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Agronomy
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Plant–Microbiome–Climate Interactions and Biogeography
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Plant–Microbiome–Climate Interactions and Biogeography

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Soil and Plant Nutrition".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 8750

Special Issue Editors

Dr. Richard Allen White III

E-Mail Website
Guest Editor
Department of Bioinfomatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
Interests: plant-microbiome interactions; plant-microbiome-virome interactions; bacteriophage therapy for crops; mycoviruses for crops; rhizosphere microbiome multi-omics
Dr. Kiwamu Tanaka

E-Mail Website
Guest Editor
Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
Interests: damage-associated molecular patterns (DAMPs) in plant defense
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues，

The plant microbiome located above/belowground may include one of the most diverse ecosystems on the planet (1011 microbial cells per gram root). The plant microbiome contains a vast interwoven network of bacteria, protists, fungi, viruses, bacteriophage, and other eukaryotes (e.g., nematodes).

Understanding the interactions within the plant microbiome is key to greater and more sustainable food production, bioenergy, controlling climate change, modeling global biogeochemistry, and our future, potentially beyond Earth.

Dr. Richard Allen White III
Dr. Kiwamu Tanaka
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

  • plants
  • rhizosphere
  • phyllosphere
  • microbiomes
  • viromes
  • multi-omics
  • climate change
  • biogeochemistry

Published Papers (4 papers)

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Research

24 pages, 14186 KiB  
Article
Genome-Resolved Metagenomics of Nitrogen Transformations in the Switchgrass Rhizosphere Microbiome on Marginal Lands
by Richard Allen White III, Aaron Garoutte, Emily E. Mclachlan, Lisa K. Tiemann, Sarah Evans and Maren L. Friesen
Agronomy 2023, 13(5), 1294; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13051294 - 03 May 2023
Cited by 1 | Viewed by 2125
Abstract
Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol, that could help displace over a quarter of the US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The [...] Read more.
Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol, that could help displace over a quarter of the US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays a critical role in nitrogen cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing to characterize the switchgrass rhizosphere microbial community before and after a nitrogen fertilization event for established stands on marginal land. We examined community structure and bulk metabolic potential, and resolved 29 individual bacteria genomes via metagenomic de novo assembly. Community structure and diversity were not significantly different before and after fertilization; however, the bulk metabolic potential of carbohydrate-active enzymes was depleted after fertilization. We resolved 29 metagenomic assembled genomes, including some from the ‘most wanted’ soil taxa such as Verrucomicrobia, Candidate phyla UBA10199, Acidobacteria (rare subgroup 23), Dormibacterota, and the very rare Candidatus Eisenbacteria. The Dormibacterota (formally candidate division AD3) we identified have the potential for autotrophic CO utilization, which may impact carbon partitioning and storage. Our study also suggests that the rhizosphere microbiome may be involved in providing associative nitrogen fixation (ANF) via the novel diazotroph Janthinobacterium to switchgrass. Full article
(This article belongs to the Special Issue Plant–Microbiome–Climate Interactions and Biogeography)
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16 pages, 3019 KiB  
Article
Study of Codon Usage Patterns and Influencing Factors in Rice Yellow Mottle Virus Based on Coding Sequence Data
by Siddiq Ur Rahman, Sajid Nawaz, Sifat Ullah, Inayat Ur Rahman, Muhammad Inam Ul Haq, Muazzam Ali Khan, Abdullah Ahmed Al-Ghamdi, Fahad M. Al-Hemaid, Mohamed S. Elshikh, Reem M. Aljowaie and Wafa Ali Eltayb
Agronomy 2022, 12(9), 1990; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12091990 - 23 Aug 2022
Cited by 3 | Viewed by 1710
Abstract
Rice yellow mottle virus (RYMV), transmitted by chrysomelids, is one of the major viral pathogens that has devastated rice production in Sub-Saharan Africa. RYMV is a member of the genus Sobemoviruses in the family Solemoviridae and harbors a positive-sense single-stranded RNA (+ssRNA). Here, [...] Read more.
Rice yellow mottle virus (RYMV), transmitted by chrysomelids, is one of the major viral pathogens that has devastated rice production in Sub-Saharan Africa. RYMV is a member of the genus Sobemoviruses in the family Solemoviridae and harbors a positive-sense single-stranded RNA (+ssRNA). Here, we used 50 RYMV strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that GC-ended codons were more frequently used in the genome of RYMV. Further low codon usage bias was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested the dominant factor of natural selection was involved in the structuring of CUB in RYMV. Based on RSCU values, the RYMV and its host relationship indicate that the RYMV develops codon usage patterns similar to its host. Generally, both natural selection and mutational pressure impact the codon usage pattern of the protein-coding genes in RYMV. This study is important because it characterized the codon usage pattern in the RYMV genomes and provided the necessary data for a basic evolutionary study on them. Additionally, we recommend that experiments such as whole genome sequencing (WGS) or dual RNA sequencing (DRS) should be considered in order to correlate these in-silico findings with viral diseases in the future. Full article
(This article belongs to the Special Issue Plant–Microbiome–Climate Interactions and Biogeography)
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18 pages, 2134 KiB  
Article
Deterministic Process Dominated Belowground Community Assembly When Suffering Tomato Bacterial Wilt Disease
by Hong Liu, Feifei Sun, Junwei Peng, Minchong Shen, Jiangang Li and Yuanhua Dong
Agronomy 2022, 12(5), 1024; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12051024 - 24 Apr 2022
Cited by 6 | Viewed by 2073
Abstract
Soil microbial communities are closely associated with ecosystem functions. However, unravelling the complex nature of the microbial world and successfully utilizing all positive interactions for multipurpose environmental benefits is still a major challenge. Here, we describe the soil bacterial communities in different niches [...] Read more.
Soil microbial communities are closely associated with ecosystem functions. However, unravelling the complex nature of the microbial world and successfully utilizing all positive interactions for multipurpose environmental benefits is still a major challenge. Here, we describe the soil bacterial communities in different niches of healthy and diseased tomatoes under natural conditions. A higher abundance of the pathogen Ralstonia solanacearum and lower bacterial diversity were observed in the disease samples. The healthy tomato rhizosphere harbored more plant-beneficial microbes, including Bacillus and Streptomyces. Also, the co-occurrence network in the healthy rhizosphere samples was more complicated, so as to better adapt to the soil-borne pathogen invasion. Both the beta nearest-taxon-index (βNTI) and normalized stochasticity ratio (NST) analyses demonstrated that healthy rhizosphere communities were less phylogenetically clustered and mainly dominated by dispersal limitation, while homogeneous selection was the major assembly process driving the rhizosphere community of diseased samples. The results obtained with community assembly methods and co-occurrence network analysis revealed that healthy rhizosphere bacterial communities possessed potentially broader environmental stress (soil-borne pathogen stress) adaptability compared with diseased rhizosphere bacterial communities. In conclusion, this study contributed to widening our understanding of the potential mechanisms of soil bacterial community composition and assembly responding to soil-borne pathogen invasion. Full article
(This article belongs to the Special Issue Plant–Microbiome–Climate Interactions and Biogeography)
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6 pages, 950 KiB  
Article
In Situ Non-Destructive Temporal Measurements of the Rhizosphere Microbiome ‘Hot-Spots’ Using Metaproteomics
by Richard Allen White III, Joshua Rosnow, Paul D. Piehowski, Colin J. Brislawn and James J. Moran
Agronomy 2021, 11(11), 2248; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11112248 - 06 Nov 2021
Cited by 5 | Viewed by 1778
Abstract
Rhizosphere arguably embodies the most diverse microbial ecosystem on the planet, yet it is largely a functional ‘black box’ of belowground plant-microbiome interactions. The rhizosphere is the primary site of entry for subsurface injection of fixed carbon (C) into soil with impacts on [...] Read more.
Rhizosphere arguably embodies the most diverse microbial ecosystem on the planet, yet it is largely a functional ‘black box’ of belowground plant-microbiome interactions. The rhizosphere is the primary site of entry for subsurface injection of fixed carbon (C) into soil with impacts on local to global scale C biogeochemistry and ultimately Earth’s climate. While spatial organization of rhizosphere is central to its function, small scale and steep microbial and geochemical gradients within this dynamic region make it easily disrupted by sampling. The significant challenge presented by sampling blocks elucidation of discreet functions, drivers, and interactions within rhizosphere ecosystems. Here, we describe a non-destructive sampling method linked to metaproteomic analysis in order to measure temporal shifts in the microbial composition and function of rhizosphere. A robust, non-destructive method of sampling microbial hotspots within rhizosphere provides an unperturbed window into the elusive functional interactome of this system over time and space. Full article
(This article belongs to the Special Issue Plant–Microbiome–Climate Interactions and Biogeography)
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