degradation, which suggests virus involvement in myriad metabolisms including fermentation and central carbon metabolism. These findings expand the scope of viral roles in microbial carbon processing and suggest viruses may be critical for understanding the fate of soil organic carbon in peatlands.

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“…Annual net ecosystem exchanges (NEE) of CO 2 and CH 4 from 2010 to 2014 were measured using transparent plexiglas autochambers (3 in each habitat for a total of 9) obtained from the Isogenie Database (Bolduc et al, 2020 , IsoGenieDB: https://isogenie‐db.asc.ohio‐state.edu/ ). The combined radiative impact of CO 2 and CH 4 fluxes was calculated using a CH 4 100 year global warming potential (GWP) of 28 (Boucher et al, 2009 ; IPCC, 2014 ).…”

Section: Methodsmentioning

confidence: 99%