Global meta-analysis and metagenomics approach on the soil microbiome associated with cover cropping

Soil nutrient loss is one of the major causes of soil degradation that threatens future global food security. Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. As one of the agricultural practices that can affect cover cropping, effects of tillage on cover cropping have been widely researched as well. Because cover cropping and tillage can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Therefore, studying their impact on the soil microbiome is necessary because the soil microbes are important drivers of soil processes including those relevant to soil health. The objectives of this MS research were i) estimate the baseline effect size of cover cropping on soil microbial abundance, activity, and diversity, ii) identify environmental and agricultural factors that affect the cover crop effects sizes on the soil microbiome, iii) further understand the cover crop effects on the soil microbial diversity by investigating the shifts in the soil microbial compositions, and iv) contribute to understanding how the relationship between cover cropping and the soil microbiome may affect the soil health. A meta-analysis was conducted to estimate the global average effects of cover cropping on the soil microbiome. This study compiled the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome. This meta-analysis revealed that cover cropping affect the overall soil microbial diversity and that tillage is a major cofactor that affect this relationship. To further investigate the cover cropping and tillage effects on the soil microbial diversity, a metagenomics study was conducted. This second part of the study was to observe compositional changes in the soil microbiome in response to cover cropping and tillage. Also, this study sought to identify microbial indicators that can be used to gauge responses of microbial guilds with functions relevant to soil health. This study used soil DNA data from a long-term cover cropping and tillage experiment on corn and soybean rotation in Illinois, USA. This study found that copiotrophic bacterial decomposers increased with legume cover crops and tillage, while oligotrophic and stress tolerant bacteria did so with bare fallow and no-till. Fungal groups responded to cover cropping and tillage based on their physiology, interaction with plant hosts, and nutrient strategies. This study also found an ammonia-oxidizing archaea species that increased with bare fallow. The consistent patterns that the microbial groups in this study display make them potential microbial indicators. Also, grass cover crops with no-till showed most potential for soil nutrient loss. Overall, this MS research found that cover cropping significantly enriches the soil microbiome. However, cover cropping effects may apply differential pressures on microbial groups with different adaptations so that the overall diversity is not changed significantly. This research suggests that timing and other agricultural practices like tillage need to be carefully considered to direct the changes in the soil microbiome to benefit the soil health

Microbial shifts following five years of cover cropping and tillage practices in fertile agroecosystems

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.Fil: Kim, Nakian. University of Illinois; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Riggins, Chance W.. University of Illinois; Estados UnidosFil: Rodríguez Zas, Sandra. University of Illinois; Estados UnidosFil: Villamil, Maria Bonita. University of Illinois; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.Fil: Behnke, Gevan D.. University of Illinois at Urbana; Estados UnidosFil: Kim, Nakian. University of Illinois at Urbana; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Riggins, Chance W.. University of Illinois at Urbana; Estados UnidosFil: Rodriguez Zas, Sandra. University of Illinois at Urbana; Estados UnidosFil: Villamil, Maria Bonita. University of Illinois at Urbana; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Microbial Signatures in Fertile Soils Under Long-Term N Management

Long-term reliance on inorganic N tomaintain 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.Fil: Villamil, Maria Bonita. University of Illinois at Urbana; Estados UnidosFil: Kim, Nakian. University of Illinois at Urbana; Estados UnidosFil: Riggins, Chance W.. University of Illinois at Urbana; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Allegrini, Marco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Investigaciones en Ciencias Agrarias de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias. Instituto de Investigaciones en Ciencias Agrarias de Rosario; ArgentinaFil: Rodríguez Zas, Sandra L.. University of Illinois at Urbana; Estados Unido

High-Resolution Indicators of Soil Microbial Responses to N Fertilization and Cover Cropping in Corn Monoculture

Cover cropping (CC) is the most promising in-field practice to improve soil health and mitigate N losses from fertilizer use. Although the soil microbiota play essential roles in soil health, their response to CC has not been well characterized by bioindicators of high taxonomic resolution within typical agricultural systems. Our objective was to fill this knowledge gap with genus-level indicators for corn [Zea mays L.] monocultures with three N fertilizer rates (N0, N202, N269; kg N ha−1), after introducing a CC mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.], using winter fallows (BF) as controls. A 3 × 2 split-plot arrangement of N rates and CC treatments was studied in a randomized complete block design with three replicates over two years. Bacterial and archaeal 16S rRNA and fungal ITS regions were sequenced with Illumina MiSeq system. Overall, our high-resolution bioindicators were able to represent specific functional or ecological shifts within the microbial community. The abundances of indicators representing acidophiles, nitrifiers, and denitrifiers increased with N fertilization, while those of heterotrophic nitrifiers, nitrite oxidizers, and complete denitrifiers increased with N0. Introducing CC decreased soil nitrate levels by up to 50% across N rates, and CC biomass increased by 73% with N fertilization. CC promoted indicators of diverse functions and niches, including N-fixers, nitrite reducers, and mycorrhizae, while only two N-cycling genera were associated with BF. Thus, CC can enhance the soil biodiversity of simplified cropping systems and reduce nitrate leaching, but might increase the risk of nitrous oxide emission without proper nutrient management. This primary information is the first of its kind in this system and provided valuable insights into the limits and potential of CC as a strategy to improve soil health.Fil: Kim, Nakian. University of Illinois at Urbana; Estados UnidosFil: Riggins, Chance W.. University of Illinois at Urbana; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Allegrini, Marco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Investigaciones en Ciencias Agrarias de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias. Instituto de Investigaciones en Ciencias Agrarias de Rosario; ArgentinaFil: Rodriguez Zas, Sandra L.. University of Illinois at Urbana; Estados UnidosFil: Villamil, Maria Bonita. University of Illinois at Urbana; Estados Unido

A Longitudinal Study of the Microbial Basis of Nitrous Oxide Emissions Within a Long-Term Agricultural Experiment

Much of the global nitrous oxide emissions are derived from agricultural management driving microbial N transformations. Crop rotation, no-till, and cover cropping are feasible conservation agronomic strategies used to prevent N losses to the environment, though their effect on soil microbial N cycling at the field scale remains relatively unknown. Our goal was to determine the effect of crop rotation (continuous corn [Zea mays L.], CCC; and continuous soybean [Glycine max (L.) Merr.], SSS), tillage (no-till, NT; and chisel tillage, T), and cover crops (cover crop mixture, CC; and no cover crop, NCC) on the quantification of functional genes related to the N cycle from different times throughout the growing season. The study was conducted during the growing season of the cash crops following the first season of cover crops introduced after 23 years of management. Using quantitative polymerase chain reaction (qPCR) techniques, we quantified nifH (N2 fixation), amoA (nitrification) and nirK, nirS, and nosZ (denitrification). Our results show that CCC increased nitrous oxide emissions by 44% compared to SSS and reduced soil pH by nearly 1 unit. The reduction in soil pH, coupled with an increase in fertilizer-derived ammonium, caused ammonia-oxidizing bacteria (AOB) and nirK copy numbers to increase. The SSS rotation showed opposite results. Bacterial denitrification via the nirK pathway was likely the N cycle mechanism behind nitrous oxide emissions in CCC. The cover crop mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth] reduced soil nitrate levels, though they did increase nitrous oxide emissions, likely due to priming and the inclusion of a legume in the cover crop mixture. Nitrous oxide emissions were affected by sampling date, crop rotation, and cover crop use, suggesting management factors that add abundantly available N alter the microbial N cycle directly or indirectly. Chisel tillage increased the abundance of all N cycle genes compared to no-till. Together, our work adds further insight into the microbial N cycle, especially nitrous oxide evolution, from three common conservation agricultural management practices, contributing to our understanding of key soil biogeochemical processes.Fil: Behnke, Gevan D.. University of Illinois at Urbana; Estados UnidosFil: Kim, Nakian. University of Illinois at Urbana; Estados UnidosFil: Riggins, Chance W.. University of Illinois at Urbana; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Rodriguez Zas, Sandra L.. University of Illinois at Urbana; Estados UnidosFil: Villamil, Maria Bonita. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Illinois at Urbana; Estados Unido

Characterization of Mollisols after Long-Term N Fertilization at Successive Rates in Continuous and Rotated Corn Systems

Modern agricultural systems rely on inorganic nitrogen (N) fertilization to enhance crop yields, but its overuse may negatively impact soil properties. Soil properties to a depth of 90 cm were studied after 36 years of inorganic N fertilization at successive rates of 0, 202, and 269 kg N ha−1 (N0, N202, and N269) in continuous corn production [Zea mays L.] (CCC), and the corn (Cs) and soybean [Glycine max (L.) Merr.] (Sc) phases of a corn-soybean (CS) rotation. Experimental plots were arranged as a split-plot in a randomized complete block design with three replications. High levels of N fertilization under CCC acidified the topsoil (N0 pH 6.6 vs. N269 pH 4.9), and increased the nitrate level eight-fold compared to unfertilized controls. Under CCC, N0 had more than twice the available phosphorus level (P) and 40% more potassium (K) than the fertilized soils. Though treatments did not impact the soil organic carbon (SOC) content, water aggregate stability (WAS) decreased during the soybean phase of the rotated treatment (Sc) when compared to CCC. Fertilization affected soil bulk density (BD), which decreased by 5% from N0 to N269 across rotations. Averaged since the start of the study, corn yields increased by 60% with N fertilizer use compared to the unfertilized controls (N0). The corn grain yield benefited from the rotation with soybeans rendering 17% more grain yield in Cs than in CCC. Yet this benefit rose to 45% more grain yield on average, when no N fertilizer was used in Cs. Our results showed that there are important trade-offs with N fertilization and long-term use of corn monocultures, as its long-term use, even in the fertile and resilient soils on the Midwestern U.S., has led to P and K depletion, soil acidification, and potentially exacerbated N losses to the environment

Do cover crops benefit soil microbiome? A meta-analysis of current research

Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. Because cover cropping can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Despite the growing number of primary literature sources investigating the relationship between cover cropping and the soil microbiome, there has not been a quantitative research synthesis that is sufficiently comprehensive and specific to this relationship. We conducted a meta-analysis by compiling the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome.Fil: Kim, Nakian. University of Illinois at Urbana; Estados UnidosFil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Guan, Kaiyu. University of Illinois at Urbana; Estados UnidosFil: Villamil, Maria Bonita. University of Illinois at Urbana; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems.

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

Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures.

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems