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Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 32485

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Dr. José David Flores-Félix

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Lab 237, Edif Departamental de Biología, Universidad de Salamanca, 37007 Salamanca, Spain
Interests: microbiology; rhizobium; PGPB
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Dear Colleagues,

In recent decades, knowledge about plant bacterial communities has shown how this environment presents an important bacterial diversity, where plants are able to model these populations. Development of next-generation sequencing (NGS) and transcriptomics techniques has allowed us to delve into bacterial diversity, contributing to give a completeness view of culturable and nonculturable plant-associated bacteria. It should also be noted that, in recent years, the study of bacterial populations associated with plants has allowed the identification of a high number of new species, and genome sequencing has revealed a more complete view of the metabolism and relationship of bacteria that inhabit these environments. These bacteria will have a key role in the development of efficient agricultural strategies to achieve higher crop production and better crop adaptation to future climatic conditions. In this way, some bacteria present a high biotechnological profile due to their ability to produce a plant growth promotion mechanism, which has a positive effect on the development and health of plants. For this reason, the integration between metagenomic and culturomic techniques is essential to achieve a global vision that allows knowing the population dynamics and their biotechnological application in modern agriculture.

This Special Issue will focus on providing a current view of the diversity and importance of bacterial populations associated with plants through a culturomic, metagenomic, and molecular approach, the relationship between community members, their relationship with the host, and their importance in plant nutrition.

Dr. José David Flores-Félix
Guest Editor

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Keywords

rhizobacteria
endophytes
epiphytes
rhizosphere
phyllosphere
plant growth promotion bacteria
plant microbiome
plant–microbe transcriptomic
plant–microbe interactions
culturomic microbiote
quorum sensing

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Related Special Issues

Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion in Microorganisms (15 articles)
Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition in Microorganisms (2 articles)

Published Papers (12 papers)

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Editorial

Jump to: Research

4 pages, 187 KiB

Open AccessEditorial

Editorial for Special Issue “Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition”

by José David Flores-Félix

Microorganisms 2024, 12(1), 190; https://doi.org/10.3390/microorganisms12010190 - 18 Jan 2024

Viewed by 1068

Abstract

The study of bacterial communities associated with plants, particularly those of agronomic interest, has been investigated since the late 19th century, revealing the relationship between nodule formation in leguminous plants, nitrogen fixation, their contribution to the plant, and the imperative presence of rhizobia [...] Read more.

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

Research

Jump to: Editorial

20 pages, 3270 KiB

Open AccessArticle

The Contribution of Hormonal Changes to the Protective Effect of Endophytic Bacterium Bacillus subtilis on Two Wheat Genotypes with Contrasting Drought Sensitivities under Osmotic Stress

by Oksana Lastochkina, Ruslan Yuldashev, Azamat Avalbaev, Chulpan Allagulova and Svetlana Veselova

Microorganisms 2023, 11(12), 2955; https://doi.org/10.3390/microorganisms11122955 - 10 Dec 2023

Cited by 2 | Viewed by 1376

Abstract

A comparative analysis was conducted to evaluate the effects of seed priming with endophytic bacterium Bacillus subtilis 10-4 (BS) on the hormonal system and cell wall tolerance (lipid peroxidation (LPO), electrolyte leakage (EL), and root lignin deposition) of two Triticum aestivum L. (wheat) varieties with contrasting drought sensitivities (Ekada 70—drought-tolerant (DT); Salavat Yulaev—drought-sensitive (DS)) under normal conditions and 12% polyethylene glycol-6000 (PEG)-induced osmotic stress. The results showed that under normal conditions, the growth stimulation in wheat plants by BS was attributed to changes in the hormonal balance, particularly an increase in endogenous indole-3-acetic acid (IAA) accumulation. However, under stress, a significant hormonal imbalance was observed in wheat seedlings, characterized by a pronounced accumulation of abscisic acid (ABA) and a decrease in the levels of IAA and cytokinins (CK). These effects were reflected in the inhibition of plant growth. BS exhibited a protective effect on stressed plants, as evidenced by a significantly lower amplitude of stress-induced changes in the hormonal system: maintaining the content of IAA at a level close to the control, reducing stress-induced ABA accumulation, and preventing CK depletion. These effects were further reflected in the normalization of growth parameters in dehydrated seedlings, as well as a decrease in leaf chlorophyll degradation, LPO, and EL, along with an increase in lignin deposition in the basal part of the roots in both genotypes. Overall, the findings demonstrate that BS, producing phytohormones, specifically IAA and ABA, had a more pronounced protective effect on DT plants, as evidenced by a smaller amplitude of stress-induced hormonal changes, higher leaf chlorophyll content, root lignin deposition, and lower cell membrane damage (LPO) and permeability (EL) compared to DS plants. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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14 pages, 603 KiB

Open AccessArticle

Legume Overseeding and P Fertilization Increases Microbial Activity and Decreases the Relative Abundance of AM Fungi in Pampas Natural Pastures

by Gastón Azziz, Cristina Frade, José M. Igual, Amabelia del Pino, Felipe Lezama and Ángel Valverde

Microorganisms 2023, 11(6), 1383; https://doi.org/10.3390/microorganisms11061383 - 24 May 2023

Cited by 3 | Viewed by 1806

Abstract

Natural grasslands provide a valuable resource for livestock grazing. In many parts of South America, legume overseeding and P fertilization are commonly used to enhance primary productivity. The effect of this practice on the plant community is well established. However, how this management regime affects the soil microbiome is less known. Here, to contribute to filling this knowledge gap, we analyzed the effect of Lotus subbiflorus overseeding, together with P fertilization, on soil microbial community diversity and activity in the Uruguayan Pampa region. The results showed that plant communities in the natural grassland paddocks significantly differed from those of the managed paddocks. In contrast, neither microbial biomass and respiration nor microbial diversity was significantly affected by management, although the structure of the bacterial and fungal communities were correlated with those of the plant communities. AM Fungi relative abundance, as well as several enzyme activities, were significantly affected by management. This could have consequences for the C, N, and P content of SOM in these soils, which in turn might affect SOM degradation. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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16 pages, 5399 KiB

Open AccessArticle

High Diversity of Bradyrhizobial Species Fix Nitrogen with Woody Legume Spartocytisus supranubius in a High Mountain Ecosystem

by Laura Pulido-Suárez, Jesús Notario del Pino, Francisco J. Díaz-Peña, Adolfo Perdomo-González, Águeda M. González-Rodríguez and Milagros León-Barrios

Microorganisms 2023, 11(5), 1244; https://doi.org/10.3390/microorganisms11051244 - 9 May 2023

Cited by 1 | Viewed by 1734

Abstract

The symbiosis between rhizobia and legumes is of pivotal importance in nitrogen-poor ecosystems. Furthermore, as it is a specific process (most legumes only establish a symbiosis with certain rhizobia), it is of great interest to know which rhizobia are able to nodulate key legumes in a specific habitat. This study describes the diversity of the rhizobia that are able to nodulate the shrub legume Spartocytisus supranubius in the harsh environmental conditions of the high mountain ecosystem of Teide National Park (Tenerife). The diversity of microsymbionts nodulating S. supranubius was estimated from a phylogenetic analysis of root nodule bacteria isolated from soils at three selected locations in the park. The results showed that a high diversity of species of Bradyrhizobium and two symbiovars can nodulate this legume. Phylogenies of ribosomal and housekeeping genes showed these strains distributed into three main clusters and a few isolates on separate branches. These clusters consist of strains representing three new phylogenetic lineages of the genus Bradyrhizobium. Two of these lineages belong to the B. japonicum superclade, which we refer to as B. canariense-like and B. hipponense-like, as the type strains of these species are the closest species to our isolates. The third main group was clustered within the B. elkanii superclade and is referred to as B. algeriense-like as B. algeriense is its closest species. This is the first time that bradyrhizobia of the B. elkanii superclade have been reported for the canarian genista. Furthermore, our results suggest that these three main groups might belong to potential new species of the genus Bradyrhizobium. Analysis of the soil physicochemical properties of the three study sites showed some significant differences in several parameters, which, however, did not have a major influence on the distribution of bradyrhizobial genotypes at the different locations. The B. algeriense-like group had a more restrictive distribution pattern, while the other two lineages were detected in all of the soils. This suggests that the microsymbionts are well adapted to the harsh environmental conditions of Teide National Park. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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24 pages, 5348 KiB

Open AccessArticle

The Friend Within: Endophytic Bacteria as a Tool for Sustainability in Strawberry Crops

by Ginaini Grazielli Doin de Moura, Aline Vieira de Barros, Franklin Machado, Caroline Marcela da Silva Dambroz, Chirlei Glienke, Desirrê Alexia Lourenço Petters-Vandresen, Eduardo Alves, Rosane Freitas Schwan, Moacir Pasqual and Joyce Dória

Microorganisms 2022, 10(12), 2341; https://doi.org/10.3390/microorganisms10122341 - 26 Nov 2022

Cited by 2 | Viewed by 2308

Abstract

Strawberry (Fragaria x ananassa, Duch.) is an important crop worldwide. However, since it is a highly demanding crop in terms of the chemical conditions of the substrate, a large part of strawberry production implies the application of large amounts of fertilizers in the production fields. This practice can cause environmental problems, in addition to increases in the fruit’s production costs. In this context, applying plant growth-promoting bacteria in production fields can be an essential strategy, especially thanks to their ability to stimulate plant growth via different mechanisms. Therefore, this study aimed to test in vitro and in vivo the potential of bacteria isolated from strawberry leaves and roots to directly promote plant growth. The isolates were tested in vitro for their ability to produce auxins, solubilize phosphate and fix nitrogen. Isolates selected in vitro were tested on strawberry plants to promote plant growth and increase the accumulation of nitrogen and phosphorus in the leaves. The tested isolates showed an effect on plant growth according to biometric parameters. Among the tested isolates, more expressive results for the studied variables were observed with the inoculation of the isolate MET12M2, belonging to the species Brevibacillus fluminis. In general, bacterial inoculation induced strain-dependent effects on strawberry growth. In vitro and in vivo assays showed the potential use of the B. fluminis MET12M2 isolate as a growth promoter for strawberries. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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21 pages, 7413 KiB

Open AccessArticle

Insight into the Taxonomic and Functional Diversity of Bacterial Communities Inhabiting Blueberries in Portugal

by Ana C. Gonçalves, Fernando Sánchez-Juanes, Sara Meirinho, Luís R. Silva, Gilberto Alves and José David Flores-Félix

Microorganisms 2022, 10(11), 2193; https://doi.org/10.3390/microorganisms10112193 - 4 Nov 2022

Cited by 6 | Viewed by 2276

Abstract

Vaccinium myrtillus is a dwarf shrub of the Ericaceae family with a Palearctic distribution, associated with temperate and cold humid climates. It is widespread on the European continent; on the Iberian Peninsula it is located on Atlantic climate mountains and glacial relicts. In Portugal, we find scattered and interesting populations; however, the majority of them are threatened by climate change and wildfires. Given that, the objective of this study is to determine the rhizospheric and root bacterial communities of this plant in the southernmost regions, and, consequently, its potential range and ability to be used as a biofertilizer. In this work, metabarcoding of 16S rRNA gene showed that the endophytic bacterial diversity is dependent on the plant and selected by it according to the observed alpha and beta diversity. Moreover, a culturomic approach allowed 142 different strains to be isolated, some of them being putative new species. Additionally, some strains belonging to the genera Bacillus, Paenibacillus, Pseudomonas, Paraburkholderia, and Caballeronia showed significant potential to be applied as multifunctional biofertilizers since they present good plant growth-promoting (PGP) mechanisms, high colonization capacities, and an increase in vegetative parameters in blueberry and tomato plants. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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17 pages, 8517 KiB

Open AccessArticle

A Comparison of Rhizospheric and Endophytic Bacteria in Early and Late-Maturing Pumpkin Varieties

by Siyu Chen, Renliu Qin, Da Yang, Wenjun Liu and Shangdong Yang

Microorganisms 2022, 10(8), 1667; https://doi.org/10.3390/microorganisms10081667 - 18 Aug 2022

Cited by 6 | Viewed by 2541

Abstract

To determine whether rhizospheric and endophytic bacteria contribute to the ripening of pumpkins, an analysis was conducted on rhizospheric and endophytic bacteria and soil fertility in the rhizospheres of early and late-maturing pumpkin varieties. The results showed higher nitrogen and abscisic acid content and more gibberellin-producing bacteria in the rhizospheres or endophytes of the early maturing varieties. Greater soil fertility and more abundant rhizospheric and endophytic bacterial genera with a greater metabolic function might be important mechanisms for early ripening. Rhodococcus, Bacillus, and Arthrobacter can be considered the functional bacteria in promoting pumpkin maturation. On the other hand, Ralstonia could be the functional bacterium that delays ripening. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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22 pages, 2219 KiB

Open AccessArticle

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

by Clara Ivette Rincón-Molina, Esperanza Martínez-Romero, José Luis Aguirre-Noyola, Luis Alberto Manzano-Gómez, Adalberto Zenteno-Rojas, Marco Antonio Rogel, Francisco Alexander Rincón-Molina, Víctor Manuel Ruíz-Valdiviezo and Reiner Rincón-Rosales

Microorganisms 2022, 10(8), 1568; https://doi.org/10.3390/microorganisms10081568 - 4 Aug 2022

Cited by 11 | Viewed by 2815

Abstract

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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13 pages, 1923 KiB

Open AccessArticle

Azospirillum brasilense Bacteria Promotes Mn²⁺ Uptake in Maize with Benefits to Leaf Photosynthesis

by Alexandra B. Housh, Spenser Waller, Stephanie Sopko, Avery Powell, Mary Benoit, Stacy L. Wilder, James Guthrie, Michael J. Schueller and Richard A. Ferrieri

Microorganisms 2022, 10(7), 1290; https://doi.org/10.3390/microorganisms10071290 - 25 Jun 2022

Cited by 3 | Viewed by 2099

Abstract

Azospirillum brasilense is a prolific grass-root colonizing bacteria well-known for its ability to promote plant growth in several cereal crops. Here we show that one of the mechanisms of action in boosting plant performance is through increased assimilation of the micronutrient manganese by the host. Using radioactive ⁵²Mn²⁺ (t_½ 5.59 d), we examined the uptake kinetics of this micronutrient in young maize plants, comparing the performance of three functional mutants of A. brasilense, including HM053, a high auxin-producing and high N₂-fixing strain; ipdC, a strain with a reduced auxin biosynthesis capacity; and FP10, a strain deficient in N₂-fixation that still produces auxin. HM053 had the greatest effect on host ⁵²Mn²⁺ uptake, with a significant increase seen in shoot radioactivity relative to non-inoculated controls. LA-ICP-MS analysis of root sections revealed higher manganese distributions in the endodermis of HM053-inoculated plants and overall higher manganese concentrations in leaves. Finally, increased leaf manganese concentration stimulated photosynthesis as determined by measuring leaf fixation of radioactive ¹¹CO₂ with commensurate increases in chlorophyll concentration. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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15 pages, 11301 KiB

Open AccessArticle

Application of Organic Fertilizer Changes the Rhizosphere Microbial Communities of a Gramineous Grass on Qinghai–Tibet Plateau

by Kun Ma, Yingcheng Wang, Xin Jin, Yangan Zhao, Huilin Yan, Haijuan Zhang, Xueli Zhou, Guangxin Lu and Ye Deng

Microorganisms 2022, 10(6), 1148; https://doi.org/10.3390/microorganisms10061148 - 2 Jun 2022

Cited by 16 | Viewed by 3282

Abstract

The effects of organic fertilizer application on the soil microbial community in grassland systems have been extensively studied. However, the effects of organic fertilizers on the structure of rhizosphere microbial communities are still limited. In this study, the diversity and composition of rhizosphere microbial communities of a gramineous grass Elymus nutans under organic fertilizer treatment were studied in an artificial pasture on Qinghai–Tibet Plateau. After a growing season, the application of organic fertilizer not only increased the height and biomass of Elymus nutans, but also changed the rhizosphere microbial compositions. In particular, organic fertilizer increased the diversity of rhizosphere bacterial community and inhibited the growth of pathogenic bacteria such as Acinetobacter, but the opposite trend was observed for the diversity of fungal community. The assembly process of fungal community was changed from a stochastic process to a deterministic process, indicating that selection was strengthened. Additionally, both the infection rate of arbuscular mycorrhizal fungi (AMF) toward host plants and the development of AMF-related structures were significantly increased after the application of organic fertilizer. Our study demonstrated that the addition of organic fertilizer to artificial pasture could improve the growth of grass through the alteration of the rhizosphere microbial communities. Organic fertilizer had a greater selectivity for the bacterial and the fungal communities that enhanced the niche filtration in this community, further benefiting the yield of forages. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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13 pages, 1270 KiB

Open AccessArticle

Phosphate-Solubilizing Bacteria Isolated from Phosphate Solid Sludge and Their Ability to Solubilize Three Inorganic Phosphate Forms: Calcium, Iron, and Aluminum Phosphates

by Fatima Zahra Aliyat, Mohamed Maldani, Mohammed El Guilli, Laila Nassiri and Jamal Ibijbijen

Microorganisms 2022, 10(5), 980; https://doi.org/10.3390/microorganisms10050980 - 7 May 2022

Cited by 31 | Viewed by 6126

Abstract

Biofertilizers are a key component of organic agriculture. Bacterial biofertilizers enhance plant growth through a variety of mechanisms, including soil compound mobilization and phosphate solubilizing bacteria (PSB), which convert insoluble phosphorus to plant-available forms. This specificity of PSB allows them to be used as biofertilizers in order to increase P availability, which is an immobile element in the soil. The objective of our study is to assess the capacity of PSB strains isolated from phosphate solid sludge to solubilize three forms of inorganic phosphates: tricalcium phosphate (Ca₃(PO₄)₂), aluminum phosphate (AlPO₄), and iron phosphate (FePO₄), in order to select efficient solubilization strains and use them as biofertilizers in any type of soil, either acidic or calcareous soil. Nine strains were selected and they were evaluated for their ability to dissolve phosphate in the National Botanical Research Institute’s Phosphate (NBRIP) medium with each form of phosphate (Ca₃(PO₄)₂, AlPO₄, and FePO₄) as the sole source of phosphorus. The phosphate solubilizing activity was assessed by the vanadate-molybdate method. All the strains tested showed significantly (p ≤ 0.05) the ability to solubilize the three different forms of phosphates, with a variation between strains, and all strains solubilized Ca₃(PO₄)₂ more than FePO₄ and AlPO₄. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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19 pages, 8011 KiB

Open AccessArticle

Metagenomic Analyses of the Soybean Root Mycobiome and Microbiome Reveal Signatures of the Healthy and Diseased Plants Affected by Taproot Decline

by Sorina C. Popescu, Maria Tomaso-Peterson, Teresa Wilkerson, Aline Bronzato-Badial, Uyen Wesser and George V. Popescu

Microorganisms 2022, 10(5), 856; https://doi.org/10.3390/microorganisms10050856 - 21 Apr 2022

Cited by 6 | Viewed by 3860

Abstract

Invading pathogens interact with plant-associated microbial communities, which can be altered under the pressure of pathogen infection. Limited information exists on plant–microbe interactions occurring during natural outbreaks in agricultural fields. Taproot decline (TRD) of soybean is an emerging disease caused by Xylaria necrophora. TRD disease occurrence and yield loss associated with TRD are outstanding issues in soybean production. We applied nuclear ribosomal DNA Internal Transcribed Spacers and 16S rRNA gene taxonomic marker sequencing to define the composition of the fungal and bacterial communities associated with healthy and diseased soybean roots collected from the Mississippi Delta. The plant compartment was a significant factor regulating taxonomic diversity, followed by the disease status of the plant. TRD impacted the root endophytes, causing imbalances; at the intermediate and advanced stages of TRD, X. necrophora decreased mycobiome diversity, whereas it increased microbiome richness. Networks of significant co-occurrence and co-exclusion relationships revealed direct and indirect associations among taxa and identified hubs with potential roles in assembling healthy and TRD-affected soybean biomes. These studies advance the understanding of host–microbe interactions in TRD and the part of biomes in plant health and disease. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition)

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