Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Benucci, Gian Maria Niccolò; Beschoren da Costa, Pedro; Wang, Xinxin; Bonito, Gregory

doi:10.1111/1462-2920.16269

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Journal Article · Wed Nov 23 23:00:00 EST 2022 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.16269· OSTI ID:1899792

^[1]; ^[2]; Wang, Xinxin ^[3]; ^[2]

DOE Great Lakes Bioenergy Research Center Michigan State University East Lansing Michigan USA, Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA, Department of Microbiology &, Molecular Genetics Michigan State University East Lansing USA
DOE Great Lakes Bioenergy Research Center Michigan State University East Lansing Michigan USA, Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA
Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA

Abstract

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant‐associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long‐term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil‐depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co‐occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal‐fungal links and an increase of bacteria–bacteria links with increasing depth in all crops, particularly in the root microbiome.

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Sponsoring Organization:: USDOE

OSTI ID:: 1899792

Alternate ID(s):: OSTI ID: 2420790
OSTI ID: 1924122

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 2 Vol. 25; ISSN 1462-2912

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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