The influence of alfalfa‐switchgrass intercropping on microbial community structure and function

Abstract

Summary The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2O, a potent greenhouse gas. Intercropping with nitrogen‐fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia‐oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia‐oxidizing bacteria abundance in fertilized plots significantly correlated to N2O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.

Weeds in the Alfalfa Field Decrease Rhizosphere Microbial Diversity and Association Networks in the North China Plain

“…Soil microorganisms are influenced by specific species as the presence of plants controls the levels of microbial diversity and drives community assembly ( Shang et al, 2021 ). Our results show that weeds significantly decreased bacterial and fungal α-diversity indices when compared with Ms., which were possibly elicited by inherent soil properties and the influence of plant growth on microbial communities ( Cha et al, 2021 ). Ms. plants may enhance microbial activity in the soil due to root depositions as increased root biomass is a significant source of C for microbial biomass, which in turn regulates soil microbial communities in their immediate vicinity ( Song et al, 2021 ).…”

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

“…The abundances of target genes (i.e. Clade I and Clade II nosZ ) were determined by calculating the ratio between normalized target reads (counts divided by the median protein length) and the genome equivalents [ 48 ]. Reference nosZ genes were also searched against the assemblies and MAGs using precompiled hidden Markov models obtained from FunGene and HMMer [ 49 , 50 ].…”

Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome

“…Moreover, the datasets from rhizosphere soils were not used in this study because they are extensively and dynamically affected by the plant roots (Zhalnina et al, 2018) and not representative of the soil microbial communities. In total, we collected 1445 datasets as listed in Table S1 (Angle et al, 2017; Bahram et al, 2018; Berkelmann et al, 2020; Black and Just, 2018; Cania et al, 2019; Cha et al, 2021; Chen et al, 2019; Chu et al, 2018; Crits-Christoph et al, 2018; Hartman et al, 2017; Huber et al, 2018; Jiang et al, 2018; Johnston et al, 2016; Li et al, 2018, 2020; Links et al, 2021; Liu et al, 2018; Ma et al, 2018; Neal et al, 2021; Nelkner et al, 2019; Orellana et al, 2018; Ouyang and Norton, 2020; Paungfoo-Lonhienne et al, 2017; Romanowicz et al, 2021; Sukhum et al, 2021; Suttner et al, 2020; Hang Wang et al, 2021; Wang et al, 2020; Woodcroft et al, 2018; Wu et al, 2021; Xiao et al, 2016; Xue et al, 2019; Yu et al, 2019; Yurgel et al, 2019; Zhang et al, 2019; Zheng et al, 2021). The latitude and longitude of each sampling site were obtained from public databases [INSDC BioSamples database (Courtot et al, 2022) and MG-RAST] and verified with the descriptions in each publication.…”