Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

CN Butterfield, Z Li, PF Andeer, S Spaulding… - PeerJ, 2016 - peerj.com
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to
CO2. However, understanding of the microbiology of this process is limited because most …

Microbial metagenomics reveals climate-relevant subsurface biogeochemical processes

PE Long, KH Williams, SS Hubbard, JF Banfield - Trends in microbiology, 2016 - cell.com
Microorganisms play key roles in terrestrial system processes, including the turnover of
natural organic carbon, such as leaf litter and woody debris that accumulate in soils and …

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

TL Swenson, U Karaoz, JM Swenson… - Nature …, 2018 - nature.com
Metagenomic sequencing provides a window into microbial community structure and
metabolic potential; however, linking these data to exogenous metabolites that …

High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

AB Narrowe, JC Angle, RA Daly… - Environmental …, 2017 - Wiley Online Library
Despite being key contributors to biogeochemical processes, archaea are frequently
outnumbered by bacteria, and consequently are underrepresented in combined molecular …

The potential of metagenomic approaches for understanding soil microbial processes

DD Myrold, LH Zeglin… - Soil Science Society of …, 2014 - Wiley Online Library
Technological advances in sequencing technologies and bioinformatics analysis tools now
enable the generation of a metagenome from soil, although the ultimate goal of obtaining …

Back to the future of soil metagenomics

J Nesme, W Achouak, SN Agathos, M Bailey… - Frontiers in …, 2016 - frontiersin.org
Direct extraction and characterization of microbial community DNA through PCR amplicon
surveys and metagenomics has revolutionized the study of environmental microbiology and …

The soil microbiome—from metagenomics to metaphenomics

JK Jansson, KS Hofmockel - Current opinion in microbiology, 2018 - Elsevier
Soil microorganisms carry out important processes, including support of plant growth and
cycling of carbon and other nutrients. However, the majority of soil microbes have not yet …

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

LH Orellana, JC Chee-Sanford… - Applied and …, 2018 - Am Soc Microbiol
The dynamics of individual microbial populations and their gene functions in agricultural
soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are …

Impact of plants on the diversity and activity of methylotrophs in soil

MC Macey, J Pratscher, AT Crombie, JC Murrell - Microbiome, 2020 - Springer
Background Methanol is the second most abundant volatile organic compound in the
atmosphere, with the majority produced as a metabolic by-product during plant growth …

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

S Diamond, PF Andeer, Z Li, A Crits-Christoph… - Nature …, 2019 - nature.com
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant
of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with …