Microbial Signatures in Fertile Soils Under Long-Term N Management

María B Villamil,Marco Allegrini,María C Zabaloy,Nakian Kim,Sandra L Rodríguez-Zas,Chance W Riggins

doi:10.3389/fsoil.2021.765901

Abstract

Long-term reliance on inorganic N to maintain and increase crop yields in overly simplified cropping systems in the U.S. Midwest region has led to soil acidification, potentially damaging biological N2 fixation and accelerating potential nitrification activities. Building on this published work, rRNA gene-based analysis via Illumina technology with QIIME 2.0 processing was used to characterize the changes in microbial communities associated with such responses. Amplicon sequence variants (ASVs) for each archaeal, bacterial, and fungal taxa were classified using the Ribosomal Database Project (RDP). Our goal was to identify bioindicators from microbes responsive to crop rotation and N fertilization rates following 34–35 years since the initiation of experiments. Research plots were established in 1981 with treatments of rotation [continuous corn (Zea mays L.) (CCC) and both the corn (Cs) and soybean (Glycine max L. Merr.) (Sc) phases of a corn-soybean rotation], and of N fertilization rates (0, 202, and 269 kg N/ha) arranged as a split-plot in a randomized complete block design with three replications. We identified a set of three archaea, and six fungal genera responding mainly to rotation; a set of three bacteria genera whose abundances were linked to N rates; and a set with the highest number of indicator genera from both bacteria (22) and fungal (12) taxa responded to N fertilizer additions only within the CCC system. Indicators associated with the N cycle were identified from each archaeal, bacterial, and fungal taxon, with a dominance of denitrifier- over nitrifier- groups. These were represented by a nitrifier archaeon Nitrososphaera, and Woesearchaeota AR15, an anaerobic denitrifier. These archaea were identified as part of the signature for CCC environments, decreasing in abundance with rotated management. The opposite response was recorded for the fungus Plectosphaerella, a potential N2O producer, less abundant under continuous corn. N fertilization in CCC or CS systems decreased the abundance of the bacteria genera Variovorax and Steroidobacter, whereas Gp22 and Nitrosospira only showed this response under CCC. In this latter system, N fertilization resulted in increased abundances of the bacterial denitrifiers Gp1, Denitratisoma, Dokdonella, and Thermomonas, along with the fungus Hypocrea, a known N2O producer. The identified signatures could help future monitoring and comparison across cropping systems as we move toward more sustainable management practices. At the same time, this is needed primary information to understand the potential for managing the soil community composition to reduce nutrient losses to the environment.

Highlights

Due to the excessive rates and inefficiencies associated with N fertilizer use, agricultural soil management is a major source of N losses to the environment [1, 2]
The archaeal taxa had 118,618 archaeal 16S rRNA region sequences clustered into 8 amplicon sequence variants (ASVs), the bacterial taxa had 14,136,085 16S V4 region sequences clustered into 1701 ASVs, whereas the fungal kingdom had 3,166,008 in the abundance of fungal counts (ITS) region sequences clustered into 342 ASVs
Results from this study indicate that both agronomic practices of crop rotation and N fertilization rates leave a significant imprint on the soil microbial groups following over three decades of management

Summary

Introduction

Due to the excessive rates and inefficiencies associated with N fertilizer use, agricultural soil management is a major source of N losses to the environment [1, 2]. All major transformative steps of the N cycle, fixation, mineralization, nitrification, and denitrification are microbially mediated [3]. Previous studies aimed to characterize the distribution and diversity of N relevant microorganisms in agroecosystems have used cultivation independent techniques targeting genes encoding phylogenic genes and critical enzymes of the microbial N cycle: nif H (N2 fixation), amoA (first step of nitrification), nirK and nirS (second step of denitrification), and nosZ (last step of denitrification) [1, 4,5,6] yet only a few long-term studies provided a complete picture of N-fertilization effects on the N transformation cycle within a single agroecosystem [7,8,9]. The identification of bioindicators from well-replicated, long-term agricultural experiments are essential, as these systems represent a unique “steady” setting to characterize baselines and evidence changes in microbiota abundance and diversity in relation to management practices [15]

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Conclusion