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

Kim, Nak Hyun (Nakian)

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https://hdl.handle.net/2142/108534 Copy

Description

Title

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

Author(s)

Kim, Nak Hyun (Nakian)

Issue Date

2020-07-23

Director of Research (if dissertation) or Advisor (if thesis)

Villamil, Maria B

Committee Member(s)

• Riggins, Chance W
• Rodriguez-Zas, Sandra L
• Zabaloy, Maria C

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• cover cropping
• soil microbiome
• soil health
• tillage
• soil nutrient
• microbial ecology

Abstract

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.

Graduation Semester

2020-08

Type of Resource

Thesis

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http://hdl.handle.net/2142/108534

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Copyright 2020 Nak Hyun (Nakian) Kim

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