Microorganisms

Editorial

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2 pages, 173 KiB

Open AccessEditorial

Special Issue “Microbial Interactions in Soil”: Editorial

by Volker S. Brozel

Microorganisms 2023, 11(5), 1260; https://doi.org/10.3390/microorganisms11051260 - 11 May 2023

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Abstract

Soils are home to a wide variety of microorganisms [...] Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

Research

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18 pages, 2256 KiB

Open AccessArticle

Continuous Sugarcane Planting Negatively Impacts Soil Microbial Community Structure, Soil Fertility, and Sugarcane Agronomic Parameters

by Ziqin Pang, Muhammad Tayyab, Chuibao Kong, Qiang Liu, Yueming Liu, Chaohua Hu, Jinwen Huang, Peiying Weng, Waqar Islam, Wenxiong Lin and Zhaonian Yuan

Microorganisms 2021, 9(10), 2008; https://doi.org/10.3390/microorganisms9102008 - 23 Sep 2021

Cited by 31 | Viewed by 4712

Abstract

Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing [...] Read more.

Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing technology, we analyzed soil samples from sugarcane fields with 1, 10, and 30 years of continuous cropping to see how monoculture time affected sugarcane yield, its rhizosphere soil characteristics and microbiota. The results showed that continuous sugarcane planting reduced sugarcane quality and yield. Continuous sugarcane planting for 30 years resulted in soil acidification, as well as C/N, alkali hydrolyzable nitrogen, organic matter, and total sulfur content significantly lower than in newly planted fields. Continuous sugarcane planting affected soil bacterial, fungal, and AM fungal communities, according to PCoA and ANOSIM analysis. Redundancy analysis (RDA) results showed that bacterial, fungal, and AM fungal community composition were strongly associated with soil properties and attributes, e.g., soil AN, OM, and TS were critical environmental factors in transforming the bacterial community. The LEfSe analysis revealed bacterial families (e.g., Gaiellaceae, Pseudomonadaceae, Micromonosporaceae, Nitrosomonadaceae, and Methyloligellaceae) were more prevalent in the newly planted field than in continuously cultivated fields (10 and 30 years), whereas Sphingomonadaceae, Coleofasciculaceae, and Oxyphotobacteria were depleted. Concerning fungal families, the newly planted field was more dominated than the continuously planted field (30 years) with Mrakiaceae and Ceratocystidaceae, whereas Piskurozymaceae, Trimorphomycetaceae, Lachnocladiaceae, and Stigmatodisc were significantly enriched in the continuously planted fields (10 and 30 years). Regarding AMF families, Diversisporaceae was considerably depleted in continuously planted fields (10 and 30 years) compared to the newly planted field. These changes in microbial composition may ultimately lead to a decrease in sugarcane yield and quality in the monoculture system, which provides a theoretical basis for the obstruction mechanism of the continuous sugarcane planting system. However, continuous planting obstacles remain uncertain and further need to be coupled with root exudates, soil metabolomics, proteomics, nematodes, and other exploratory methods. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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15 pages, 1562 KiB

Open AccessArticle

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

by Kishan Mahmud, Kendall Lee, Nicholas S. Hill, Anaas Mergoum and Ali Missaoui

Microorganisms 2021, 9(9), 1843; https://doi.org/10.3390/microorganisms9091843 - 31 Aug 2021

Cited by 13 | Viewed by 3406

Abstract

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue [...] Read more.

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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12 pages, 1338 KiB

Open AccessArticle

Biodiversity of Actinomycetes from Heavy Metal Contaminated Technosols

by Michaela Cimermanova, Peter Pristas and Maria Piknova

Microorganisms 2021, 9(8), 1635; https://doi.org/10.3390/microorganisms9081635 - 30 Jul 2021

Cited by 16 | Viewed by 3027

Abstract

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, [...] Read more.

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, including streptomycetes, known as a tremendous source of biotechnologically important molecules. In this study, the biodiversity of streptomycete-like isolates from several technosols, mainly mine soils and wastes (landfills and sludge) in Slovakia, was investigated. The combination of basic morphological and biochemical characterisations, including heavy metal resistance determination, and molecular approaches based on 16S rRNA gene analysis were used for the identification of the bacterial strains. From nine isolates of Actinobacteria collected from different habitats, one was found to represent a new species within the Crossiella genus. Eight other isolates were assigned to the genus Streptomyces, of which at least one could represent a new bacterial species. Some isolates showed high resistance to Pb, Zn, Cu or Ni. The most tolerated metal was Pb. The results obtained in this study indicate that technosols are a prospective source of new actinomycete species resistant to heavy metals what underlines their bioremediation potential. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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13 pages, 3032 KiB

Open AccessArticle

Response of Soil Fungal Diversity and Community Composition to Varying Levels of Bamboo Biochar in Red Soils

by Muhammad Waqqas Khan Tarin, Lili Fan, Dejin Xie, Muhammad Tayyab, Jundong Rong, Lingyan Chen, Muhammad Atif Muneer and Yushan Zheng

Microorganisms 2021, 9(7), 1385; https://doi.org/10.3390/microorganisms9071385 - 25 Jun 2021

Cited by 36 | Viewed by 3766

Abstract

Soil fungi play a vital role in soil nutrient dynamics, but knowledge of their diversity and community composition in response to biochar addition into red soil is either limited or inconsistent. Therefore, we determined the impact of bamboo biochar (BB) with increasing concentrations [...] Read more.

Soil fungi play a vital role in soil nutrient dynamics, but knowledge of their diversity and community composition in response to biochar addition into red soil is either limited or inconsistent. Therefore, we determined the impact of bamboo biochar (BB) with increasing concentrations (0, 5, 20, and 80 g kg⁻¹ of soil, referred to as B0, BB5, BB20, and BB80, respectively) on soil physicochemical properties and fungal communities (Illumina high-throughput sequencing) in red soil under Fokenia hodginsii (Fujian cypress). We found that increasing BB levels effectively raised the soil pH and soil nutrients, particularly under BB80. BB addition significantly increased the relative abundance of important genera, i.e., Basidiomycota, Mucoromycota, and Chytridiomycota that could play a key role in ecological functioning, e.g., wood degradation and litter decomposition, improvement in plant nutrients uptake, and resistance to several abiotic stress factors. Soil amended with BB exhibited a substantial ability to increase the fungal richness and diversity; BB80 > BB20 > BB5 > B0. Basidiomycota, Mucoromycota, Glomeromycota, Rozellomycota, Aphelidiomycota, Kickxellomycota, and Planctomycetes were positively associated with soil pH, total nitrogen, phosphorous, and carbon, and available potassium and phosphorous. Besides, the correlation analysis between the soil fungal communities and soil properties also showed that soil pH was the most influential factor in shaping the soil fungal communities in the red soil. These findings have significant implications for a comprehensive understanding of how to ameliorate acidic soils with BB addition, as well as for future research on sustainable forest management, which might increase soil fungi richness, diversity, and functionality in acidic soils. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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17 pages, 1237 KiB

Open AccessArticle

Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities

by Lucas Dantas Lopes, Yen Ning Chai, Ellen L. Marsh, John F. Rajewski, Ismail Dweikat and Daniel P. Schachtman

Microorganisms 2021, 9(6), 1329; https://doi.org/10.3390/microorganisms9061329 - 18 Jun 2021

Cited by 11 | Viewed by 2956

Abstract

The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of [...] Read more.

The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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16 pages, 1999 KiB

Open AccessArticle

Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere

by Jingjing Chang, Shaohua Shi, Lei Tian, Marcio F. A. Leite, Chunling Chang, Li Ji, Lina Ma, Chunjie Tian and Eiko E. Kuramae

Microorganisms 2021, 9(1), 175; https://doi.org/10.3390/microorganisms9010175 - 15 Jan 2021

Cited by 10 | Viewed by 3259

Abstract

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the [...] Read more.

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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Review

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19 pages, 1405 KiB

Open AccessReview

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments

by Beatrice Farda, Rihab Djebaili, Ilaria Vaccarelli, Maddalena Del Gallo and Marika Pellegrini

Microorganisms 2022, 10(2), 453; https://doi.org/10.3390/microorganisms10020453 - 16 Feb 2022

Cited by 39 | Viewed by 7514

Abstract

The environmental conditions of caves shape microbiota. Within caves’ microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role [...] Read more.

The environmental conditions of caves shape microbiota. Within caves’ microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves’ actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves’ actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes’ outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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18 pages, 882 KiB

Open AccessReview

Pathogen Biocontrol Using Plant Growth-Promoting Bacteria (PGPR): Role of Bacterial Diversity

by Hao Wang, Runjin Liu, Ming Pei You, Martin J. Barbetti and Yinglong Chen

Microorganisms 2021, 9(9), 1988; https://doi.org/10.3390/microorganisms9091988 - 18 Sep 2021

Cited by 102 | Viewed by 11928

Abstract

A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading [...] Read more.

A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading plant pathogens. However, a cumulative or synergistic effect does not always ensue when a bacterial consortium is used. In this review, we reassess the disease-suppressive mechanisms of PGPR and present explanations and illustrations for functional diversity and/or stability among PGPR taxa regarding these mechanisms. We also provide evidence of benefits when PGPR mixtures, rather than individuals, are used for protecting crops from various diseases, and underscore the critical determinant factors for successful use of PGPR mixtures. Then, we evaluate the challenges of and limitations to achieving the desired outcomes from strain/species-rich bacterial assemblages, particularly in relation to their role for plant disease management. In addition, towards locating additive or synergistic outcomes, we highlight why and how the benefits conferred need to be categorized and quantified when different strains/species of PGPR are used in combinations. Finally, we highlight the critical approaches needed for developing PGPR mixtures with improved efficacy and stability as biocontrols for utilization in agricultural fields. Full article

(This article belongs to the Special Issue Microbial Interactions in Soil)

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