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Microorganisms
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Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd...
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Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 5877

Special Issue Editors

Dr. Blanca R. López

E-Mail Website
Guest Editor
1. Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
2. Bashan Institute of Science, Auburn, AL, USA
Interests: bacterial endophytes; microbial inoculants; plant–soil interaction; microbial communities
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Luz De-Bashan

E-Mail Website
Guest Editor
Bashan Institute of Science, Auburn, AL, USA
Interests: plant–bacteria interaction; microbial inoculants; plant growth promoting bacteria; microbial-assisted restoration of degraded soils
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant-growth-promoting bacteria (PGPBs) are a diverse group of bacteria which induce beneficial effects in plants, both directly and indirectly. Many bacterial isolates have been characterized and used as inoculants to improve nutrient acquisition and mitigate environmental stress or for the biocontrol of pathogens. At present, PGPBs offer an alternative to sustainable agriculture, although their practical use for soil rehabilitation and other environmental purposes has received less attention.  

In a changing world, there is a need to explore new sources of PGPBs and investigate their metabolic potential, enabling plants to cope with intense drought, inundation, increasing salinity, soil degradation, etc.

Consequently, for this Special Issue, we encourage contributions which enhance our understanding of how PGPBs interact with plants and soils in challenging environments.

We especially welcome works on the following topics:

  • Prospection of endophytic/rhizosphere/phyllosphere bacteria with plant-growth potential.
  • Exploring the role of PGPBs on wild and cultivated plants.
  • Interaction of PGPBs on the microbial communities of their host and soil.
  • Validation of bacterial inoculants interacting with plants used in soil rehabilitation.
  • Elucidation of new mechanisms of plant growth promotion.

Dr. Blanca R. López
Prof. Dr. Luz De-Bashan
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. Microorganisms 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 2700 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

  • plant growth-promoting bacteria
  • endophytes
  • environmental stress
  • nitrogen fixing bacteria
  • P and K solubilizing bacteria
  • mechanisms of plant growth
  • PGPB-plant interaction soil microbial communities
  • soil rehabilitation
  • bacterial inoculants and biosafety

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Published Papers (5 papers)

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Research

22 pages, 4398 KiB  
Article
Genome-Driven Functional Validation of Bacillus amyloliquefaciens Strain MEPW12: A Multifunctional Endophyte for Sustainable Sweet Potato Cultivation
by Yiming Wang, Jingwen Hao, Jingsheng Gu, Jiaying Wu, Yongjing Zhang, Ting Liang, Haimeng Bai, Qinghe Cao, Jihong Jiang, Ludan Li and Xiaoying Cao
Microorganisms 2025, 13(6), 1322; https://doi.org/10.3390/microorganisms13061322 - 6 Jun 2025
Viewed by 507
Abstract
Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can [...] Read more.
Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can protect the environment and effectively promote the sustainable development of the sweet potato industry. In this study, 12 strains of endophytic bacteria were isolated from sweet potato. Through nitrogen fixation, phosphorus solubilization, indoleacetic acid production, siderophore production, ACC deaminase production, and carboxymethyl cellulose production, three strains with multiple biological activities were screened out. Among them, MEPW12 had the most plant growth-promoting functions. In addition, MEPW12 promoted host chlorophyll accumulation and inhibited pathogen growth and colonization in sweet potato roots and can utilize various carbon sources and salts for growth. It can also grow in extreme environments of high salt and weak acid. MEPW12 was identified as Bacillus amyloliquefaciens with a genome size of 3,928,046 bp and a GC content of 46.59%. After the annotation of multiple databases, it was found that MEPW12 had multiple enzymatic activities and metabolic potential. Comparative genomics and pan-genomics analyses revealed that other Bacillus sp. strains of MEPW12 have similar functions. However, due to adaptation to different growth environments, there are still genomic differences and changes. Inoculation with MEPW12 induced the high expression of IbGH3.10, IbERF1, and other genes, thereby promoting the growth of sweet potatoes. Bacillus amyloliquefaciens strain MEPW12 is a sweet potato endophyte with multiple growth-promoting functions, which can promote the growth of sweet potato seedlings. This study provides new microbial resources for developing microbial agents and improving the quality of sweet potatoes. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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21 pages, 3120 KiB  
Article
Bacillus tropicus YJ33 and Medicago sativa L. Synergistically Enhance Soil Aggregate Stability in Saline–Alkali Environments
by Jingjing Li, Yajuan Che, Shiyang Chen, Mengge Liu, Mengmeng Diao, Chao Yang and Wenke Jia
Microorganisms 2025, 13(6), 1291; https://doi.org/10.3390/microorganisms13061291 - 31 May 2025
Viewed by 552
Abstract
Soil salinization represents a significant global environmental challenge, necessitating the urgent amelioration of saline–alkali lands. As a critical functional component of the soil system, soil aggregates play a pivotal role in enhancing soil structure and are essential for nutrient cycling and plant growth. [...] Read more.
Soil salinization represents a significant global environmental challenge, necessitating the urgent amelioration of saline–alkali lands. As a critical functional component of the soil system, soil aggregates play a pivotal role in enhancing soil structure and are essential for nutrient cycling and plant growth. However, the synergistic effects of plants and microorganisms on alterations in soil aggregate composition, stability, and nutrient content in saline–alkali soils remain inadequately understood. In this study, three saline soil gradients from the Yellow River Delta were analyzed: low saline soil (S1, 1.65 g/kg), medium saline soil (S2, 4.54 g/kg), and high saline soil (S3, 6.57 g/kg). For each gradient, four experimental treatments were established: (1) inoculation of Bacillus tropicus YJ33 alone (B), (2) planting of alfalfa alone (M), (3) combined alfalfa cultivation with B. tropicus YJ33 inoculation (MB), and (4) an unamended control (CK). These treatments were implemented in controlled laboratory pot experiments to evaluate the individual and synergistic impacts of alfalfa and B. tropicus YJ33 on saline soil aggregate stability and structural organization. Overall, B. tropicus YJ33 inoculation significantly promoted the growth and nutritional quality of alfalfa. B, M, and MB treatment increased the contents of total carbon (TC), total nitrogen (TN), and available phosphorus (AP) and promoted the activities of soil alkaline phosphatase (S-ALP) and soil urease (S-UE) in the soil. Simultaneously, these treatments resulted in a reduction in the proportion of micro-aggregates, an increase in the proportion of large and small aggregates, and significantly enhanced mean weight diameter (MWD) and geometric mean diameter (GMD), improving the stability of soil aggregates. Random forest analysis identified AP, B. tropicus YJ33, salinity, TC, and available nitrogen (AN) as key determinants of alfalfa biomass. Partial least squares (PLS) modeling further corroborated the role of B. tropicus YJ33 in enhancing soil nutrient content, improving aggregate stability, and increasing alfalfa yield. In conclusion, B. tropicus YJ33 was demonstrated to enhance the stability of soil aggregates and nutrient availability in saline–alkali soils, thereby significantly promoting the growth, yield, and nutritional quality of alfalfa. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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13 pages, 2054 KiB  
Article
The Rhizobacterium Bacillus amyloliquefaciens MHR24 Has Biocontrol Ability Against Fungal Phytopathogens and Promotes Growth in Arabidopsis thaliana
by Mónica Hernández-Rodríguez, Diana Jasso-de Rodríguez, Francisco Daniel Hernández-Castillo, Ivana Moggio, Eduardo Arias, José Humberto Valenzuela-Soto and Alberto Flores-Olivas
Microorganisms 2024, 12(11), 2380; https://doi.org/10.3390/microorganisms12112380 - 20 Nov 2024
Viewed by 1207
Abstract
A novel rhizobacteria Bacillus was isolated from rhizosphere of soil associated with tomato (Solanum lycopersicum L.) under open field conditions. The Bacillus amyloliquefaciens strain MHR24 (MHR24) is a promising biocontrol agent against several fungal phytopathogens. In this research, MHR24 was characterized by [...] Read more.
A novel rhizobacteria Bacillus was isolated from rhizosphere of soil associated with tomato (Solanum lycopersicum L.) under open field conditions. The Bacillus amyloliquefaciens strain MHR24 (MHR24) is a promising biocontrol agent against several fungal phytopathogens. In this research, MHR24 was characterized by an effective antagonistic ability against Alternaria alternata (Aa), Botrytis cinerea (Bc), Fusarium oxysporum F1 (F1), F. oxysporum F2 (F2), F. oxysporum R3 (F3), and Sclerotinia sclerotiorum (Sc). In particular, MHR24 showed a strong inhibition via airborne volatiles against Bc, F3, Aa, and F2 fungal strains. MHR24 also showed elevated saline stress tolerance at 1% and 25% to NaCl and KCl. The molecular sequence analysis of 16S rDNA confirmed the identity of the isolate as Bacillus amyloliquefaciens strain MHR24. Bioassays on Arabidopsis thaliana Col-0 inoculated with MHR24 showed in in vitro conditions that MHR24 significantly increases the foliar and root area, while in growth chamber conditions, it strongly increases the dry shoot biomass of A. thaliana. The observed results indicate that B. amyloliquefaciens MHR24 has a broad-spectrum biocontrol against fungal phytopathogens and can be used as a biofertilizer and biocontrol agent to improve horticultural crops. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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13 pages, 2526 KiB  
Article
The Impact of Rhizospheric and Endophytic Bacteria on the Germination of Carajasia cangae: A Threatened Rubiaceae of the Amazon Cangas
by Daniela Boanares, Aline Figueiredo Cardoso, Diego Fernando Escobar Escobar, Keila Jamille Alves Costa, José Augusto Bitencourt, Paulo Henrique O. Costa, Silvio Ramos, Markus Gastauer and Cecilio Frois Caldeira
Microorganisms 2024, 12(9), 1843; https://doi.org/10.3390/microorganisms12091843 - 6 Sep 2024
Cited by 2 | Viewed by 1447
Abstract
Carajasia cangae (Rubiaceae) is a narrow endemic species from the canga ecosystems of the Carajás National Forest that is facing extinction due to a limited range and habitat disturbance from hydroclimatological changes and mining activities. This study examines the influence of rhizospheric and [...] Read more.
Carajasia cangae (Rubiaceae) is a narrow endemic species from the canga ecosystems of the Carajás National Forest that is facing extinction due to a limited range and habitat disturbance from hydroclimatological changes and mining activities. This study examines the influence of rhizospheric and endophytic bacteria on C. cangae seed germination to support conservation efforts. Soil samples, both rhizospheric and non-rhizospheric, as well as plant root tissues, were collected. Bacteria from these samples were subsequently isolated, cultured, and identified. DNA sequencing revealed the presence of 16 isolates (9 rhizospheric and 7 endophytic), representing 19 genera and 6 phyla: Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. The endophytic isolates of Bacillus and the rhizospheric isolates of Planococcus and Lysinibacillus reduced the median germination time and initiation time, while the rhizospheric isolates Serratia and Comamonas increased the germination time and decreased the germination percentage in comparison to the control sample. These findings emphasize the crucial role of endophytic bacteria in the germination of C. cangae and highlight isolates that could have beneficial effects in the following stages of plant growth. Understanding the impact of endophytic and rhizospheric bacterial isolates on seed germination can enhance conservation efforts by shortening the germination period of this species and thereby improving seedling production. Additionally, this knowledge will pave the way for future research on the role of bacteria in the establishment of C. cangae. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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18 pages, 14747 KiB  
Article
Performance of Halo-Alkali-Tolerant Endophytic Bacteria on Hybrid Pennisetum and Bacterial Community under Varying Soil Conditions
by Xia Li, Yiming Ding, Charles Obinwanne Okoye, Xiaoyan Geng, Huifang Jiang, Yongli Wang, Yanfang Wu, Lu Gao, Lei Fu, Jianxiong Jiang and Jianzhong Sun
Microorganisms 2024, 12(6), 1062; https://doi.org/10.3390/microorganisms12061062 - 24 May 2024
Cited by 1 | Viewed by 1289
Abstract
Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the potential of halo-alkali-tolerant endophytic bacteria strains Sphingomonas sp. pp01, Bacillus sp. pp02, Pantoea sp. pp04, and Enterobacter sp. pp06 to enhance [...] Read more.
Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the potential of halo-alkali-tolerant endophytic bacteria strains Sphingomonas sp. pp01, Bacillus sp. pp02, Pantoea sp. pp04, and Enterobacter sp. pp06 to enhance the growth of hybrid Pennisetum under varying saline conditions. The strains exhibited tolerance to high salt concentrations, alkaline pH, and high temperatures. Under controlled conditions, all four strains showed significant growth-promoting effects on hybrid Pennisetum inoculated individually or in combination. However, the effects were significantly reduced in coastal saline soil. The best growth-promoting effect was achieved under greenhouse conditions, increasing shoot fresh and dry weights of hybrid Pennisetum by up to 457.7% and 374.7%, respectively, using irrigating trials. Metagenomic sequencing analysis revealed that the diversity and composition of rhizosphere microbiota underwent significant changes after inoculation with endophytic bacteria. Specifically, pp02 and co-inoculation significantly increased the Dyella and Pseudomonas population. Firmicutes, Mycobacteria, and Proteobacteria phyla were enriched in Bacillus PP02 samples. These may explain the best growth-promoting effects of pp02 and co-inoculation on hybrid Pennisetum under greenhouse conditions. Our findings reveal the performance of endophytic bacterial inoculants in enhancing beneficial microbiota, salt stress tolerance, and hybrid Pennisetum growth. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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