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Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and...
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Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 38353

Special Issue Editors

Dr. Ana Alexandre

E-Mail Website
Guest Editor
Department of Biology, Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora, 7004-516 Évora, Portugal
Interests: plant beneficial bacteria, in particular the rhizobia-legume symbiosis; bacteria-plant interaction; plant protection against biotic and abiotic stresses
Dr. Kathrin Wippel

E-Mail Website
Guest Editor
Max Planck Institute for Plant Breeding Research, Cologne, Germany
Interests: plant-microbe interactions; microbiota assembly; microbial colonization of plant roots; root nodule symbiosis; microbial host preference

Special Issue Information

Dear Colleagues,

Agriculture is currently facing a number of ecologic and economic challenges. On the one hand, climate change has highlighted the importance of crop resilience and genetic diversity, and there is a demand for a more efficient use of resources and the implementation of sustainable and eco-friendly practices. On the other hand, these aspects are often neglected due to the constant pressure to increase food production in the light of a growing world population.

Soil bacteria have the potential to promote plant growth and contribute to plant protection against biotic and abiotic stresses in an ecologically sustainable way. From fundamental research focusing on individual genes or metabolic networks to large-scale applied field studies, there are many diverse approaches to further our understanding of the role and impact of beneficial soil bacteria on crop production.

This Special Issue is dedicated to research performed on all aspects of the biology of these bacteria as well as host interaction mechanisms. We invite scientists to contribute with original research and review articles that report progress on the current knowledge of soil beneficial bacteria, including:

- Rhizobia–legume symbiosis;
- Broad host range plant-growth-promoting bacteria;
- Bacterial bio-control agents for crop protection;
- Soil and rhizosphere bacterial communities.

Dr. Ana Alexandre
Dr. Kathrin Wippel
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. Biology 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
  • rhizobia
  • endophytes
  • symbiosis
  • agriculture
  • diversity
  • plant protection

Published Papers (7 papers)

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Research

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21 pages, 3743 KiB  
Article
Protective and Curative Activities of Paenibacillus polymyxa against Zucchini yellow mosaic virus Infestation in Squash Plants
by Ahmed Abdelkhalek, Abdulaziz A. Al-Askar, Toufic Elbeaino, Hassan Moawad and Hamada El-Gendi
Biology 2022, 11(8), 1150; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11081150 - 30 Jul 2022
Cited by 11 | Viewed by 2319
Abstract
The use of microbial products as natural biocontrol agents to increase a plant’s systemic resistance to viral infections is a promising way to make agriculture more sustainable and less harmful to the environment. The rhizobacterium Paenibacillus polymyxa has been shown to have strong [...] Read more.
The use of microbial products as natural biocontrol agents to increase a plant’s systemic resistance to viral infections is a promising way to make agriculture more sustainable and less harmful to the environment. The rhizobacterium Paenibacillus polymyxa has been shown to have strong biocontrol action against plant diseases, but its antiviral activity has been little investigated. Here, the efficiency of the culture filtrate of the P. polymyxa strain SZYM (Acc# ON149452) to protect squash (Cucurbita pepo L.) plants against a Zucchini yellow mosaic virus (ZYMV, Acc# ON159933) infection was evaluated. Under greenhouse conditions, the foliar application of the culture filtrate of SZYM either in protective or curative treatment conditions enhanced squash growth, reduced disease severity, and decreased ZYMV accumulation levels in the treated plants when compared to the non-treated plants. The protective treatment group exhibited the highest inhibitory effect (80%), with significant increases in their total soluble carbohydrates, total soluble protein content, ascorbic acid content, and free radical scavenging activity. Furthermore, a considerable increase in the activities of reactive oxygen species scavenging enzymes (superoxide dismutase, polyphenol oxidase, and peroxidase) were also found. In addition, the induction of systemic resistance with a significant elevation in the transcriptional levels of polyphenolic pathway genes (CHS, PAL, and C3H) and pathogenesis-related genes (PR-1 and PR-3) was observed. Out of the 14 detected compounds in the GC–MS analysis, propanoic acid, benzenedicarboxylic acid, tetradecanoic acid, and their derivatives, as well as pyrrolo [1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl) were the primary ingredient compounds in the ethyl acetate extract of the SZYM-culture filtrate. Such compounds may act as elicitor molecules that induce systemic resistance against viral infection. Consequently, P. polymyxa can be considered a powerful plant growth-promoting bacterium (PGPB) in agricultural applications as well as a source of bioactive compounds for sustainable disease management. As far as we know, this is the first time that P. polymyxa has been shown to fight viruses in plants. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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15 pages, 2344 KiB  
Article
Microbial Consortia: An Engineering Tool to Suppress Clubroot of Chinese Cabbage by Changing the Rhizosphere Bacterial Community Composition
by Jinhao Zhang, Waqar Ahmed, Zhenlin Dai, Xinghai Zhou, Zulei He, Lanfang Wei and Guanghai Ji
Biology 2022, 11(6), 918; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11060918 - 15 Jun 2022
Cited by 10 | Viewed by 2324
Abstract
Clubroot disease, caused by Plasmodiophora brassicae, is a serious threat to Chinese cabbage (Brassica rapa subsp. pekinensis) production, which results in extensive yield losses. At present, clubroot control mainly depends upon pesticides, which provoke food-safety concerns, and the application of [...] Read more.
Clubroot disease, caused by Plasmodiophora brassicae, is a serious threat to Chinese cabbage (Brassica rapa subsp. pekinensis) production, which results in extensive yield losses. At present, clubroot control mainly depends upon pesticides, which provoke food-safety concerns, and the application of sole biocontrol agents cannot successfully control the disease. In this study, we investigated the effect of Bacillus cereus BT-23, Lysobacter antibioticus 13-6, and Lysobacter capsici ZST1-2 as sole strains, intra-/inter-genus co-culture, and microbial consortia on clubroot disease, plant growth, and rhizosphere bacterial diversity in a field experiment. The microbial consortia efficiently controlled the incidence of clubroot disease, with a biocontrol effect of about 65.78%, by decreasing the soil acidity and enhancing the yield (17,662.49 kg/acre). The high-throughput sequencing results demonstrated that the phyla Proteobacteria and Bacteroidetes were present in high relative abundance in the rhizosphere soil of the Chinese cabbage. Furthermore, Firmicutes was found as a unique phylum in the rhizosphere soil of CK-H and T1-T7, except for CK-D. The application of microbial consortia recovers the imbalance in indigenous microbial communities. Therefore, we conclude that microbial consortia can reduce the clubroot incidence in Chinese cabbage by decreasing the soil acidity and altering the diversity and structure of rhizosphere bacterial communities. This study highlights the potential of microbial consortia as an engineering tool to control devastating soilborne diseases in commercial crops. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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27 pages, 7976 KiB  
Article
Drought Tolerant Enterobacter sp./Leclercia adecarboxylata Secretes Indole-3-acetic Acid and Other Biomolecules and Enhances the Biological Attributes of Vigna radiata (L.) R. Wilczek in Water Deficit Conditions
by Bilal Ahmed, Mohammad Shahid, Asad Syed, Vishnu D. Rajput, Abdallah M. Elgorban, Tatiana Minkina, Ali H. Bahkali and Jintae Lee
Biology 2021, 10(11), 1149; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10111149 - 08 Nov 2021
Cited by 32 | Viewed by 3148
Abstract
Drought or water stress is a limiting factor that hampers the growth and yield of edible crops. Drought-tolerant plant growth-promoting rhizobacteria (PGPR) can mitigate water stress in crops by synthesizing multiple bioactive molecules. Here, strain PAB19 recovered from rhizospheric soil was biochemically and [...] Read more.
Drought or water stress is a limiting factor that hampers the growth and yield of edible crops. Drought-tolerant plant growth-promoting rhizobacteria (PGPR) can mitigate water stress in crops by synthesizing multiple bioactive molecules. Here, strain PAB19 recovered from rhizospheric soil was biochemically and molecularly characterized, and identified as Enterobacter sp./Leclercia adecarboxylata (MT672579.1). Strain PAB19 tolerated an exceptionally high level of drought (18% PEG-6000) and produced indole-3-acetic acid (176.2 ± 5.6 µg mL−1), ACC deaminase (56.6 ± 5.0 µg mL−1), salicylic acid (42.5 ± 3.0 µg mL−1), 2,3-dihydroxy benzoic acid (DHBA) (44.3 ± 2.3 µg mL−1), exopolysaccharide (204 ± 14.7 µg mL−1), alginate (82.3 ± 6.5 µg mL−1), and solubilized tricalcium phosphate (98.3 ± 3.5 µg mL−1), in the presence of 15% polyethylene glycol. Furthermore, strain PAB19 alleviated water stress and significantly (p ≤ 0.05) improved the overall growth and biochemical attributes of Vigna radiata (L.) R. Wilczek. For instance, at 2% PEG stress, PAB19 inoculation maximally increased germination, root dry biomass, leaf carotenoid content, nodule biomass, leghaemoglobin (LHb) content, leaf water potential (ΨL), membrane stability index (MSI), and pod yield by 10%, 7%, 14%, 38%, 9%, 17%, 11%, and 11%, respectively, over un-inoculated plants. Additionally, PAB19 inoculation reduced two stressor metabolites, proline and malondialdehyde, and antioxidant enzymes (POD, SOD, CAT, and GR) levels in V. radiata foliage in water stress conditions. Following inoculation of strain PAB19 with 15% PEG in soil, stomatal conductance, intercellular CO2 concentration, transpiration rate, water vapor deficit, intrinsic water use efficiency, and photosynthetic rate were significantly improved by 12%, 8%, 42%, 10%, 9% and 16%, respectively. Rhizospheric CFU counts of PAB19 were 2.33 and 2.11 log CFU g−1 after treatment with 15% PEG solution and 8.46 and 6.67 log CFU g−1 for untreated controls at 40 and 80 DAS, respectively. Conclusively, this study suggests the potential of Enterobacter sp./L. adecarboxylata PAB19 to alleviate water stress by improving the biological and biochemical features and of V. radiata under water-deficit conditions. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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16 pages, 3227 KiB  
Article
Enhancement of the Aroma Compound 2-Acetyl-1-pyrroline in Thai Jasmine Rice (Oryza sativa) by Rhizobacteria under Salt Stress
by Kawiporn Chinachanta, Arawan Shutsrirung, Laetitia Herrmann, Didier Lesueur and Wasu Pathom-aree
Biology 2021, 10(10), 1065; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10101065 - 19 Oct 2021
Cited by 6 | Viewed by 3530
Abstract
Thai jasmine rice (Oryza sativa L. KDML105), particularly from inland salt-affected areas in Thailand, is both domestically and globally valued for its unique aroma and high grain quality. The key aroma compound, 2-acetyl-1-pyrroline (2AP), has undergone a gradual degradation due to anthropogenic [...] Read more.
Thai jasmine rice (Oryza sativa L. KDML105), particularly from inland salt-affected areas in Thailand, is both domestically and globally valued for its unique aroma and high grain quality. The key aroma compound, 2-acetyl-1-pyrroline (2AP), has undergone a gradual degradation due to anthropogenic soil salinization driven by excessive chemical input and climate change. Here, we propose a cheaper and an ecofriendly solution to improve the 2AP levels, based on the application of plant growth-promoting rhizobacteria (PGPR). In the present study, nine PGPR isolates from rice rhizosphere were investigated for the 2AP production in liquid culture and the promotion potential for 2AP content in KDML105 rice seedlings under four NaCl concentrations (0, 50, 100, and 150 mM NaCl). The inoculation of 2AP-producing rhizobacteria resulted in an increase in 2AP content in rice seedling leaves with the maximum enhancement from Sinomonas sp. ORF15-23 at 50 mM NaCl (19.6 µg·kg−1), corresponding to a 90.2% increase as compared to the control. Scanning electron microscopy confirmed the colonization of Sinomonas sp. ORF15-23 in the roots of salinity-stressed KDML105 seedlings. Our results provide evidence that Sinomonas sp. ORF15-23 could be a promising PGPR isolate in promoting aroma level of Thai jasmine rice KDML105 under salt stress. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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23 pages, 3528 KiB  
Article
Contrasting Effects of Forest Type and Stand Age on Soil Microbial Activities: An Analysis of Local Scale Variability
by Anna Walkiewicz, Andrzej Bieganowski, Adrianna Rafalska, Mohammad I. Khalil and Bruce Osborne
Biology 2021, 10(9), 850; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10090850 - 31 Aug 2021
Cited by 6 | Viewed by 2946
Abstract
Understanding the functioning of different forest ecosystems is important due to their key role in strategies for climate change mitigation, especially through soil C sequestration. In controlled laboratory conditions, we conducted a preliminary study on six different forest soils (two coniferous, two deciduous, [...] Read more.
Understanding the functioning of different forest ecosystems is important due to their key role in strategies for climate change mitigation, especially through soil C sequestration. In controlled laboratory conditions, we conducted a preliminary study on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region. The aim was to explore any differences and assess seasonal changes in soil microbial parameters (basal respiration BR, microbial biomass Cmic, metabolic quotient qCO2, dehydrogenase activity DHA, and Cmic:Corg ratio). Indicator- and forest-specific seasonality was assessed. In addition to litter input, soil parameters (pH, nutrient content, texture and moisture) strongly regulated the analyzed microbial indicators. PCA analysis indicated similarity between mature mixed and deciduous forests. Among annual mean values, high Cmic and DHA with simultaneously low qCO2 suggest that the mature deciduous stand was the most sustainable in microbial activities among the investigated forest soils. Research on the interrelationship between soil parameters and forest types with different tree ages needs to be continued and extended to analyze a greater number of forest and soil types. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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Review

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22 pages, 1692 KiB  
Review
Utilization of Microbial Consortia as Biofertilizers and Biopesticides for the Production of Feasible Agricultural Product
by Renganathan Seenivasagan and Olubukola Oluranti Babalola
Biology 2021, 10(11), 1111; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10111111 - 28 Oct 2021
Cited by 38 | Viewed by 11448
Abstract
Farmers are now facing a reduction in agricultural crop yield, due to the infertility of soils and poor farming. The application of chemical fertilizers distresses soil fertility and also human health. Inappropriate use of chemical fertilizer leads to the rapid decline in production [...] Read more.
Farmers are now facing a reduction in agricultural crop yield, due to the infertility of soils and poor farming. The application of chemical fertilizers distresses soil fertility and also human health. Inappropriate use of chemical fertilizer leads to the rapid decline in production levels in most parts of the world, and hence requires the necessary standards of good cultivation practice. Biofertilizers and biopesticides have been used in recent years by farmers worldwide to preserve natural soil conditions. Biofertilizer, a replacement for chemical fertilizer, is cost-effective and prevents environmental contamination to the atmosphere, and is a source of renewable energy. In contrast to chemical fertilizers, biofertilizers are cost-effective and a source of renewable energy that preserves long-term soil fertility. The use of biofertilizers is, therefore, inevitable to increase the earth’s productivity. A low-input scheme is feasible to achieve farm sustainability through the use of biological and organic fertilizers. This study investigates the use of microbial inoculants as biofertilizers to increase crop production. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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23 pages, 3663 KiB  
Review
The Role of Plant Growth-Promoting Bacteria in Alleviating the Adverse Effects of Drought on Plants
by Khaled Abdelaal, Muneera AlKahtani, Kotb Attia, Yaser Hafez, Lóránt Király and András Künstler
Biology 2021, 10(6), 520; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10060520 - 11 Jun 2021
Cited by 119 | Viewed by 10022
Abstract
Plant growth-promoting bacteria play an essential role in enhancing the physical, chemical and biological characters of soils by facilitating nutrient uptake and water flow, especially under abiotic stress conditions, which are major constrains to agricultural development and production. Drought is one of the [...] Read more.
Plant growth-promoting bacteria play an essential role in enhancing the physical, chemical and biological characters of soils by facilitating nutrient uptake and water flow, especially under abiotic stress conditions, which are major constrains to agricultural development and production. Drought is one of the most harmful abiotic stress and perhaps the most severe problem facing agricultural sustainability, leading to a severe shortage in crop productivity. Drought affects plant growth by causing hormonal and membrane stability perturbations, nutrient imbalance and physiological disorders. Furthermore, drought causes a remarkable decrease in leaf numbers, relative water content, sugar yield, root yield, chlorophyll a and b and ascorbic acid concentrations. However, the concentrations of total phenolic compounds, electrolyte leakage, lipid peroxidation, amounts of proline, and reactive oxygen species are considerably increased because of drought stress. This negative impact of drought can be eliminated by using plant growth-promoting bacteria (PGPB). Under drought conditions, application of PGPB can improve plant growth by adjusting hormonal balance, maintaining nutrient status and producing plant growth regulators. This role of PGPB positively affects physiological and biochemical characteristics, resulting in increased leaf numbers, sugar yield, relative water content, amounts of photosynthetic pigments and ascorbic acid. Conversely, lipid peroxidation, electrolyte leakage and amounts of proline, total phenolic compounds and reactive oxygen species are decreased under drought in the presence of PGPB. The current review gives an overview on the impact of drought on plants and the pivotal role of PGPB in mitigating the negative effects of drought by enhancing antioxidant defense systems and increasing plant growth and yield to improve sustainable agriculture. Full article
(This article belongs to the Special Issue Beneficial Soil Bacteria: Many Recipes to Promote Plant Growth and Protection)
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