Abstract
Metagenomics in agricultural research allows for searching for bioindicators of soil health to characterize changes caused by management practices. Cover cropping (CC) improves soil health by mitigating nutrient losses, yet the benefits depend on the tillage system used. Field studies searching for indicator taxa within these systems are scarce and narrow in their scope. Our goal was to identify bioindicators of soil health from microbes that were responsive to CC (three levels) and tillage (chisel tillage, no-till) treatments after five years under field conditions. We used rRNA gene-based analysis via Illumina HiSeq2500 technology with QIIME 2.0 processing to characterize the microbial communities. Our results indicated that CC and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds. Corn–soybean rotations with legume–grass CC increased the RA of copiotrophic decomposers more than rotations with grass CC, whereas rotations with only bare fallows favored stress-tolerant oligotrophs, including nitrifiers and denitrifiers. Unlike bacteria, fewer indicator fungi and archaea were detected; fungi were poorly identified, and their responses were inconsistent, while the archaea RA increased under bare fallow treatments. This is primary information that allows for understanding the potential for managing the soil community compositions using cover crops to reduce nutrient losses to the environment.
Highlights
Ecological intensification is defined by Bender et al [1] as an approach “to enhance agricultural sustainability through the promotion of biodiversity and targeted management of soil communities.” Within this framework, cover cropping is one of the main tools that is widely researched and promoted as a promising strategy to mitigate soil nutrient loss, greenhouse gas emissions, and water pollution [2,3,4]
This study showed that cover cropping and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds, mainly through changing the soil nutrient availability, aeration, and moisture conditions
We found fewer indicator fungi and archaea; fungi were poorly identified and their responses were inconsistent, while the ammonia-oxidizing archaea (AOA) family Nitrososphaeraceae responded positively to control treatments (CT)
Summary
Ecological intensification is defined by Bender et al [1] as an approach “to enhance agricultural sustainability through the promotion of biodiversity and targeted management of soil communities.” Within this framework, cover cropping is one of the main tools that is widely researched and promoted as a promising strategy to mitigate soil nutrient loss, greenhouse gas emissions, and water pollution [2,3,4]. Ecological intensification is defined by Bender et al [1] as an approach “to enhance agricultural sustainability through the promotion of biodiversity and targeted management of soil communities.”. Within this framework, cover cropping is one of the main tools that is widely researched and promoted as a promising strategy to mitigate soil nutrient loss, greenhouse gas emissions, and water pollution [2,3,4]. Cover cropping (CC) benefits agroecosystem by improving soil organic matter (SOM) and water retention [5,6], suppressing weeds [7,8], reducing soil erosion [7], and preventing soil nutrient loss by scavenging excess nutrients [9,10,11,12]. Tillage reduces the provision of benefits from CC to soil organic C (SOC) content [16] and soil N [17] by increasing the N-leaching potential of legume CC and reducing the N-scavenging capability of grass CC [18]
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