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Diversity
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Ecology of Crop-Associated Communities of Bacteria and Fungi
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Ecology of Crop-Associated Communities of Bacteria and Fungi

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (19 November 2021) | Viewed by 12108

Special Issue Editors

Dr. David Johnston-Monje

E-Mail Website
Guest Editor
1. Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali, Valle del Cauca, Colombia
2. Max Planck Institute for Plant Breeding Research, Cologne, Germany
Interests: microbial ecology; soil microbiology; plant microbiomes; agricultural biotechnology; agroecology
Special Issues, Collections and Topics in MDPI journals
Dr. Alejandro Caro-Quintero

E-Mail Website
Guest Editor
Colombian Agricultural Research Corporation (AGROSAVIA), Bogota, Colombia
Interests: microbial evolution; bacterial genome; genomics and metagenomics

Special Issue Information

Dear Colleagues,

Plants co-evolved with an impressive diversity of microorganisms that help stimulate their hosts to grow and resist stress, aid in nutrient acquisition, and control pathogens. Advances in molecular and systems biology have empowered the study of these complex microbial networks, providing valuable reference tools for our development of agroecological biotechnologies to help address the grand challenges facing humanity, such as food security, food safety, and environmental sustainability. This Special Issue provides a platform to highlight new research that adds to our knowledge of the microbiology of crop plants, especially as it relates to: i) the dynamics, distribution, and diversity of bacteria and fungi on or inside crop plants; ii) the effect of agricultural practices (e.g., fertilization, pesticide use, planting method, etc.) or environmental variation (e.g., soil type, moisture levels, temperature) on plant microbiomes; iii) the provenance of plant-inhabiting bacteria and fungi; iv) the use of plant microbiome data to diagnose plant health or guide bioprospecting for beneficial microbes; and/or v) the loss (and reintroduction) of beneficial microbes in modern agriculture. We look forward to reading your submissions.

Dr. David Johnston-Monje
Dr. Alejandro Caro-Quintero
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. Diversity 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

  • phytobiome
  • rhizosphere
  • phyllosphere
  • spermosphere
  • endosphere
  • plant microbiome
  • plant mycobiome
  • plant microbial ecology
  • bioprospecting
  • microbial inoculation
  • farming practices
  • agricultural microbiology
  • agroecology
  • bacteria
  • fungi
  • endophytes
  • population dynamics
  • microbiome dynamics

Published Papers (4 papers)

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Research

15 pages, 1497 KiB  
Article
Cultivable Endophytic Bacteria in Seeds of Dongxiang Wild Rice and Their Role in Plant-Growth Promotion
by Zhibin Zhang, Tingting Liu, Xiao Zhang, Jing Xie, Ya Wang, Riming Yan, Yumei Jiang and Du Zhu
Diversity 2021, 13(12), 665; https://doi.org/10.3390/d13120665 - 12 Dec 2021
Cited by 11 | Viewed by 3062
Abstract
Dongxiang wild rice (Oryza rufipogon Griff.) germplasm is a precious resource for the improvement of agronomic traits in rice. Rice seeds also harbor a diverse endophytic bacterial community, and their interactions with their hosts and each other can influence plant growth and [...] Read more.
Dongxiang wild rice (Oryza rufipogon Griff.) germplasm is a precious resource for the improvement of agronomic traits in rice. Rice seeds also harbor a diverse endophytic bacterial community, and their interactions with their hosts and each other can influence plant growth and adaptability. Here, we investigated the community composition of cultivable endophytic bacteria obtained from the surface-sterilized seeds of Dongxiang wild rice and screened them for plant growth-promoting traits. Phylogenetic analysis of 16S rRNA gene sequences indicated that the 47 isolates were affiliated with five classes and 13 discrete genera, and Bacillus and Microbacterium predominated. Evaluations of plant growth promoting (PGP) traits showed that 45 endophytic bacteria isolates produced between 3.37 and 90.11 μg mL−1 of Indole-3-acetic acid (IAA), with the highest yield of 90.11 μg mL−1 (Fse28). Further, 37 of the isolates were able to solubilize mineral phosphate, while 28 other isolates had the ability of N2-fixation, 17 isolates possessed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity with the highest yield of 20.72 μmol mg−1 protein h−1 (Fse35), and 17 isolates were also able to produce siderophores. The two strains Fse28 and Fse35 had multiple PGP traits that significantly improved the agronomic traits (root length, shoot length, dry matter, and chlorophyll content) of cultivated rice seedlings. Our results illustrate the rich diversity of seed endophytic bacteria in Dongxiang wild rice and their potential for developing novel efficient bioinoculants to enhance soil fertility and favor seedling growth. Full article
(This article belongs to the Special Issue Ecology of Crop-Associated Communities of Bacteria and Fungi)
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15 pages, 3255 KiB  
Article
Assessing the Cultivability of Bacteria and Fungi from Arable Crop Residues Using Metabarcoding Data as a Reference
by Valérie Laval, Lydie Kerdraon, Matthieu Barret, Anne-Lise Liabot, Coralie Marais, Benjamin Boudier, Marie-Hélène Balesdent, Marion Fischer-Le Saux and Frédéric Suffert
Diversity 2021, 13(9), 404; https://doi.org/10.3390/d13090404 - 26 Aug 2021
Cited by 1 | Viewed by 3055
Abstract
This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish [...] Read more.
This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue microbial communities for further study, i.e., testing potential interactions within these communities and characterizing groups of beneficial taxa that could be used as biological control agents against plant pathogens. We generated community-based culture collections. We adapted the isolation strategy to the potential differences in the spatial and temporal distribution of diversity between bacteria and fungi. We performed (i) a high-throughput isolation from few samples with no a priori for bacteria and (ii) a low-throughput isolation from several samples with a priori—i.e., morphotype selection—for fungi. Although isolation using a single medium did not allow us to characterize the microbiome as precisely as metabarcoding, the bacterial diversity (158 ASVs, 36 genera) was relatively higher than the fungal diversity (131 ASVs, 17 genera) known to be limited by competition for growth on non-selective solid media. Isolation and metabarcoding provided consistent and complementary information: they revealed several common but also specific ASVs, leading to close microbial community profiles of the most abundant fungal and bacterial taxa in residues. Finally, by empirically comparing the different profiles, we assessed the cultivability of the most abundant fungal and bacterial taxa obtained in metabarcoding. Full article
(This article belongs to the Special Issue Ecology of Crop-Associated Communities of Bacteria and Fungi)
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15 pages, 3392 KiB  
Article
Bacterial Diversity and Community in Response to Long-Term Nitrogen Fertilization Gradient in Citrus Orchard Soils
by Yu Wan, Wenjie Li, Jie Wang and Xiaojun Shi
Diversity 2021, 13(7), 282; https://doi.org/10.3390/d13070282 - 23 Jun 2021
Cited by 9 | Viewed by 2220
Abstract
Citrus orchards receive increasing amounts of nitrogen fertilizer for the purpose of optimal yields and good quality of citrus fruits. Although the effects of increased nitrogen fertilizer on citrus fruit trees have been reasonably well studied, few comparable studies have examined impacts on [...] Read more.
Citrus orchards receive increasing amounts of nitrogen fertilizer for the purpose of optimal yields and good quality of citrus fruits. Although the effects of increased nitrogen fertilizer on citrus fruit trees have been reasonably well studied, few comparable studies have examined impacts on soil bacterial communities and diversity, even though they play critical roles in orchard ecosystem functioning. In our study, Illumina MiSeq sequencing was used to investigate bacterial community structure and diversity under 5-years long-term nitrogen fertilization gradients (N0, N1, N2, N3, N4, and N5) in citrus orchard soils. The sequencing result showed that nitrogen fertilizer addition increased bacterial diversity along the N0 to N3 gradient but decreased bacterial diversity along the N3 to N5 gradient. The increase in the nitrogen fertilizer rate altered bacterial community composition by increasing the relative abundance of Delta-proteobacteria, Nitrospirae, SBR1093, and Latescibacteria and decreasing the relative abundance of Alpha-proteobacteria. Finally, regression analysis revealed that bacterial diversity and the relative abundance of Nitrosomonadales, Rhodobiaceae, Gemmatimonas, and Variibacter exhibited a significant positive correlation with citrus yield. The study revealed that a reasonable nitrogen fertilizer rate applied to citrus orchards could improve bacterial community structure and diversity and increase citrus yield. Full article
(This article belongs to the Special Issue Ecology of Crop-Associated Communities of Bacteria and Fungi)
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15 pages, 2133 KiB  
Article
Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota
by Alejandra Cabrera-Rodríguez, Erika Nava-Reyna, Ricardo Trejo-Calzada, Cristina García-De la Peña, Jesús G. Arreola-Ávila, Mónica M. Collavino, Felipe Vaca-Paniagua, Clara Díaz-Velásquez and Vicenta Constante-García
Diversity 2020, 12(11), 436; https://doi.org/10.3390/d12110436 - 19 Nov 2020
Cited by 3 | Viewed by 3005
Abstract
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) [...] Read more.
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics. Full article
(This article belongs to the Special Issue Ecology of Crop-Associated Communities of Bacteria and Fungi)
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