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Agronomy
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Effect of Agricultural Management Practices on Soil Microbial Community Composition,...
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Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Farming Sustainability".

Deadline for manuscript submissions: 25 August 2024 | Viewed by 3996

Special Issue Editors

Prof. Dr. Yajun Hu

E-Mail Website
Guest Editor
College of Agronomy, Hunan Agricultural University, Changsha 410125, China
Interests: fungal diversity; soil fertility; microbial functional genes; phosphorus mobilization
Prof. Dr. Xiangbi Chen

E-Mail Website
Guest Editor
Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
Interests: soil carbon sequestration; carbon-nitrogen coupling; functional microorganism; lignin

Special Issue Information

Dear Colleagues,

A fundamental challenge in agriculture is to increase crop yield while preserving a healthy soil environment. Agricultural practices significantly influence soil properties and biodiversity, particularly by shaping the microbial communities within the soil. The profound impact of these practices extends to various soil ecosystem processes, influencing the potential for developing sustainable agriculture to meet the global food demand. Considering the spatial heterogeneity in microbial community structures, the outcomes of specific management practices may vary across different agricultural regions. Therefore, a thorough comprehension of the effects of agricultural management practices on microbial diversity and function in diverse agricultural regions enhances the applicability of agricultural measures.

In this Special Issue, we invite the latest advancements that elucidate the impact of agricultural practices on soil microbial ecology. Submissions are welcome to cover topics like soil health, soil fertility, microbial biogeography, and related subjects.

Prof. Dr. Yajun Hu
Prof. Dr. Xiangbi Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • tillage
  • irrigation
  • organic agriculture
  • crop rotation
  • biochar
  • CNP cycling
  • soil fertility
  • biodiversity
  • amplicon sequencing
  • microbial community assembly

Published Papers (7 papers)

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19 pages, 2791 KiB  
Article
Analysis of Tobacco Straw Return to the Field to Improve the Chemical, Physical, and Biological Soil Properties and Rice Yield
by Jie Huang, Xinyue Wang, Lili Yang, Yuanhuan Li, Bing Xia, Hailin Li and Xiaohua Deng
Agronomy 2024, 14(5), 1025; https://doi.org/10.3390/agronomy14051025 - 11 May 2024
Viewed by 282
Abstract
Straw incorporation into soil contributes significantly to the sustainable development of agriculture. To investigate the impact of tobacco straw returns on a tobacco–rice replanting system, we designed an experiment with two straw return levels and a control group: T1 (full return), T2 (root [...] Read more.
Straw incorporation into soil contributes significantly to the sustainable development of agriculture. To investigate the impact of tobacco straw returns on a tobacco–rice replanting system, we designed an experiment with two straw return levels and a control group: T1 (full return), T2 (root return), and CK (no straw return). Over a three-year field experiment in rice fields in South China, we assessed the effects of tobacco straw return on soil quality, microbial diversity, dry matter accumulation, and yield composition of rice. The results demonstrated that returning tobacco straw to the field effectively enhanced rice yield by positively influencing various soil physical, chemical, and biological properties. Compared to those in the CK treatment, as the soil porosity increased from 9.0% to 12.4%, the mean weight diameter of the soil aggregates substantially increased, ranging from 28.7% to 45.2%. There were significant increases in soil organic matter, total nitrogen, and alkaline dissolved nitrogen. Soil sucrase activity increased between 29.8% and 44.9%, and urease activity increased between 4.3% and 62.2% over the three consecutive years of straw return. The diversity index of soil fungi significantly increased. Additionally, rice yield increased markedly, ranging from 1.8% to 5.1%. Overall, the enhancement effect of T1 surpassed that of T2. According to our comprehensive analysis, the incorporation of tobacco straw into the field was found to enhance the physical properties of the soil, elevate soil enzyme activity, and increase the abundance of soil microorganisms. Consequently, this practice led to improved rice yield and a reduction in agricultural waste output. Overall, the return of tobacco straw to the field represents a clean and dependable approach in rice-cultivated tobacco areas to improve soil health and rice productivity. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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13 pages, 2312 KiB  
Article
From Residue to Resource: A Physicochemical and Microbiological Analysis of Soil Microbial Communities through Film Mulch-Enhanced Rice Straw Return Strategies
by Xinyue Wang, Jie Huang, Lili Yang, Yuanhuan Li, Bing Xia, Hailin Li and Xiaohua Deng
Agronomy 2024, 14(5), 1001; https://doi.org/10.3390/agronomy14051001 - 9 May 2024
Viewed by 294
Abstract
Promoting rice straw in situ return is an important strategy for improving soil quality. From 2018 to 2021, we investigated the effects of rice straw return with microbial agents and film covering technology on soil physical and chemical properties at different layer depths, [...] Read more.
Promoting rice straw in situ return is an important strategy for improving soil quality. From 2018 to 2021, we investigated the effects of rice straw return with microbial agents and film covering technology on soil physical and chemical properties at different layer depths, as well as the soil microbial community structure, in Hunan, southern China. This study was designed to evaluate the effects of microbial agents (T1), film mulch covering (T2), and the application of microbial agents combined with film mulch (T3) on the soil physicochemical properties and microbial community after rice straw in situ return. The results show that, after three years of continuous treatment, T3 significantly increased the soil temperature by 17.76–22.97%, T2 significantly increased the water content by 34.27–46.23%, and T1 and T3 significantly increased the soil pH. The addition of microbial agents combined with film mulch resulted in a notable increase in both the number of OTUs and the Chao1 index of soil microorganisms. Additionally, the model of promoting rice straw in situ return (the application of a microbial agent combined with film mulch) was shown to promote the growth of beneficial soil microorganisms. RDA was used for the investigation, and the findings showed that soil microorganisms were significantly influenced by the TOC content, pH, and water content. These findings provide evidence of an effective method for accelerating the decomposition of late rice straw and guiding soil improvement in tobacco–rice rotation regions. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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17 pages, 2703 KiB  
Article
Changes in the Rhizosphere Biome Depending on the Variety of Wheat, Timing of Its Growing Season, and Agrochemical Components in the Soils of Italy
by Tommaso Bardelli, Flavio Fornasier, Elena Novarina, Antonella Donniacuo, Elio Romano, Pier Giacomo Bianchi and Anna Pia Maria Giulini
Agronomy 2024, 14(4), 832; https://doi.org/10.3390/agronomy14040832 - 17 Apr 2024
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Abstract
The purpose of this research is to investigate the interactions among wheat varieties and microorganisms within rhizosphere and how conventional agriculture affects these dynamics during the growing season. Indeed, little is known about how commercial bread varieties modulate root exudates and how agrochemicals [...] Read more.
The purpose of this research is to investigate the interactions among wheat varieties and microorganisms within rhizosphere and how conventional agriculture affects these dynamics during the growing season. Indeed, little is known about how commercial bread varieties modulate root exudates and how agrochemicals affect the microbiological processes. Therefore, this study investigated the changes in soil microbiological features such as enzyme activities (β-glucosidase, xylosidase, glucoronidase, chitinase, leucine-aminopeptidase, acid and alkaline phosphomonoesterases, inositol phosphatase, phosphodiesterase, pyrophosphatase–phosphodiesterase, arylsulphatase) and microbial biomass as a function of treatment (fungicides and plant growth regulator—PGR) and wheat varieties (Skyfall, SY Moisson, Aquilante, Bandera, Tintoretto, Antille, and Bologna) at the sowing, heading, and harvesting stage. A total of 168 samples (2 treatments × 7 varieties × 3 field replicates × 4 sub-samples taken in each plot) were collected in each period and analyzed. We found that soil microbial biomass was a sensible indicator in the fungicide/PGR application, with reduced values in treated plots at the heading. At this stage, the soil enzymatic activities were in general more expressed, confirming that the microbial processes are more proactive due to the growth of plants. Overall, the soil enzymatic activities responded differently according to the wheat varieties, highlighting specific capabilities to interact with microbes. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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16 pages, 1759 KiB  
Article
Enzymatic Activity in Different Crop Succession Systems in the Cerrado Region
by Vanessa Brenda Souza Chaves, Tiara Moraes Guimarães, Aracy Camilla Tardin Pinheiro Bezerra, Claudio Hideo Martins da Costa and Simério Carlos Silva Cruz
Agronomy 2024, 14(4), 810; https://doi.org/10.3390/agronomy14040810 - 13 Apr 2024
Viewed by 460
Abstract
The enzymatic activity of soil arylsulfatase and β-glucosidase enzymes are biological parameters used to measure the biological activity of soils, an important tool for identifying disturbances in agricultural systems, as they are more sensitive to differentiate changes in soil management when compared to [...] Read more.
The enzymatic activity of soil arylsulfatase and β-glucosidase enzymes are biological parameters used to measure the biological activity of soils, an important tool for identifying disturbances in agricultural systems, as they are more sensitive to differentiate changes in soil management when compared to physical and chemical attributes. Thus, the aim was to evaluate arylsulfatase and β-glucosidase levels in different succession systems. Soil samples were collected in agricultural areas with 5 years of experimentation, with four treatments: (1) soybean/corn + brachiaria (Urochloa ruzizienses), (2) soybean/corn, (3) soybean/brachiaria (Urochloa ruzizienses) and (4) soybean/millet. Routine chemical analyses were performed, and the determination of β-glucosidase and arylsulfatase was carried out according to the p-nitrophenyl colorimetric method. As a result, both enzymes presented higher average values in treatment 3. In the biological IQS, treatment 3 differed from treatments 1 and 2. Under the study circumstances, the use of soil with soybean, corn, millet and brachiaria crops provided adequate sustainability conditions, providing high arylsulfatase and β-glucosidase levels. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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14 pages, 5642 KiB  
Article
The ptxD Gene Confers Rapeseed the Ability to Utilize Phosphite and a Competitive Advantage against Weeds
by Dinghui Xu, Teng Xiong, Wenbin Lu, Jinsheng Zhao, Zhenqian Zhang and Gang Xiao
Agronomy 2024, 14(4), 727; https://doi.org/10.3390/agronomy14040727 - 1 Apr 2024
Viewed by 565
Abstract
Weed infestation has seriously affected the yield and quality of rapeseed, which is a globally significant oil crop. While the application of chemical herbicides in agriculture has greatly boosted agricultural efficiency and crop yield, it has also unfortunately led to escalating environmental pollution [...] Read more.
Weed infestation has seriously affected the yield and quality of rapeseed, which is a globally significant oil crop. While the application of chemical herbicides in agriculture has greatly boosted agricultural efficiency and crop yield, it has also unfortunately led to escalating environmental pollution and the emergence of herbicide-resistant weeds. The ptxD gene, originating from bacteria, encodes the phosphite dehydrogenase enzyme that is responsible for converting phosphite (Phi) into orthophosphate (Pi). Phi remains unusable by plants and most microorganisms, but upon its conversion into Pi, it becomes a viable nutrient source for plants. This unique function of the ptxD gene offers promising avenues for the development of innovative weed control technologies. We tested the Phi tolerance of weeds and ptxD-expressing rapeseed (Brassica napus) through greenhouse experiments in rapeseed fields. The results revealed that a Phi concentration of 200 mg·kg of soil−1 inhibited the growth of all weeds in the rapeseed fields, while the ptxD-expressing rapeseed exhibited robust tolerance to this concentration of Phi. In field experiments, the application of 60 g·m−2 of Phi allowed the ptxD-expressing rapeseed to grow normally, while the weeds grew slowly due to phosphorus deficiency, resulting in the rapeseed having a strong competitive advantage over the weeds. The leaves of the transgenic rapeseed plants covered gaps in the field as they grew, further inhibiting weed growth and completely eliminating their harm due to shading effects. The combination of ptxD-expressing rapeseed and the application of phosphite offers a sustainable alternative to herbicides for weed management in rapeseed fields. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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15 pages, 4323 KiB  
Article
Microbial Nutrient Limitation of Different Tea Cultivars: Evidence from Five Representative Cultivars
by Shijie Yuan, Chengwen Shen, Kun Gao, Shuzhen Feng, Dejun Li, Qiulong Hu, Yu Liu and Ze Luo
Agronomy 2024, 14(3), 467; https://doi.org/10.3390/agronomy14030467 - 27 Feb 2024
Viewed by 560
Abstract
Soil microbial activity is generally limited by the availability of carbon (C), nitrogen (N), or phosphorus (P) in agricultural ecosystems. Soil ecoenzymatic activity (EEA), ecoenzymatic stoichiometry (EES), and vector characteristics were examined to assess microbial nutrient limitation. Investigating soil microbial nutrient limitation can [...] Read more.
Soil microbial activity is generally limited by the availability of carbon (C), nitrogen (N), or phosphorus (P) in agricultural ecosystems. Soil ecoenzymatic activity (EEA), ecoenzymatic stoichiometry (EES), and vector characteristics were examined to assess microbial nutrient limitation. Investigating soil microbial nutrient limitation can provide insight into nutrient cycling in tea plantations with different tea cultivars. However, the dynamics of different tea cultivars on soil microbial nutrient limitations and their effect on tea quality remains poor. To address this issue, soil and plant samples were collected from a tea plantation cultivating five representative tea cultivars in Hunan Province, China. Baojing Huangjincha No. 1 (HJC1) and Huangjincha No. 2 (HJC2) were the extra early-sprouting cultivars, Zhuyeqi (ZYQ) and Zijuan (ZJ) were the middle-sprouting cultivars, and Zhenghedabai (ZHDB) was the late-sprouting cultivar, respectively. The results indicated that differences in EEA and EES were significant among five treatments. Notably, ZYQ and ZJ exhibited markedly lower activities of carbon (C), nitrogen (N), and phosphorus (P) acquiring enzymes compared to HJC1 and HJC2, whereas ZHDB showed significantly higher ecoenzymatic activities. Despite a general limitation in C and P for soil microorganisms across all cultivars (VL ranging from 1.42 to 1.59 and VA ranging from 58.70° to 62.66°), the degree of microbial nutrient limitation varied. Specifically, ZYQ experienced a pronounced P limitation (VA = 62.66°, N:P enzyme = 0.52), as evidenced by increased vector angles and decreased N:P enzyme values. Although C limitation was most pronounced in ZYQ (VL = 1.59), it did not significantly differ among the cultivars. These findings suggest that tea cultivars can influence the P limitation of microbial communities. Further analysis revealed that microbial nutrient limitations might adversely affect tea quality via impeding enzyme secretion. This study highlights the critical role of nutrient cycling within the soil-microorganism-plant ecosystem and emphasizes the influence of soil microbial nutrient limitations on tea quality within tea plantations. It is recommended that in the management of tea plantation fertilization, managers need to consider the influence of cultivars and develop specialized cultivar fertilizers. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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12 pages, 1033 KiB  
Perspective
Soil Microorganisms in Agricultural Fields and Agronomic Regulation Pathways
by Qiming Wang, Qiang Chai, Xuecheng Dou, Cai Zhao, Wen Yin, Hanting Li and Jingui Wei
Agronomy 2024, 14(4), 669; https://doi.org/10.3390/agronomy14040669 - 26 Mar 2024
Viewed by 712
Abstract
Agricultural soil microorganisms play a crucial role in farmland ecosystems and are integral to the material cycle in these environments. The composition and abundance of soil microorganisms are influenced by agronomic measures that alter the soil microenvironment. These changes are pivotal to enhancing [...] Read more.
Agricultural soil microorganisms play a crucial role in farmland ecosystems and are integral to the material cycle in these environments. The composition and abundance of soil microorganisms are influenced by agronomic measures that alter the soil microenvironment. These changes are pivotal to enhancing crop resistance, maximizing yield, and facilitating nutrient cycling in farmlands. Drawing on prior research advancements, this study systematically examined the functions of soil microorganisms, the effects of various agronomic measures on their populations, and the ways in which agronomic measures regulate soil microorganisms, and this article offers a comprehensive study of agricultural influences on microorganisms. Additionally, it outlines key areas for future research on soil microorganisms in farmlands, aiming to provide valuable insights for the sustainable development of farmland ecosystems. Full article
(This article belongs to the Special Issue Effect of Agricultural Management Practices on Soil Microbial Community Composition, Diversity and Function)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. Effects of combined inoculation of AM fungi and PGPR on tobacco seedling growth and its rhizosphere microecological mechanism

2. Contrasting effects of straw and straw–derived biochar application on phosphorus fractions and phoD-harboring bacterial community in subtropical paddy soil

3. The combined application of organic fertilizers enhances rice yield by increasing the soil microbial diversity in paddy fields

4. Comparison of phosphorus mobilization strategies caused by microbe between upland and paddy soils in subtropical of China

5. Soil ecoenzymatic stoichiometry reveals microbial phosphorus limitation is linked to different tea varieties: Evidence from five representative varieties

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