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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 (30 November 2023) | Viewed by 19412

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Dr. Taegun Seo

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Department of Life Science, Dongguk University, Goyang 10326, Republic of Korea
Interests: symbiosis; plant growth promoting rhizobacteria (PGPR); rhizosphere; endophytes; plant-microbe interactions
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue "Rhizosphere Microbial Community".

The bacterial community found in the rhizosphere, known for its colonization around the roots due to the availability of nutrients, plays an important role in plant growth and adaptability both directly and indirectly. Various bacteria promote plant root growth to establish their ecological niche in the rhizosphere. Rhizobacteria are involved in plant-growth promotion and are often utilized to improve crop health and productivity. The rhizosphere microbe community has been the focus of extensive research during recent decades, due to its impact on plant sustainability.

More than 99% of soil bacterial species are assumed to be uncultured bacteria. The development of a next-generation sequencing (NGS) technique has allowed us to explore bacterial diversity, providing additional information about culturable and non-culturable plant-associated bacteria. In recent years, many studies have shown that bacterial populations associated with plants have allowed the identification of a large number of novel genera and species. Moreover, whole genome sequencing has enhanced our knowledge of the metabolism and relationship between bacteria and their host.

This Special Issue seeks contributions that explore the native bacterial community and diversity in the rhizosphere of plants, with the aim of sharing new findings on microorganisms’ interactions with plants in the rhizosphere environment. Moreover, it will consist of articles that cover the isolation and characterization of microbes, genomic analyses and agronomic applications. Submissions of research articles, review articles, or short communications related to the rhizosphere microbial community are all welcome, and will help us to make unexpected new discoveries in this area.

Dr. Taegun Seo
Guest Editor

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.

Related Special Issue

Rhizosphere Microbial Community 3.0 in Microorganisms

Published Papers (10 papers)

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Research

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18 pages, 2148 KiB

Open AccessArticle

The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon

by Rosiane do Socorro dos Reis de Sousa, Giulia Victória Silva Lima, Josinete Torres Garcias, Graziane de Oliveira Gomes, Jackeline Rossetti Mateus, Lucimar Di Paula dos Santos Madeira, Lucy Seldin, Hervé Louis Ghislain Rogez and Joana Montezano Marques

Microorganisms 2024, 12(2), 398; https://doi.org/10.3390/microorganisms12020398 - 17 Feb 2024

Viewed by 989

Abstract

This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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15 pages, 3687 KiB

Open AccessArticle

Microecological Shifts in the Rhizosphere of Perennial Large Trees and Seedlings in Continuous Cropping of Poplar

by Junkang Sui, Chenyu Li, Yinping Wang, Xiangyu Li, Rui Liu, Xuewen Hua, Xunli Liu and Hui Qi

Microorganisms 2024, 12(1), 58; https://doi.org/10.3390/microorganisms12010058 - 28 Dec 2023

Viewed by 655

Abstract

The cultivation of poplar trees is hindered by persistent cropping challenges, resulting in reduced wood productivity and increased susceptibility to soil-borne diseases. These issues primarily arise from alterations in microbial structure and the infiltration of pathogenic fungi. To investigate the impact on soil fertility, we conducted an analysis using soil samples from both perennial poplar trees and three successive generations of continuously cropped poplar trees. The quantity and community composition of bacteria and fungi in the rhizosphere were assessed using the Illumina MiSeq platform. The objective of this study is to elucidate the impact of continuous cropping challenges on soil fertility and rhizosphere microorganisms in poplar trees, thereby establishing a theoretical foundation for investigating the mechanisms underlying these challenges. The study found that the total bacteria in the BT group is 0.42 times higher than the CK group, and the total fungi is 0.33 times lower than the CK group. The BT and CK groups presented relatively similar bacterial richness and diversity, while the indices showed a significant (p < 0.05) higher fungal richness and diversity in the CK group. The fractions of Bacillus were 2.22% and 2.41% in the BT and CK groups, respectively. There was a 35.29% fraction of Inocybe in the BT group, whereas this was barely observed in the CK group. The fractions of Geopora were 26.25% and 5.99%, respectively in the BT and CK groups. Modifying the microbial community structure in soil subjected to continuous cropping is deemed as the most effective approach to mitigate the challenges associated with this agricultural practice. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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29 pages, 5077 KiB

Open AccessArticle

Nutrient and Microbiome-Mediated Plant–Soil Feedback in Domesticated and Wild Andropogoneae: Implications for Agroecosystems

by Amanda Quattrone, Yuguo Yang, Pooja Yadav, Karrie A. Weber and Sabrina E. Russo

Microorganisms 2023, 11(12), 2978; https://doi.org/10.3390/microorganisms11122978 - 13 Dec 2023

Viewed by 1070

Abstract

Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73-wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative PSF based on growth, phenotypic traits, and foliar nutrient concentrations for maize B73-wt, which grew slower in maize-conditioned soil than prairie grass-conditioned soil. In contrast, teosinte and A. gerardii showed few consistent feedback responses. Both rhizobiome and nutrient-mediated mechanisms were implicated in PSF. Based on 16S rRNA gene amplicon sequencing, the rhizosphere bacterial community composition differed significantly after conditioning by prairie grass and maize plants, and the final soil nutrients were significantly influenced by conditioning, more so than by the feedback plants. These results suggest PSF-mediated soil domestication in agricultural settings can develop quickly and reduce crop productivity mediated by PSF involving changes to both the soil rhizobiomes and nutrient availability. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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15 pages, 4465 KiB

Open AccessArticle

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils

by John M. Santiago, Lukas M. Hallman, John-Paul Fox, Marco Pitino, Robert G. Shatters, Jr., Liliana M. Cano and Lorenzo Rossi

Microorganisms 2023, 11(11), 2764; https://doi.org/10.3390/microorganisms11112764 - 14 Nov 2023

Viewed by 850

Abstract

Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of ‘Valencia’ sweet orange (Citrus × sinensis) trees grafted on ‘US-812’ (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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20 pages, 5305 KiB

Open AccessArticle

Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L.

by Inhyup Kim, Geeta Chhetri, Yoonseop So, Sunho Park, Yonghee Jung, Haejin Woo and Taegun Seo

Microorganisms 2023, 11(8), 1900; https://doi.org/10.3390/microorganisms11081900 - 27 Jul 2023

Cited by 3 | Viewed by 1224

Abstract

Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11^T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11^T fermentation broth. The exopolysaccharide’s average molecular weight was 0.93 × 10⁵ Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11^T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11^T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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21 pages, 2519 KiB

Open AccessArticle

The Plant Growth-Promoting Potential of Halotolerant Bacteria Is Not Phylogenetically Determined: Evidence from Two Bacillus megaterium Strains Isolated from Saline Soils Used to Grow Wheat

by Sylia Ait Bessai, Joana Cruz, Pablo Carril, Juliana Melo, Margarida M. Santana, Abdul M. Mouazen, Cristina Cruz, Ajar Nath Yadav, Teresa Dias and El-hafid Nabti

Microorganisms 2023, 11(7), 1687; https://doi.org/10.3390/microorganisms11071687 - 28 Jun 2023

Cited by 1 | Viewed by 1513

Abstract

(1) Background: Increasing salinity, further potentiated by climate change and soil degradation, will jeopardize food security even more. Therefore, there is an urgent need for sustainable agricultural practices capable of maintaining high crop yields despite adverse conditions. Here, we tested if wheat, a salt-sensitive crop, could be a good reservoir for halotolerant bacteria with plant growth-promoting (PGP) capabilities. (2) Methods: We used two agricultural soils from Algeria, which differ in salinity but are both used to grow wheat. Soil halotolerant bacterial strains were isolated and screened for 12 PGP traits related to phytohormone production, improved nitrogen and phosphorus availability, nutrient cycling, and plant defence. The four ‘most promising’ halotolerant PGPB strains were tested hydroponically on wheat by measuring their effect on germination, survival, and biomass along a salinity gradient. (3) Results: Two halotolerant bacterial strains with PGP traits were isolated from the non-saline soil and were identified as Bacillus subtilis and Pseudomonas fluorescens, and another two halotolerant bacterial strains with PGP traits were isolated from the saline soil and identified as B. megaterium. When grown under 250 mM of NaCl, only the inoculated wheat seedlings survived. The halotolerant bacterial strain that displayed all 12 PGP traits and promoted seed germination and plant growth the most was one of the B. megaterium strains isolated from the saline soil. Although they both belonged to the B. megaterium clade and displayed a remarkable halotolerance, the two bacterial strains isolated from the saline soil differed in two PGP traits and had different effects on plant performance, which clearly shows that PGP potential is not phylogenetically determined. (4) Conclusions: Our data highlight that salt-sensitive plants and non-saline soils can be reservoirs for halotolerant microbes with the potential to become effective and sustainable strategies to improve plant tolerance to salinity. However, these strains need to be tested under field conditions and with more crops before being considered biofertilizer candidates. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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11 pages, 1034 KiB

Open AccessArticle

On the Negative Impact of Mycorrhiza Application on Maize Plants (Zea mays) Amended with Mineral and Organic Fertilizer

by Matthias Thielicke, Julian Ahlborn, Bettina Eichler-Löbermann and Frank Eulenstein

Microorganisms 2023, 11(7), 1663; https://doi.org/10.3390/microorganisms11071663 - 26 Jun 2023

Cited by 3 | Viewed by 1374

Abstract

Many studies describe the positive effect of mycorrhiza, but few report on negative effects. Furthermore, there is a research gap on the mechanisms under which conditions the symbiotic mycorrhizal plant interaction or a parasitic one predominates. The study was conducted as a field experiment over three years to investigate the effect of mycorrhiza (Rhizoglomus intraradices) and soil bacteria applications on fertile soil. A standard fertilizer (diammonium phosphate) and two microgranular fertilizers (mineral and organomineral) were applied alone or in combination with the biostimulants mycorrhiza and/or soil bacteria (Bacillus velezensis). The application of the mycorrhiza as the only biostimulant resulted in lower yields compared to all fertilizer variants without the mycorrhiza or with mycorrhiza in combination with soil bacteria in the dry years 2015 (p = 0.0241) and 2016 (p = 0.0003). The usage of soil bacteria alone, or soil bacteria with fertilizer, resulted in few occasional significant differences. The combination with soil bacteria raised the yield of mycorrhiza-treated fertilizer variants to a significant extent in 2015 (p = 0.0007) and 2016 (p = 0.0019). The negative effects of mycorrhiza application in this study were alleviated by the simultaneous use of soil bacteria. Treatments with organomineral microgranular fertilizer, which were expected to promote the naturally occurring soil microbiome more than the mineral fertilizer variants, were most negatively affected by the mycorrhiza. We hypothesize that the naturally occurring microbiome of the study site was already optimal for maize plants, and thus the successful introduction of other microorganisms through the application of the mycorrhiza and soil bacteria tended not to be beneficial. The present study is the first report on the negative influence of arbuscular mycorrhiza on maize yields gained with a standard fertilizer (diammonium phosphate) and two microgranular fertilizer, and the alleviation of that impact by combined application of soil bacteria. We conclude that the application of the used biostimulants may have negative impacts on maize yield if the soil is already rich in nutrients and water is the limiting factor. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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Review

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27 pages, 2271 KiB

Open AccessReview

Bacterial Communities Associated with the Roots of Typha spp. and Its Relationship in Phytoremediation Processes

by Joana Guadalupe Martínez-Martínez, Stephanie Rosales-Loredo, Alejandro Hernández-Morales, Jackeline Lizzeta Arvizu-Gómez, Candy Carranza-Álvarez, José Roberto Macías-Pérez, Gisela Adelina Rolón-Cárdenas and Juan Ramiro Pacheco-Aguilar

Microorganisms 2023, 11(6), 1587; https://doi.org/10.3390/microorganisms11061587 - 15 Jun 2023

Cited by 5 | Viewed by 1733

Abstract

Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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18 pages, 1164 KiB

Open AccessReview

Evaluation of Legume–Rhizobial Symbiotic Interactions Beyond Nitrogen Fixation That Help the Host Survival and Diversification in Hostile Environments

by Ravinder K. Goyal and Jemaneh Z. Habtewold

Microorganisms 2023, 11(6), 1454; https://doi.org/10.3390/microorganisms11061454 - 31 May 2023

Cited by 10 | Viewed by 3073

Abstract

Plants often experience unfavorable conditions during their life cycle that impact their growth and sometimes their survival. A temporary phase of such stress, which can result from heavy metals, drought, salinity, or extremes of temperature or pH, can cause mild to enormous damage to the plant depending on its duration and intensity. Besides environmental stress, plants are the target of many microbial pathogens, causing diseases of varying severity. In plants that harbor mutualistic bacteria, stress can affect the symbiotic interaction and its outcome. To achieve the full potential of a symbiotic relationship between the host and rhizobia, it is important that the host plant maintains good growth characteristics and stay healthy under challenging environmental conditions. The host plant cannot provide good accommodation for the symbiont if it is infested with diseases and prone to other predators. Because the bacterium relies on metabolites for survival and multiplication, it is in its best interests to keep the host plant as stress-free as possible and to keep the supply stable. Although plants have developed many mitigation strategies to cope with stress, the symbiotic bacterium has developed the capability to augment the plant’s defense mechanisms against environmental stress. They also provide the host with protection against certain diseases. The protective features of rhizobial–host interaction along with nitrogen fixation appear to have played a significant role in legume diversification. When considering a legume–rhizobial symbiosis, extra benefits to the host are sometimes overlooked in favor of the symbionts’ nitrogen fixation efficiency. This review examines all of those additional considerations of a symbiotic interaction that enable the host to withstand a wide range of stresses, enabling plant survival under hostile regimes. In addition, the review focuses on the rhizosphere microbiome, which has emerged as a strong pillar of evolutionary reserve to equip the symbiotic interaction in the interests of both the rhizobia and host. The evaluation would draw the researchers’ attention to the symbiotic relationship as being advantageous to the host plant as a whole and the role it plays in the plant’s adaptation to unfavorable environmental conditions. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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17 pages, 2645 KiB

Open AccessReview

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

by Phil Thomas, Oliver G. G. Knox, Jeff R. Powell, Brian Sindel and Gal Winter

Microorganisms 2023, 11(4), 835; https://doi.org/10.3390/microorganisms11040835 - 24 Mar 2023

Cited by 5 | Viewed by 4374

Abstract

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)

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