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  1. Article ; Online: Variation in genomic traits of microbial communities among ecosystems.

    Chuckran, Peter F / Hungate, Bruce A / Schwartz, Egbert / Dijkstra, Paul

    FEMS microbes

    2021  Volume 2, Page(s) xtab020

    Abstract: Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these ... ...

    Abstract Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of
    Language English
    Publishing date 2021-12-01
    Publishing country England
    Document type Journal Article
    ISSN 2633-6685
    ISSN (online) 2633-6685
    DOI 10.1093/femsmc/xtab020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Multiple mechanisms determine the effect of warming on plant litter decomposition in a dryland

    Chuckran, Peter F / Reibold, Robin / Throop, Heather L / Reed, Sasha C

    Elsevier Ltd Soil biology & biochemistry. 2020 June, v. 145

    2020  

    Abstract: In drylands, where soil fertility is typically low, plant litter decomposition provides particularly critical carbon and nitrogen inputs into soil. Although climate change is projected to increase the already large global extent of drylands, it is ... ...

    Abstract In drylands, where soil fertility is typically low, plant litter decomposition provides particularly critical carbon and nitrogen inputs into soil. Although climate change is projected to increase the already large global extent of drylands, it is unknown how warmer temperatures will affect core ecosystem processes, such as plant litter decomposition, in these systems. To address this key unknown, we conducted a litterbag study in a long-term dryland warming experiment in southeastern Utah, USA. Unexpectedly, we did not find an overall effect of warming on leaf litter mass loss over time. Instead, our results indicated both positive and negative effects of warming on mass loss which offset one another. In particular, our findings suggested that a warming-induced degradation of biological soil crusts (soil surface community of mosses, lichens, and/or cyanobacteria that live in drylands worldwide) increased soil-litter mixing, thereby accelerating decomposition. Results also suggested that a warming-induced reduction in litter moisture slowed decomposition. In addition, we found that warming lowered the carbon-to-nitrogen ratio of the decomposing litter. These results showed that warming did not alter the total litter mass-loss rates in this ecosystem, but that decomposition patterns were affected through more nuanced changes to both the biological and physical environment of dryland soils.
    Keywords Cyanobacteria ; arid lands ; biological soil crusts ; carbon ; carbon nitrogen ratio ; climate change ; ecosystems ; lichens ; mixing ; mosses and liverworts ; nitrogen ; plant litter ; soil fertility ; temperature ; Utah
    Language English
    Dates of publication 2020-06
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 280810-9
    ISSN 0038-0717
    ISSN 0038-0717
    DOI 10.1016/j.soilbio.2020.107799
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  3. Article: Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.

    Chuckran, Peter F / Fofanov, Viacheslav / Hungate, Bruce A / Morrissey, Ember M / Schwartz, Egbert / Walkup, Jeth / Dijkstra, Paul

    mSystems

    2021  Volume 6, Issue 3

    Abstract: Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N ... ...

    Abstract Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.
    Language English
    Publishing date 2021-05-11
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00161-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled.

    Antoninka, Anita / Chuckran, Peter F / Mau, Rebecca L / Slate, Mandy L / Mishler, Brent D / Oliver, Melvin J / Coe, Kirsten K / Stark, Llo R / Fisher, Kirsten M / Bowker, Matthew A

    Frontiers in microbiology

    2022  Volume 13, Page(s) 821860

    Abstract: Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth's terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical ... ...

    Abstract Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth's terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.
    Language English
    Publishing date 2022-04-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.821860
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

    Chuckran, Peter F / Huntemann, Marcel / Clum, Alicia / Foster, Brian / Foster, Bryce / Roux, Simon / Palaniappan, Krishnaveni / Varghese, Neha / Mukherjee, Supratim / Reddy, T B K / Daum, Chris / Copeland, Alex / Ivanova, Natalia N / Kyrpides, Nikos C / Del Rio, Tijana Glavina / Eloe-Fadrosh, Emiley A / Morrissey, Ember M / Schwartz, Egbert / Fofanov, Viacheslav /
    Hungate, Bruce / Dijkstra, Paul

    Microbiology resource announcements

    2020  Volume 9, Issue 44

    Abstract: The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and ... ...

    Abstract The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.
    Language English
    Publishing date 2020-10-29
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00895-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Functional Significance of Bacterial Predators.

    Hungate, Bruce A / Marks, Jane C / Power, Mary E / Schwartz, Egbert / van Groenigen, Kees Jan / Blazewicz, Steven J / Chuckran, Peter / Dijkstra, Paul / Finley, Brianna K / Firestone, Mary K / Foley, Megan / Greenlon, Alex / Hayer, Michaela / Hofmockel, Kirsten S / Koch, Benjamin J / Mack, Michelle C / Mau, Rebecca L / Miller, Samantha N / Morrissey, Ember M /
    Propster, Jeffrey R / Purcell, Alicia M / Sieradzki, Ella / Starr, Evan P / Stone, Bram W G / Terrer, César / Pett-Ridge, Jennifer

    mBio

    2021  Volume 12, Issue 2

    Abstract: Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is ...

    Abstract Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera
    MeSH term(s) Animals ; Bacteria/classification ; Bacteria/genetics ; Bacteria/growth & development ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Bacteriophages ; Carbon/metabolism ; DNA, Bacterial/genetics ; Deltaproteobacteria/genetics ; Deltaproteobacteria/physiology
    Chemical Substances DNA, Bacterial ; Carbon (7440-44-0)
    Language English
    Publishing date 2021-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.00466-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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