Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.

Martı́nez, Miguel Ángel; Woodcroft, Ben J.; Ignacio‐Espinoza, J. Cesar; Zayed, Ahmed A.; Singleton, Caitlin M.; Boyd, Joel A.; Li, Yueh-Fen; Purvine, Samuel O.; Maughan, Heather; Hodgkins, S. B.; Anderson, Darya; Sederholm, Maya; Temperton, Ben; Bolduc, Benjamin; Saleska, S. R.; Tyson, Gene W.; Rich, V. I.

doi:10.1016/j.syapm.2018.12.003

Cited by 48 publications

(13 citation statements)

References 69 publications

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“…Further studies provided growing evidence that representatives of the phylum can occupy other environmental niches as well. Interestingly, their high contribution (reaching as much as 60% of the total community) has been confirmed in permafrost [52,53], which denies their exclusively thermophilic character. Additionally, a negative effect of the increased temperature has been observed in this specific location [52].…”

Section: Discussionmentioning

confidence: 99%

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Szafranek-Nakonieczna

Pytlak

Grządziel

et al. 2019

IJMS

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Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO2/H2). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH4 L−1 d−1) was highest in the culture grown with tryptone, yeast extract, and CO2/H2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.

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Section: Discussionmentioning

confidence: 99%

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Szafranek-Nakonieczna

Pytlak

Grządziel

et al. 2019

IJMS

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“…1B). By integrating these myriad types of datasets, the project has characterized how thaw-induced changes in hydrology and vegetation (Malmer et al, 2005;Johansson et al, 2006;Bäckstrand et al, 2010;Palace et al, 2018) drive changes in organic matter (Hodgkins et al, 2014(Hodgkins et al, , 2016Wilson et al, 2017;Wilson & Tfaily, 2018) and microbial and viral communities (Mondav et al, 2014;Trubl et al, 2016Trubl et al, , 2018Trubl et al, , 2019Singleton et al, 2018;Emerson et al, 2018;Woodcroft et al, 2018;Martinez et al, 2019;Wilson et al, 2019;Roux et al, 2019), giving rise to changes in carbon gas emissions (Wik et al, 2013(Wik et al, , 2018Hodgkins et al, 2014Hodgkins et al, , 2015McCalley et al, 2014;Burke et al, 2019;Perryman et al, 2020), and collectively these insights are allowing improvements in predictive models (Deng et al, 2014(Deng et al, , 2017Chang et al, 2019aChang et al, , 2019bWilson et al, 2019).…”

Section: Assembly Of Interdisciplinary Project Datasets In Need Of Inmentioning

confidence: 99%

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

Bolduc¹,

Hodgkins²,

Varner³

et al. 2020

PeerJ

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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

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“…Data from the IsoGenie and related projects (Table 1; Figure 1A) span multiple levels of study, with temporal scales ranging from minute-to decadal-resolution, and spatial scales ranging from nanoscale (e.g., elemental composition of soil and pore water), to microscale (e.g., microbial composition and metabolic processes), to macroscale (e.g., vegetation surveys and drone and satellite imagery) ( Figure 1B). By integrating these myriad types of datasets, the project has characterized how thawinduced changes in hydrology and vegetation (Malmer et al, 2005;Johansson et al, 2006;Bäckstrand et al, 2010;Palace et al, 2018) drive changes in organic matter (Hodgkins et al, 2014(Hodgkins et al, , 2016Wilson et al, 2017;Wilson & Tfaily, 2018) and microbial and viral communities (Mondav & Woodcroft et al, 2014;Trubl et al, 2016Trubl et al, , 2018Trubl et al, , 2019Singleton et al, 2018;Emerson et al, 2018;Woodcroft & Singleton et al, 2018;Martinez et al, 2019;Wilson et al, 2019;Roux et al, 2019), giving rise to changes in carbon gas emissions (Wik et al, 2013(Wik et al, , 2018Hodgkins et al, 2014Hodgkins et al, , 2015McCalley et al, 2014;Burke et al, 2019;Perryman et al, 2020), and collectively these insights are allowing improvements in predictive models (Deng et al, 2014(Deng et al, , 2017Chang et al, 2019b,a;Wilson et al, 2019).…”

Section: Assembly Of Interdisciplinary Project Datasets In Need Of Inmentioning

confidence: 99%

Peer Review #1 of "The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research (v0.2)"

2020

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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in 'speaking' to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10-year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example

show abstract

Cited by 48 publications

References 69 publications

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

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

Peer Review #1 of "The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research (v0.2)"

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