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Agriculture
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Soil Microbial Communities in Agriculture and Environmental Resilience
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Soil Microbial Communities in Agriculture and Environmental Resilience

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Agricultural Soils".

Deadline for manuscript submissions: closed (20 November 2022) | Viewed by 15076

Special Issue Editors

Dr. Sandipan Samaddar

E-Mail Website
Guest Editor
Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
Interests: microbial soil community; microbial ecology; soil analysis
Dr. Poulami Chatterjee

E-Mail Website
Guest Editor
Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
Interests: plant-microbe interaction; microbial genetics; plant and microbial transcriptome analysis

Special Issue Information

Dear colleagues,

Soil is the most diverse habitat on the planet. The soil microbiome includes archaea, bacteria, viruses, fungi, protists and other eukaryotes.  Development of high throughput sequencing technology and ever-expanding microbial culture libraries document the vast tree of life dominated by microbial diversification. Soil microbiome are essential in regulating ecosystem multifunctionality, nutrient cycling, litter decomposition, plant productivity, and also in reducing the potential for pathogenicity. However, several beneficial functions performed by soil microbiome are currently under great threat due to change in climate and patterns of precipitation, soil degradation and poor land management practices. The technological advances in DNA and RNA based studies of soil microbiome, the knowledge on phylogenetic and taxonomic structure of soil microbial community has improved, however, there are unfolded areas to understand the complex organization of below ground biotic interactions in relation with changing environmental factors.

In this special issue we invite submissions documenting how agricultural management practices influence the structural and functional composition of soil microbiome. Both research and review articles are open to submission in this issue.

Dr. Sandipan Samaddar
Dr. Poulami Chatterjee
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. Agriculture 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

  • Soil microbial community
  • soil microbiome
  • agricultural management practices
  • sustainable agriculture
  • soil health

Published Papers (5 papers)

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Research

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13 pages, 1474 KiB  
Article
The Endophytic Plant Growth Promoting Methylobacterium oryzae CBMB20 Integrates and Persists into the Seed-Borne Endophytic Bacterial Community of Rice
by Denver I. Walitang, Aritra Roy Choudhury, Yi Lee, Geon Choi, Bowon Jeong, Aysha Rizwana Jamal and Tongmin Sa
Agriculture 2023, 13(2), 355; https://doi.org/10.3390/agriculture13020355 - 31 Jan 2023
Cited by 6 | Viewed by 2105
Abstract
Endophytic persistence of inoculated plant growth promoting bacteria (PGPB) involves interaction with the host plant and the host’s indigenous endophytic bacterial communities. This study investigated the persistence of Methylobacterium oryzae CBMB20 into the rice endosphere together with the impact of inoculation on the [...] Read more.
Endophytic persistence of inoculated plant growth promoting bacteria (PGPB) involves interaction with the host plant and the host’s indigenous endophytic bacterial communities. This study investigated the persistence of Methylobacterium oryzae CBMB20 into the rice endosphere together with the impact of inoculation on the diversity and community structure of the root and shoot bacterial endophytes in Oryza sativa L. spp. indica cv. IR29. Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis of the root and shoot showed that M. oryzae CBMB20 was able to integrate and persist in the rice endosphere without causing drastic shifts in bacterial endophytic diversity and community composition. The bacterial communities in the root and shoot are very similar to the seeds of IR29, suggesting that most of them are seed-borne. The root endosphere bacterial communities of inoculated and uninoculated IR29 plants are more diverse compared to the shoots in terms of richness and diversity indices. The dominant bacterial T-RFs of the root endosphere of IR29 belong to Microbacterium, Delftia, Pseudomonas, Xanthomonas and Stenotrophomonas, Herbaspirillum, Enterobacter, and Sphingomonas, as observed in the three restriction enzyme T-RFLP profiles. Bacterial clades identified as Curtobacterium, Enterobacter, Stenotrophomonas, and Xanthomonas were distinctly observed in both the root and shoot communities, and these bacterial groups are also the dominant endophytes of the shoot endosphere. This study showed that Methylobacterium oryzae CBMB20 could persist and incorporate into the endophytic bacterial community of the endosphere without causing long-term antagonistic interactions with its host plant and with the native microbiota. Full article
(This article belongs to the Special Issue Soil Microbial Communities in Agriculture and Environmental Resilience)
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17 pages, 3785 KiB  
Article
The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights
by Pugazhenthi Davidson Rokins, Nellaiappan Olaganathan Gopal, Rangasamy Anandham and Ramasamy Saraswathi
Agriculture 2022, 12(10), 1624; https://doi.org/10.3390/agriculture12101624 - 6 Oct 2022
Cited by 3 | Viewed by 2027
Abstract
Soil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems [...] Read more.
Soil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems (conventional, aerobic and System of Rice Intensification (SRI)) under saline conditions. The physicochemical properties and urease, soil dehydrogenase, alkaline phosphatase and arylsulphatase activity of soil samples were evaluated to understand their influence on the bacterial communities of the soil. Electrical conductivity (EC) of soil was lower in SRI soil samples, while the available major soil nutrients (nitrogen, phosphorous and potassium) content and soil enzyme activities such as dehydrogenase, alkaline phosphatase, urease and arylsulphatase were higher. A total of 2,516,700 reads were generated by amplicon sequencing of the hypervariable V3–V4 regions of bacterial 16S rRNA gene and were clustered into 273,447 OTU operational taxonomic units. The total number of Operational Taxonomic Units (OTUs) was higher in the conventional soil samples compared to the SRI and aerobic soil samples. Metagenomic analysis revealed that Proteobacteria was the most dominant phyla in all the planting systems followed by Actinobacteria, Firmicutes and Chloroflexi. The alpha diversity index was higher in conventional soil samples compared to other samples and more species diversity was found in SRI soil samples. KEGG analysis revealed that bacterial communities in different soil samples showed varied functional properties. The bacterial diversity of saline soil in this study can be utilised to identify microbial communities with biotechnological potential that can be employed for plant growth promotion in saline environments. Full article
(This article belongs to the Special Issue Soil Microbial Communities in Agriculture and Environmental Resilience)
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20 pages, 4555 KiB  
Article
Alleviation of Sodic Stress in Rice by Exploring the Exopolysaccharide-Producing Sodic-Tolerant Bacteria
by Yazhini Gunasekaran, Subramaniam Thiyageshwari, Manikandan Ariyan, Aritra Roy Choudhury, Jung-Ho Park, Duraisamy Selvi, Lakshmanan Chithra and Rangasamy Anandham
Agriculture 2022, 12(9), 1451; https://doi.org/10.3390/agriculture12091451 - 13 Sep 2022
Cited by 6 | Viewed by 2291
Abstract
Sodicity is one of the major salt stresses that impair crop production. Exopolysaccharide-producing sodic tolerant bacteria (EPS-STB) play a significant role in reducing the sodic stress in plants by hampering the uptake of sodium. In this context, this study aims to isolate the [...] Read more.
Sodicity is one of the major salt stresses that impair crop production. Exopolysaccharide-producing sodic tolerant bacteria (EPS-STB) play a significant role in reducing the sodic stress in plants by hampering the uptake of sodium. In this context, this study aims to isolate the EPS-STB for alleviating sodic stress in rice under a sodic environment. Thus, artificial sodicity was created in culture media, and 253 bacteria were isolated from the rice rhizosphere of sodic soils in Trichy and Chinna Salem of Tamil Nadu in India. Fifty bacterial isolates were initially screened based on EPS production, sodic tolerant ability, and plant growth-promoting activities. Further, these bacterial isolates were identified using 16S rDNA sequencing. The results suggested that the isolated bacteria possessed biofilm-forming abilities along with plant growth-promoting activities and osmolyte accumulation under sodic stress conditions. Bacillus rugosus L1C7T, Bacillus paralicheniformis L1C5L, Pseudomonas sp. L5C14T and Franconibacter helveticus L2C1L2 were chosen as better EPS-STB plant growth-promoting bacteria, and their impact on rice under sodic conditions was evaluated. Among the sodic tolerant bacteria, Franconibacter helveticus L2C1L2-inoculated rice plants increased dry matter production compared to the control. Thus, this study showed that the utilization of EPS-STB will become a promising tool to alleviate sodic stress in rice. Full article
(This article belongs to the Special Issue Soil Microbial Communities in Agriculture and Environmental Resilience)
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17 pages, 3387 KiB  
Article
Assessing the Effect of Physicochemical Properties of Saline and Sodic Soil on Soil Microbial Communities
by Junzhi Gao, Qingzhou Zhao, Dongdong Chang, Fabrice Ndayisenga and Zhisheng Yu
Agriculture 2022, 12(6), 782; https://doi.org/10.3390/agriculture12060782 - 29 May 2022
Cited by 9 | Viewed by 2786
Abstract
Soil physicochemical properties are the main driving factors affecting the stability and diversity of the soil microbial community. The impacts of the saline–alkali situation and associated soil degradation need to be understood and reversed as soil diversity and communities are increasingly affected by [...] Read more.
Soil physicochemical properties are the main driving factors affecting the stability and diversity of the soil microbial community. The impacts of the saline–alkali situation and associated soil degradation need to be understood and reversed as soil diversity and communities are increasingly affected by saline–alkaline soil. However, the differences between salinization and alkalization soil and their impact on microbiota have been overlooked. The object of this study is to demonstrate the differences in salinization and alkalization soil and the driving factors affecting microbiota. In this study, 12 soil samples collected from saline–alkaline spots were used to detect the differences in soil physicochemical properties. The soil microbial community was sequenced by high-throughput sequencing. The results of ESP and EC in the soil samples indicated that the soil samples were categorized as saline soil and sodic soil. Venn diagrams indicated that unique OTUs in saline soil showed higher adaptation and environmental tolerance. Partial Mantel tests showed that the differences in pH, exchangeable sodium percentage (ESP), C/N, Na, and K between saline and sodic soil were the primary determinants affecting the relative abundance of bacterial and fungal communities, besides electrical conductivity (EC). In the KEGG analysis, ESP mainly affected the cellular processes in the archaea. Metabolism in the bacterial function was positively correlated with K only in sodic soil. These results indicated that the proportions in sodic soil were more strongly affecting soil microbiota. Full article
(This article belongs to the Special Issue Soil Microbial Communities in Agriculture and Environmental Resilience)
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Review

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21 pages, 336 KiB  
Review
Influence of Agricultural Practices on Bacterial Community of Cultivated Soils
by Ludmila Eugenevna Khmelevtsova, Ivan Sergeevich Sazykin, Tatiana Nikolaevna Azhogina and Marina Alexandrovna Sazykina
Agriculture 2022, 12(3), 371; https://doi.org/10.3390/agriculture12030371 - 6 Mar 2022
Cited by 19 | Viewed by 4909
Abstract
Bacterial communities play an important role in maintaining stable functioning of soil ecosystems, participating in decomposition of plant residues, accumulation of organic matter, formation of soil aggregates and in the cycle of nutrients. For agroecosystems, maintaining the diversity of microbiocenosis is especially critical [...] Read more.
Bacterial communities play an important role in maintaining stable functioning of soil ecosystems, participating in decomposition of plant residues, accumulation of organic matter, formation of soil aggregates and in the cycle of nutrients. For agroecosystems, maintaining the diversity of microbiocenosis is especially critical because they are essentially less stable and are dependent on external control. The agricultural practices used today (plowing, application of synthetic fertilizers) can negatively affect the richness and diversity of the soil bacterial communities. The solution to this problem may be the application of alternative farming methods to preserve the structural and functional richness of soil (reduced tillage, conservation tillage, no tillage, organic farming). Data on composition and diversity of soil microbiocenosis are important for further forecasting the impact of agriculture and development of effective methods on preserving and increasing soil fertility. This review presents the results of recent studies on the impact of agriculture on the soil bacterial communities. Attention is mainly paid to the effects of applying inorganic and organic fertilizers on the structure and diversity of soil microbiocenosis; the influence of the farming system (different methods of soil cultivation, organic and traditional systems); the influence of cover crops and crop rotation on the microbial community of agricultural soils. Full article
(This article belongs to the Special Issue Soil Microbial Communities in Agriculture and Environmental Resilience)
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