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Article ; Online: Microbes on decomposing litter in streams: entering on the leaf or colonizing in the water?

Hayer, Michaela / Wymore, Adam S / Hungate, Bruce A / Schwartz, Egbert / Koch, Benjamin J / Marks, Jane C

2021 Volume 16, Issue 3, Page(s) 717–725

Abstract: When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ... ...

Abstract	When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ecosystems, fungi and bacteria that enter soils with dead leaves often play prominent roles in decomposition, but their role in aquatic decomposition is less known. Here, we test whether fungi and bacteria that enter streams on senesced leaves are growing during decomposition and compare their abundances and growth to bacteria and fungi that colonize leaves in the water. We employ quantitative stable isotope probing to identify growing microbes across four leaf litter species and two decomposition times. We find that most of the growing fungal species on decomposing leaves enter the water with the leaf, whereas most growing bacteria colonize from the water column. Results indicate that the majority of bacteria found on litter are growing, whereas the majority of fungi are dormant. Both bacterial and fungal assemblages differed with leaf type on the dried leaves and throughout decomposition. This research demonstrates the importance of fungal species that enter with the leaf on aquatic decomposition and the prominence of bacteria that colonize decomposing leaves in the water.
MeSH term(s)	Ecosystem ; Fungi/genetics ; Plant Leaves/microbiology ; Rivers/microbiology ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-021-01114-6
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Article: Substrate stoichiometric regulation of microbial respiration and community dynamics across four different ecosystems

Liu, Xiao Jun Allen / Hayer, Michaela / Mau, Rebecca L. / Schwartz, Egbert / Dijkstra, Paul / Hungate, Bruce A.

Soil biology & biochemistry. 2021 Dec., v. 163

2021

Abstract: Microbes decompose soil organic matter (SOM), yet it is unclear how substrate inputs (i.e., stoichiometry) directly mediate microbial activities and community dynamics. We hypothesized that C+N input has the largest effect on microbial respiration and ... ...

Abstract	Microbes decompose soil organic matter (SOM), yet it is unclear how substrate inputs (i.e., stoichiometry) directly mediate microbial activities and community dynamics. We hypothesized that C+N input has the largest effect on microbial respiration and community structure, followed by C input and N input. Soils were collected from four ecosystems (grassland, piñon-juniper, ponderosa pine, mixed conifer) and amended with NH₄NO₃ (N only; 100 μg g⁻¹ wk⁻¹), ¹³C-glucose (C only; 1000 μg g⁻¹ wk⁻¹), or C+N in a five-week laboratory incubation. We found that C+N input induced the greatest total respiration while C input induced the greatest SOM-derived respiration (i.e., priming effect) across ecosystems. Shifts in community composition were the largest with C+N input, followed by C input, and showed little response to N input. C only and C+N inputs increased both of the relative and absolute abundances of Actinobacteria and Proteobacteria (α, β, γ), but reduced the relative abundances of Verrucomicrobia and δ-Proteobacteria. C+N input increased the relative abundances of Bacillales, Rhizobiales, Burkholderiales and of 9 families, and reduced the relative abundances of Myxococcales and of 12 families, but showed little effect on the absolute abundances of these bacterial taxa. N input reduced the absolute abundances of Actinobacteria, Proteobacteria, and Verrucomicrobia but did not affect their relative abundances in the mixed conifer soil; by contrast, N input reduced relative abundances of δ-Proteobacteria and increased the relative abundances of γ-Proteobacteria but did not affect their absolute abundances in the ponderosa pine soil. We also found that substrate inputs were the main driver of SOM decomposition, microbial respiration and diversity, while soil ecosystem was the main driver of community composition and abundances of most bacterial phyla. Our work suggests that substrate stoichiometry has predictable effects on soil C cycling, microbial diversity and community composition, but has variable effects on microbial abundances, and that incorporating bacterial gene copies in abundance calculations can help more accurately estimate microbial responses across taxonomic levels and ecosystems.
Keywords	Actinobacteria ; Bacillales ; Burkholderiales ; Myxococcales ; Pinus ponderosa ; Rhizobiales ; Verrucomicrobia ; biochemistry ; community structure ; conifers ; genes ; grasslands ; pinyon-juniper ; soil ; soil ecosystems ; soil organic matter ; stoichiometry
Language	English
Dates of publication	2021-12
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2021.108458
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Stable Isotope Probing of Microorganisms in Environmental Samples with H

Schwartz, Egbert / Hayer, Michaela / Hungate, Bruce A / Mau, Rebecca L

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2046, Page(s) 129–136

Abstract: We describe a protocol for investigating microbial growth in environmental samples via stable isotope probing (SIP) with ... ...

Abstract	We describe a protocol for investigating microbial growth in environmental samples via stable isotope probing (SIP) with H
MeSH term(s)	Bacteria/genetics ; Bacteria/metabolism ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Environmental Microbiology ; Isotope Labeling/methods ; Oxygen Isotopes/metabolism ; Water/chemistry
Chemical Substances	DNA, Bacterial ; Oxygen Isotopes ; Water (059QF0KO0R)
Language	English
Publishing date	2019-08-12
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9721-3_10
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Article ; Online: Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community

Stone, Bram W. / Blazewicz, Steven J. / Koch, Benjamin J. / Dijkstra, Paul / Hayer, Michaela / Hofmockel, Kirsten S. / Liu, Xiao Jun Allen / Mau, Rebecca L. / Pett-Ridge, Jennifer / Schwartz, Egbert / Hungate, Bruce A.

Oecologia. 2023 Mar., v. 201, no. 3 p.771-782

2023

Abstract: Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative ...

Abstract	Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.
Keywords	altitude ; ammonium sulfate ; biodiversity ; carbon ; data analysis ; ecological communities ; genome ; glucose ; mortality ; nitrogen ; population size ; soil ; soil bacteria ; stable isotopes
Language	English
Dates of publication	2023-03
Size	p. 771-782.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	123369-5
ISSN	1432-1939 ; 0029-8549
ISSN (online)	1432-1939
ISSN	0029-8549
DOI	10.1007/s00442-023-05322-z
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Article ; Online: The predictive power of phylogeny on growth rates in soil bacterial communities.

Walkup, Jeth / Dang, Chansotheary / Mau, Rebecca L / Hayer, Michaela / Schwartz, Egbert / Stone, Bram W / Hofmockel, Kirsten S / Koch, Benjamin J / Purcell, Alicia M / Pett-Ridge, Jennifer / Wang, Chao / Hungate, Bruce A / Morrissey, Ember M

ISME communications

2023 Volume 3, Issue 1, Page(s) 73

Abstract: Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement ... ...

Abstract	Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
Language	English
Publishing date	2023-07-15
Publishing country	England
Document type	Journal Article
ISSN	2730-6151
ISSN (online)	2730-6151
DOI	10.1038/s43705-023-00281-1
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Article ; Online: Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming.

Propster, Jeffrey R / Schwartz, Egbert / Hayer, Michaela / Miller, Samantha / Monsaint-Queeney, Victoria / Koch, Benjamin J / Morrissey, Ember M / Mack, Michelle C / Hungate, Bruce A

Applied and environmental microbiology

2023 Volume 89, Issue 3, Page(s) e0154322

Abstract: Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input ...

Abstract	Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using
MeSH term(s)	Soil ; Ecosystem ; Phylogeny ; Tundra ; Arctic Regions ; Climate Change ; Carbon/metabolism
Chemical Substances	Soil ; Carbon (7440-44-0)
Language	English
Publishing date	2023-02-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.01543-22
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Article ; Online: Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community.

Stone, Bram W / Blazewicz, Steven J / Koch, Benjamin J / Dijkstra, Paul / Hayer, Michaela / Hofmockel, Kirsten S / Liu, Xiao Jun Allen / Mau, Rebecca L / Pett-Ridge, Jennifer / Schwartz, Egbert / Hungate, Bruce A

Oecologia

2023 Volume 201, Issue 3, Page(s) 771–782

Abstract	Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.
MeSH term(s)	Ecosystem ; Soil ; Soil Microbiology ; Bacteria ; Carbon
Chemical Substances	Soil ; Carbon (7440-44-0)
Language	English
Publishing date	2023-02-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	123369-5
ISSN	1432-1939 ; 0029-8549
ISSN (online)	1432-1939
ISSN	0029-8549
DOI	10.1007/s00442-023-05322-z
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Article ; Online: Resource partitioning and amino acid assimilation in a terrestrial geothermal spring.

Lai, Dengxun / Hedlund, Brian P / Mau, Rebecca L / Jiao, Jian-Yu / Li, Junhui / Hayer, Michaela / Dijkstra, Paul / Schwartz, Egbert / Li, Wen-Jun / Dong, Hailiang / Palmer, Marike / Dodsworth, Jeremy A / Zhou, En-Min / Hungate, Bruce A

The ISME journal

2023 Volume 17, Issue 11, Page(s) 2112–2122

Abstract: High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was ... ...

Abstract	High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of
MeSH term(s)	Hot Springs/chemistry ; Phylogeny ; Amino Acids ; Aspartic Acid ; Isotopes ; DNA ; Acetates
Chemical Substances	Amino Acids ; Aspartic Acid (30KYC7MIAI) ; Isotopes ; DNA (9007-49-2) ; Acetates
Language	English
Publishing date	2023-09-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-023-01517-7
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Article ; Online: Opposing effects of bacterial endophytes on biomass allocation of a wild donor and agricultural recipient.

Rubin, Rachel L / Jones, Ashley N / Hayer, Michaela / Shuman-Goodier, Molly E / Andrews, Lela V / Hungate, Bruce A

FEMS microbiology ecology

2020 Volume 96, Issue 3

Abstract: Root endophytes are a promising tool for increasing plant growth, but it is unclear whether they perform consistently across plant hosts. We characterized the blue grama (Bouteloua gracilis) root microbiome using two sequencing methods, quantified the ... ...

Abstract	Root endophytes are a promising tool for increasing plant growth, but it is unclear whether they perform consistently across plant hosts. We characterized the blue grama (Bouteloua gracilis) root microbiome using two sequencing methods, quantified the effects of root endophytes in the original host (blue grama) and an agricultural recipient, corn (Zea mays), under drought and well-watered conditions and examined in vitro mechanisms for plant growth promotion. 16S rRNA amplicon sequencing revealed that the blue grama root microbiome was similar across an elevation gradient, with the exception of four genera. Culturing and Sanger sequencing revealed eight unique endophytes belonging to the genera Bacillus, Lysinibacillus and Pseudomonas. All eight endophytes colonized corn roots, but had opposing effects on aboveground and belowground biomass in each plant species: they increased blue grama shoot mass by 45% (19) (mean +/- SE) while decreasing corn shoot mass by 10% (19), and increased corn root:shoot by 44% (7), while decreasing blue grama root:shoot by 17% (7). Furthermore, contrary to our expectations, endophytes had stronger effects on plant growth under well-watered conditions rather than drought conditions. Collectively, these results suggest that ecological features, including host identity, bacterial traits, climate conditions and morphological outcomes, should be carefully considered in the design and implementation of agricultural inocula.
MeSH term(s)	Biomass ; Endophytes/genetics ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Resource Allocation
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2020-01-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiaa012
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Article ; Online: Quantitative stable isotope probing with H

Papp, Katerina / Mau, Rebecca L / Hayer, Michaela / Koch, Benjamin J / Hungate, Bruce A / Schwartz, Egbert

The ISME journal

2018 Volume 12, Issue 12, Page(s) 3043–3045

Abstract: Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We ... ...

Abstract	Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Deuterium/analysis ; Microbiota/genetics ; Oxygen Isotopes/analysis ; RNA, Bacterial/biosynthesis ; RNA, Bacterial/genetics ; RNA, Ribosomal/biosynthesis ; RNA, Ribosomal/genetics ; Soil Microbiology
Chemical Substances	Oxygen Isotopes ; RNA, Bacterial ; RNA, Ribosomal ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2018-07-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-018-0233-7
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