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Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes

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A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 40749

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Special Issue Editors

Dr. Milko A. Jorquera

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Guest Editor

Department of Chemical Science and Environmental Resources, La Frontera University, Temuco 4811-230, Chile
Interests: airborne microbiomes; algae-associated microbiomes; bacterial community diversity; extremophilic bacteria; plant-associated microbiomes; plant growth-promoting bacteria; sediment-associated microbiomes; soil microbiology
Special Issues, Collections and Topics in MDPI journals

Dr. Jacquelinne Acuña

E-Mail Website
Guest Editor

Universidad de la Frontera, Temuco, Chile
Interests: plant-microbe interactions; soil microbiology; microbial ecology; bacterial communities; culturomics; plant-growth promoting bacteria; microbe-microbe interactions; plant microbiome

Special Issue Information

Dear Colleagues,

Numerous studies in the last few decades have demonstrated that microbiomes are pivotal for the growth and fitness of plants in diverse ecosystems. These studies have revealed that plants are able to recruit a varied and specific microbial community according to their genotype, phenological stages, and plant niches. In this sense, diverse niches have been identified in plants, such as rhizosphere, endosphere, phyllosphere, spermosphere, and plant detritusphere, where the local conditions influence the colonization, proliferation, and plant–microbe interactions.

In addition, studies have also revealed that plant-associated microbiomes not only harbor a wide diversity of specific microbial communities but also can harbor beneficial microbes, commonly termed plant growth-promoting microorganisms (PGPMs), which have been extensively studied, bioprospected, and applied as commercial microbial inoculants. Thus, PGPMs have been used by farmers as biofertilizers to improve plant nutrition and as biocontrol agents to prevent the attack of phytopathogens. In this context, prolonged drought periods and sudden heavy rains and cold/hot waves have affected diverse agricultural regions worldwide as result of climate change. This world challenge has also motivated the search and the potential use of PGPMs as agents to mitigate the effect of abiotic stress (e.g., increased soil salinity, water shortages, flooding, etc.) on crops, orchards, and pastures in arid and semiarid agricultural areas.

On the other hand, the use of culture-independent approaches and next-generation omics technologies have opened a new window for the study of plant-associated microbiomes, revealing the wide diversity of microorganisms in plant niches as never before seen. However, the functions and interconnectivity of microbe–microbe and microbe–plant interactions is still considered a black box, where traditionally culture-based approaches are used toward the isolation and characterization of selected beneficial microbes and bioprospecting for their potential biotechnological applications in agriculture and degraded soil recovery under a changing world.

For this Special Issue, we invite microbiologists, biologists, agriculturists, biochemists, and biotechnologists to contribute to a new understanding of microbial diversity, ecological interactions, and bioprospecting of microbiomes associated with plants living in a wide variety of ecosystems, including agricultural systems, pristine or undisturbed environments, extreme environments, etc.

Contributions can be focused on (but are not limited to):

Microbial diversity and coevolution in plant niches (rhizosphere soil, endosphere, phyllosphere, spermosphere, and detritusphere or plant litters);
Role and influence of plant-associated microbiomes on growth, nutrition, and tolerance of plants;
Effect of soil management, fertilization, and/or abiotic stress on microbial diversity and functioning of plant-associated microbiomes;
Plant-associated microbiomes’ response to climate change;
Use of molecular and culture-based approaches in the monitoring and/or tracking of specific microbes in plant-associated microbiomes;
Bioprospecting of novel plant growth-promoting microorganisms (and/or their biomolecules) isolated from plant-associated microbiomes.

Interdisciplinary approaches to investigate microbial-mediated processes in plant niches are welcome, such as next-generation multi-omics, microbial ecology, conservation and management of soils, and microbial bioprospecting for the sustainable development and study of plant–microbe interactions, among others.

Dr. Milko A. Jorquera
Dr. Jacquelinne Acuña
Guest Editors

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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. Diversity 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 2600 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.

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Editorial

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4 pages, 180 KiB

Open AccessEditorial

Diversity, Interaction, and Bioprospecting of Plant-Associated Microbiomes

by Jacquelinne J. Acuña and Milko A. Jorquera

Diversity 2020, 12(10), 390; https://doi.org/10.3390/d12100390 - 13 Oct 2020

Cited by 2 | Viewed by 2044

Abstract

Plant-associated microbiomes have been suggested as pivotal for the growth and health of natural vegetation and agronomic plants. In this sense, plant-associated microbiomes harbor a huge diversity of microorganisms (such as bacteria and fungi) which can modulate the plant host response against pathogens and changing environmental conditions through a complex network of genetic, biochemical, physical, and metabolomics interactions. Advances on next-generation omic technologies have opened the possibility to unravel this complex microbial diversity and their interactive networks as never described before. In parallel, the develop of novel culture-dependent methods are also crucial to the study of the biology of members of plant-associated microbiomes and their bioprospecting as sources of bioactive compounds, or as tools to improve the productivity of agriculture. This Special Issue aims to motivate and collect recent studies which are focused on exploring the diversity and ecology of plant-associated microbiomes and their genetic and metabolic interactions with other microorganisms or their plant hosts, as well as their potential biotechnological applications in diverse fields, such as inoculants for agriculture. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

Research

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16 pages, 3089 KiB

Open AccessArticle

Bioprospecting of Plant Growth-Promoting Traits of Pseudomonas sp. Strain C3 Isolated from the Atacama Desert: Molecular and Culture-Based Analysis

by Alexis Gaete, Constanza Andreani-Gerard, Jonathan E. Maldonado, Patricio A. Muñoz-Torres, Germán F. Sepúlveda-Chavera and Mauricio González

Diversity 2022, 14(5), 388; https://doi.org/10.3390/d14050388 - 13 May 2022

Cited by 4 | Viewed by 2736

Abstract

Soil microorganisms that inhabit extreme environments have unique metabolic capacities and/or physical structures that allow them to survive in oligotrophic conditions. The bioprospecting of unknown bacteria in the context of current advances in genome mining is fundamental for the discovery of natural products with novel properties or applications. In this study, the plant growth-promoting and biocontrol traits of a Pseudomonas isolated from soil associated with plants from the Atacama Desert were characterized by whole-genome sequencing and in vitro assays. A high-quality genome draft of Pseudomonas sp. isolate C3 was obtained. An automated biosynthetic gene cluster analysis using antiSMASH 6.0 revealed the presence of a cluster of genes for the biosynthesis, regulation, and transport of the metabolite 2,4-diacetylphloroglucinol, which showed a high protein sequence identity (>89%) with a validated orthologous gene cluster from another Pseudomonas. In addition, via an in vitro assay, the biocontrol activity of Pseudomonas sp. isolate C3 against Botrytis cinerea, Monilinia fructicola, Phytium sp., Alternaria sp., Geotrichum candidum, and Fusarium oxysporum was corroborated. Finally, through KofamKOALA, the presence of genes involved in different metabolic pathways of plant growth-promoting traits was identified, which was corroborated by in vitro assays. This study provides information obtained from genomic analyses and culture tools on a bacterial isolate from the Atacama Desert characterized by plant growth-promoting capacities and biocontrol activity. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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16 pages, 1994 KiB

Open AccessArticle

Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication

by Jianfeng Zhang, Zongmu Yao, Yalin Chen, Jiafan Zhang, Shouyang Luo, Chunjie Tian and Lei Tian

Diversity 2022, 14(2), 67; https://doi.org/10.3390/d14020067 - 20 Jan 2022

Cited by 4 | Viewed by 2629

Abstract

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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15 pages, 3783 KiB

Open AccessArticle

Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano

by Qian Zhang, Macarena M. Araya, Marcia Astorga-Eló, Gabriela Velasquez, Joaquin I. Rilling, Marco Campos, Michael J. Sadowsky, Milko A. Jorquera and Jacquelinne J. Acuña

Diversity 2022, 14(1), 14; https://doi.org/10.3390/d14010014 - 28 Dec 2021

Cited by 5 | Viewed by 2202

Abstract

Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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15 pages, 1767 KiB

Open AccessArticle

Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

by Geon Seung Lee, Mahesh Adhikari, Jae E. Yang, Hyuck Soo Kim, Kyu Suk Han, Kean-Soo Ha and Duck Hwan Park

Diversity 2021, 13(12), 659; https://doi.org/10.3390/d13120659 - 11 Dec 2021

Cited by 1 | Viewed by 2572

Abstract

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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15 pages, 2933 KiB

Open AccessArticle

Analysis of Ficus hirta Fig Endosymbionts Diversity and Species Composition

by Yifeng Liu, Songle Fan and Hui Yu

Diversity 2021, 13(12), 636; https://doi.org/10.3390/d13120636 - 02 Dec 2021

Cited by 2 | Viewed by 2940

Abstract

Endosymbionts living in plants and insects are pervasive. Ficus (Moraceae) has very special inflorescences (which we also call figs) enclosed like an urn, and such inflorescence is usually parasitized by fig wasps. Ficus breeds fig wasp larvae in its figs and adult fig wasps pollinate for Ficus, Ficus and its obligated pollinator formed fig-fig wasp mutualism. Previous studies have found that this confined environment in figs may have provided protection for fig wasps and that this has left some imprints on the genome of fig wasps during the coevolution history of figs and fig wasps. Research on the diversity of both bacteria and fungi in figs are fewer. Our study explored the diversity of endosymbionts in Ficus hirta figs. We utilized high-throughput sequencing and biological database to identify the specific microorganism in figs, then conducted microorganism communities’ diversity analysis and function annotation analysis. As a result, we identified the dominant endosymbionts in figs, mainly some insect internal parasitic bacteria and fungi, plant pathogen, endophytes, and saprotroph. Then we also found bacteria in Ficus hirta figs were more diversified than fungi, and bacteria communities in female figs and functional male figs were different. These findings may give us more insight into the coevolution and interaction among endosymbiont, fig, and fig wasp. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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17 pages, 1652 KiB

Open AccessArticle

Bacterial Communities Associated with the Cycling of Non-Starch Polysaccharides and Phytate in Aquaponics Systems

by Daniel Menezes-Blackburn, Nahad Al-Mahrouqi, Buthaina Al-Siyabi, Adhari Al-Kalbani, Ralf Greiner and Sergey Dobretsov

Diversity 2021, 13(12), 631; https://doi.org/10.3390/d13120631 - 30 Nov 2021

Cited by 3 | Viewed by 2380

Abstract

Aquaponics are efficient systems that associate aquatic organisms’ production and plants by recirculating water and nutrients between aquaculture and hydroponic tanks. In this study, we characterised the bacterial communities in the freshwater aquaponics system that can mineralise polysaccharides and phytate by producing carbohydrate-degrading enzymes and phytases, by 16S rRNA gene sequencing and in vitro culture techniques. Around 20% of the operational taxonomic units (zOTUs) identified were previously reported to carry fibre-degrading enzyme putative genes, namely β-glucanase (1%), xylanase (5%), or cellulases (17%). Ten % of the zOTUs were previously reported to carry putative genes of phytases with different catalytic mechanisms, namely β-propeller (6%), histidine acid phytases (3%), and protein tyrosine phytase (<1%). Thirty-eight morphologically different bacteria were isolated from biofilms accumulated in fish and plant compartments, and identified to belong to the Bacilli class. Among these, 7 could produce xylanase, 8 produced β-glucanase, 14 produced cellulase, and 11 isolates could secrete amylases. In addition, Staphylococcus sp. and Rossellomorea sp. could produce consistent extracellular phytate-degrading activity. The PCR amplification of β-propeller genes both in environmental samples and in the isolates obtained showed that this is the most ecologically relevant phytase type in the aquaponics systems used. In summary, the aquaponics system is abundant with bacteria carrying enzymes responsible for plant-nutrient mineralisation. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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19 pages, 3564 KiB

Open AccessArticle

Diversity of Endophytic and Pathogenic Fungi of Saffron (Crocus sativus) Plants from Cultivation Sites in Italy

by Beatrice Belfiori, Andrea Rubini and Claudia Riccioni

Diversity 2021, 13(11), 535; https://doi.org/10.3390/d13110535 - 26 Oct 2021

Cited by 8 | Viewed by 2594

Abstract

Crocus sativus is an important crop for the production of saffron and bioactive compounds. Plant endophytic fungi are a source of secondary metabolites additional to those produced by the plant itself. We analysed the biodiversity of endophytic fungi present in corms, stems, leaves, tepals, and stigmas of C. sativus from ten Italian sites; furthermore, we isolated putative pathogenic fungi from rotten plants. We used an in vitro isolation approach followed by molecular analysis of the internal transcribed spacer (ITS rDNA) region. We obtained 165 strains belonging to 39 OTUs, spreading over 26 genera and 29 species. Dark septate endophytes of the genus Cadophora and the species Talaromyces pinophilus dominated in corms, while Alternaria alternata, Epicoccum spp., T. pinophilus, Mucor fragilis, and Stemphylium vesicarium dominated in other tissues. The most frequently isolated pathogens were Fusarium oxysporum and Rhizopus oryzae. Endophytic communities significantly differed among tissues and life stages, whereas differences among cultivation sites were not statistically supported. Several endophytes were hypothesized to have changing trophic modes and/or to be latent pathogens in C. sativus. All strains were conserved ex-situ for future bioactivity tests and production of metabolites. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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15 pages, 4053 KiB

Open AccessArticle

Streptomyces Application Triggers Reassembly and Optimization of the Rhizosphere Microbiome of Cucumber

by Yanjiang Zhang, Tian Zhang, Zhijing Xue, Yifan Liu, Yongzhe Li, Yulong Li and Qin Chen

Diversity 2021, 13(9), 413; https://doi.org/10.3390/d13090413 - 29 Aug 2021

Cited by 2 | Viewed by 2471

Abstract

Streptomyces partum Act12 and Streptomyces roche D74 are biocontrol strains that can promote plant growth and enhance stress resistance in different crops. However, their effects on the rhizosphere microbiome and the role of the reassembled microbiome in plant growth promotion and stress resistance enhancement remain unclear. This study investigated the variation in the rhizosphere microbiome induced by Streptomyces application through a cucumber (Cucumis sativus L. cv. “Youliang”) pot experiment. The bacterial and fungal communities of rhizosphere soils inoculated with and without Streptomyces were, respectively, compared based on 16S rRNA and internal transcribed spacer rRNA gene sequences. Following Streptomyces application, the bacterial alpha diversity increased significantly, while the fungal alpha diversity exhibited the opposite trend. The bacterial and fungal communities’ compositions clearly shifted in the inoculated soil. Compared with the uninoculated control, the relative abundance of the genus Streptomyces increased by 68.3%, and the bacterial co-occurrence network in the rhizosphere soil was enriched significantly. The relative abundance of bacteria associated with nitrogen fixation was increased by 7.5% following Streptomyces application. Based on the results of this study, we conclude that the application of Streptomyces Act12 and D74 can be used to reassemble and optimize the rhizosphere microbiome of cucumber, which is conducive to plant survival. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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15 pages, 2453 KiB

Open AccessArticle

Effects of Continuous Cropping of Codonopsis tangshen on Rhizospheric Soil Bacterial Community as Determined by Pyrosequencing

by Meide Zhang, Yinsheng He, Wuxian Zhou, Lunqiang Ai, Haihua Liu, Liang Chen and Yan Xie

Diversity 2021, 13(7), 317; https://doi.org/10.3390/d13070317 - 12 Jul 2021

Cited by 7 | Viewed by 2017

Abstract

Codonopsis tangshen, a perennial herbaceous, has been shown to be affected by continuous cropping, with significant decline in both yield and quality. In this study, we studied the effect of continuous cropping on the abundance and composition of rhizospheric soil bacterial community. Results showed that continuous cropping causes a significant decline in both yield and quality. The nutrient content in continuous cropping soil was higher than that of soil in main cropping. Pyrosequencing analyses revealed Proteobacteria and Acidobacteria as the main phyla in two types of soils. Relative abundance of Acidobacteria, Nitrospirae, TM7, and AD3 phyla was observed to be high in continuous cropping soils, whereas Chloroflexi, Bacteroidetes, and Planctomycetes phyla were richer in main cropping soils. At the genus level, high relative abundance of Pseudomonas (γ-Proteobacteria), Rhodanobacter, Candidatus Koribacter, and Candidatus were observed in continuous cropping soil. Different patterns of bacterial community structure were observed between different soils. Redundancy analysis indicated that organic matter content and available nitrogen content exhibited the strongest effect on bacterial community structure in the continuous cropping soil. Taken together, continuous cropping led to a significant decline in yield and quality, decrease in rhizospheric soil bacterial abundance, and alteration of rhizospheric soil microbial community structure, thereby resulting in poor growth of C. tangshen in the continuous cropping system. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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19 pages, 1487 KiB

Open AccessArticle

Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass

by Cristina P. Fernández-Baca, Adam R. Rivers, Jude E. Maul, Woojae Kim, Ravin Poudel, Anna M. McClung, Daniel P. Roberts, Vangimalla R. Reddy and Jinyoung Y. Barnaby

Diversity 2021, 13(3), 125; https://doi.org/10.3390/d13030125 - 15 Mar 2021

Cited by 3 | Viewed by 3227

Abstract

Plant–soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizosphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Two plant developmental stages were studied, heading and physiological maturity, based on root and shoot biomass growth patterns across the selected genotypes. We used partial least squares (PLS) regression analysis to examine plant trait-driven microbial populations and identify microbial species, functions, and genes corresponding to root and shoot biomass as well as developmental stage patterns. Species identified correlated with increases in either root or shoot biomass were widely present in soil and included species involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocellaavoryzae), as well as known endophytes (Bradyrhizobium spp.). Additionally, PLS analysis allowed us to explore the relationship of developmental stage with species, microbial functions, and genes. Many of the community functions and genes observed during the heading stage were representative of cell growth (e.g., carbohydrate and nitrogen metabolism), while functions correlated with physiological maturity were indicative of cell decay. These results are consistent with the hypothesis that microbial communities exist whose metabolic and gene functions correspond to plant biomass traits. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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12 pages, 2431 KiB

Open AccessArticle

Insights into the Fungal Community and Functional Roles of Pepper Rhizosphere Soil under Plastic Shed Cultivation

by Shi Yao, Xiaona Li, Hu Cheng, Kaining Sun, Xin Jiang and Yang Song

Diversity 2020, 12(11), 432; https://doi.org/10.3390/d12110432 - 17 Nov 2020

Cited by 3 | Viewed by 2614

Abstract

The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between the rhizosphere and non-rhizosphere soils. The greatest abundance variation was observed for the rare fungal members with relative abundances <0.1%. In the rhizosphere soil of pepper, the abundance of the genera Purpureocillium, Metacorgyceps, Arthrobotrys, Cephalotheca, and Scedosporium increased significantly, among which, Purpureocillium, Arthrobotrys and Metacorgyceps exhibited biocontrol characteristics. Co-occurrence network analysis revealed different interactions of fungal communities in the rhizosphere and non-rhizosphere soils, both of which were dominated by low abundance members. More positive correlation was identified among the rare members, the fungal pathotroph functions and phthalate acid ester in the rhizosphere soil. This study highlights the important niche of the rare fungal members in soil microbial ecology under plastic shed cultivation. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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19 pages, 2767 KiB

Open AccessArticle

Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota

by Hend Elsawey, Sascha Patz, Rahma A. Nemr, Mohamed S. Sarhan, Mervat A. Hamza, Hanan H. Youssef, Mohamed R. Abdelfadeel, Hassan-Sibroe A. Daanaa, Mahmoud El-Tahan, Mohamed Abbas, Mohamed Fayez, Katja Witzel, Silke Ruppel and Nabil A. Hegazi

Diversity 2020, 12(11), 418; https://doi.org/10.3390/d12110418 - 04 Nov 2020

Cited by 7 | Viewed by 8542

Abstract

Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation of hub taxa. Despite recent advances in high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably the human microbiome. As a plant-based culturing strategy, we developed culture media based on a broth of cooked aqueous mixtures of host plants. This improved the in vitro growth of representative isolates of plant microbiota and extended the in situ recovery of plant microbiota. With clover, 16S rRNA gene sequencing of representative isolates confirmed the predominance of Firmicutes, Alphaproteobacteria and Gammaproteobacteria, and less frequently Bacteroidetes and Actinobacteria. Whereas bovine-based culture media (modified R2A) confined the diversity to Firmicutes, the plant broth-based culture media revealed a wider scope of endophytes beyond rhizobia, i.e., multiple genera such as Chryseobacterium, Cronobacter, Kosakonia, Tsukamurella, and a potentially/presumptive novel species. Matrix-assisted laser desorption/ionization time-of-flight (MADI-TOF) analysis clustered isolates according to their plant niches, the endo-phyllosphere/endo-rhizosphere. We recommend the plant broth for simplicity, reproducibility and perdurable storage, supporting future culturomics applications, good laboratory practice (GLP) and good manufacturing practice (GMP). The strategy creates an “in-situ-similis” vegan nutritional matrix to analyze microbial diversity and reveal novel microbial resources pertinent to biotechnological and environmental applications. Full article

(This article belongs to the Special Issue Diversity, Interaction and Bioprospecting of Plant-Associated Microbiomes)

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