Impact of storage and extraction methods on peat soil microbiomes DOI Creative Commons
Dylan Cronin,

Yueh-Fen Li,

Paul N. Evans

et al.

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e18745 - e18745

Published: Dec. 23, 2024

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, the impact varies type. Peat soils store a large portion of soil carbon their microbiomes mediate climate feedbacks. Here, we tested three five protocols on peat from physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts (here, meaning bacteria archaea) structure. Initial preservation method impacted alpha but not beta diversity, with in-field LifeGuard buffer yielding roughly two-thirds richness flash-freezing or transport field ice (all samples were stored at −80 °C after return field). Nucleic both diversity; one ( PowerSoil Total RNA Isolation kit DNA Elution Accessory ki t) diverged others PowerMax Soil kit-High Humic Acid Protocol , variations modified DNA/RNA isolation kit) capturing more diverse taxa, divergent structures. Although habitat depth still consistently dominated variation, method-based biases microbiome recovery for these climatologically-relevant are significant, underscore importance consistency accurate inter-study comparisons, long-term monitoring, consistent ecological interpretations.

Language: Английский

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle DOI Creative Commons
Bridget McGivern, Dylan Cronin, Jared B. Ellenbogen

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(6), P. 1454 - 1466

Published: May 28, 2024

Abstract With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due diminished phenol oxidase activity, inhibiting resident microbes and promoting stabilization. Pairing microbiome geochemical measurements along a thaw-induced saturation gradient Stordalen Mire, model Arctic peatland, we confirmed negative relationship between expression but failed support other trends predicted by the latch. To inventory alternative polyphenol removal strategies, built CAMPER, gene annotation tool leveraging knowledge gleaned across ecosystems. Applying CAMPER genome-resolved metatranscriptomes, identified genes for diverse polyphenol-active enzymes expressed various lineages under range of redox conditions. This shifts paradigm stabilize soils highlights need consider both oxic anoxic metabolisms understand cycling changing

Language: Английский

Citations

9
Multi-Omics Reveal Microbial Succession and Metabolomic Adaptations to Flood in a Hypersaline Coastal Lagoon DOI Creative Commons
Christopher Keneally, Daniel Chilton, Tyler Dornan

et al.

Water Research, Journal Year: 2025, Volume and Issue: unknown, P. 123511 - 123511

Published: March 1, 2025

Language: Английский

Citations

1
Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands DOI Creative Commons
Emily K. Bechtold, Jared B. Ellenbogen, Jorge A. Villa

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 22, 2025

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from methane-emitting wetlands. Microorganisms drive cycling, but little is known about their conservation across To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual flux data 9 wetlands, creating Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource used link microbiome composition function emissions, focusing on methane-cycling microbes networks driving carbon decomposition. We identify eight genera shared wetlands show wetland-specific metabolic interactions marshes, revealing low connections between methanogens methanotrophs high-emitting Methanoregula emerged as a hub methanogen strong predictor flux. In these it also displays functional potential methylotrophic methanogenesis, highlighting importance this pathway ecosystems. Collectively, our findings illuminate trends microbial decomposition while providing an extensive publicly available database advance future research. The authors created multisite CH4 fluxes diverse differences cross-feeding dynamics that improve predictions

Language: Английский

Citations

0
Reduction of iron-organic carbon associations shifts net greenhouse gas release after initial permafrost thaw DOI Creative Commons
Eva Voggenreiter, Laurel K. ThomasArrigo, Joachim Kilian

et al.

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109735 - 109735

Published: Jan. 1, 2025

Language: Английский

Citations

0
Role of permafrost thaw transitions in biogeochemical nitrogen cycling DOI Creative Commons
Merritt Logan, Monique Patzner, Jacob P. VanderRoest

et al.

Soil & Environmental Health, Journal Year: 2025, Volume and Issue: unknown, P. 100148 - 100148

Published: March 1, 2025

Language: Английский

Citations

0
Vertical distribution patterns and potential activities of methanogenic and methanotrophic communities in permafrost peatlands of Greater Khingan Mountains DOI

Anwen Liu,

Yin Wei-ping,

Dalong Ma

et al.

Ecological Indicators, Journal Year: 2025, Volume and Issue: 175, P. 113539 - 113539

Published: May 5, 2025

Language: Английский

Citations

0
Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism DOI
John A. Bouranis, Malak Tfaily

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(12), P. 1170 - 1178

Published: June 1, 2024

Language: Английский

Citations

2
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA DOI Creative Commons
Anna Rasmussen, Bradley B. Tolar, John Bargar

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(7)

Published: June 28, 2024

ABSTRACT We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling—particularly methane-cycling—microorganisms in montane riparian floodplain sediments. generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- 150-cm depth below the sediment surface capturing transition between oxic, unsaturated sediments anoxic, saturated Slate River (SR) (Crested Butte, CO, USA). recovered of putative methanogens, methanotrophs, methylotrophs ( n = 57). Methanogens, found only deep, anoxic depths at SR, originate three different clades Methanoregulaceae , Methanotrichaceae Methanomassiliicoccales ), each with a methanogenesis pathway; methanotrophic within Archaea Candidatus Methanoperedens) uncultured bacteria Ca . Binatia) oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens exceptionally abundant (~1,400× coverage, >50% abundance MAG library) one sample that also contained aceticlastic indicating potential C1/methane-cycling hotspot. Methylomirabilis SR encode pathways methylotrophy but do harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports clade genus is methanotrophic. The genetic was widespread, over 10% 19% encoding methanol dehydrogenase substrate-specific methyltransferase, respectively. Thermoplasmata archaea Gimiplasmatales (UBA10834) contain may allow anaerobic methylotrophic acetogenesis. Overall, reveal production consumption system robust methylotrophy. IMPORTANCE cycling carbon by microorganisms subsurface environments particular relevance face global climate change. Riparian high organic can be degraded into C1 compounds such as methane, methanol, methylamines, fate which depends on microbial metabolisms present well hydrological conditions availability oxygen. In study, we 1,000 river are capable producing consuming other compounds, highlighting both without sample, hotspot system.

Language: Английский

Citations

2
Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands DOI Open Access
Emily K. Bechtold, Jared B. Ellenbogen, Jorge A. Villa

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 15, 2024

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from methane-emitting wetlands. Microorganisms mediate cycling, yet knowledge their conservation across wetlands remains scarce. To address this, we integrated 1,118 16S rRNA amplicon datasets (116 new), 305 metagenomes (20 new) that yielded 4,745 medium and high-quality metagenome assembled genomes (MAGs; 617 133 metatranscriptomes, annual flux data 9 create Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This new resource was leveraged link microbiome compositional profiles encoded functions emissions, with specific focus on methane-cycling populations microbial carbon decomposition networks fuel them. We identified eight genera were conserved wetlands, deciphered metabolic interactions marshes, revealing low methanogen-methanotroph connectivity high-emitting Methanoregula emerged as a hub methanogen strong predictor flux, demonstrating potential broad relevance methylotrophic methanogenesis these ecosystems. Collectively, our findings illuminate trends between provide an extensive publicly available database advance future research.

Language: Английский

Citations

1
Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands DOI Creative Commons
Michael J. Wilkins, Emily K. Bechtold, Jared B. Ellenbogen

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: June 12, 2024

Abstract Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from methane-emitting wetlands. Microorganisms mediate cycling, yet knowledge their conservation across wetlands remains scarce. To address this, we integrated 1,118 16S rRNA amplicon datasets (116 new), 305 metagenomes (20 new) that yielded 4,745 medium and high-quality metagenome assembled genomes (MAGs; 617 133 metatranscriptomes, annual flux data 9 create Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This new resource was leveraged link microbiome compositional profiles encoded functions emissions, with specific focus on methane-cycling populations microbial carbon decomposition networks fuel them. We identified eight genera were conserved wetlands, deciphered metabolic interactions marshes, revealing low methanogen-methanotroph connectivity high-emitting Methanoregula emerged as a hub methanogen strong predictor flux, demonstrating potential broad relevance methylotrophic methanogenesis these ecosystems. Collectively, our findings illuminate trends between provide an extensive publicly available database advance future research.

Language: Английский

Citations

0