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Diversity
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Microbiota Diversity in Plants and Forest
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Microbiota Diversity in Plants and Forest

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 4645

Special Issue Editor

Dr. Yaara Oppenheimer-Shaanan

E-Mail Website
Guest Editor
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
Interests: soil microbial communities; fungi; bacteria; plant microbiota; plant health

Special Issue Information

Dear Colleagues,

Research on the forest underworld is significantly changing our fundamental understanding of the ecological systems of plants. The ecology system is a complex of competing and symbiotic interactions between microbiota and plants. Large networks of symbiotic fungi, bacteria, trees, and plants supply each other with the necessary resources to thrive.

To better understand the symbiotic biological processes below the ground, we would like to highlight the exchange of water, carbon, and nutrients in forests and the associated fungal and bacterial species. We aim to significantly expand our understanding of the microbiota networks in the soil, the rate at which they transfer matter between them and trees, and the chemical compounds used by tree roots to communicate with the soil microbiota. Omics data of molecular identification, metabolomic analysis, stable isotope labeling, and microbiome analysis will help us to understand the diversity in these ecology environments.

In addition, we must improve our knowledge of the root zone symbiotic processes to uncover the interactions between above- and below-ground organisms.

New insights from this Special Issue will provide scientists with a complete picture of forest systems and their role in the environment.

Dr. Yaara Oppenheimer-Shaanan
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. 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.

Keywords

  • forest microbiome
  • plant microbiome
  • habitat
  • ecosystem dynamics
  • decomposition
  • microbial plant interactions
  • microbiome diversity

Published Papers (5 papers)

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Research

18 pages, 4898 KiB  
Article
Abundant Species Govern the Altitude Patterns of Bacterial Community in Natural and Disturbed Subalpine Forest Soils
by Chaonan Li, Haijun Liao, Dehui Li and Yanli Jing
Diversity 2024, 16(4), 242; https://doi.org/10.3390/d16040242 - 18 Apr 2024
Viewed by 357
Abstract
Abundant and rare bacteria exhibit unequal responses to environmental changes and disturbances, potentially resulting in differential contributions to the altitudinal characteristics of total community in natural and disturbed soils. Although the altitude patterns of soil bacteria have been widely studied, it remains unclear [...] Read more.
Abundant and rare bacteria exhibit unequal responses to environmental changes and disturbances, potentially resulting in differential contributions to the altitudinal characteristics of total community in natural and disturbed soils. Although the altitude patterns of soil bacteria have been widely studied, it remains unclear whether these patterns are consistent among bacteria with varying predominance levels, and which subpopulation contributes more to maintaining these patterns in natural and disturbed subalpine forest soils. In this study, we collected 18 natural subalpine forest soil samples and 18 disturbed ones from three altitudes (2900 m a.s.l., 3102 m a.s.l., and 3194 m a.s.l.) along the Wenma highway in Miyaluo, Lixian, Sichuan, Southwest China. By partitioning total bacterial communities based on species predominance, we found that bacteria with higher predominance levels tended to exhibit altitude patterns (α-diversity, community structure, and functional redundancy) similar to those of total bacteria in both natural and disturbed subalpine forest soils, although they only occupied a small portion of the community. Abundant bacteria might play critical roles in maintaining the regional ecological characteristics of total community across the altitude gradient, while the rare and hyper-rare ones might contribute more to local diversity and functional redundancy. In natural soils, the altitude patterns of α-diversity inferred from total, abundant, and rare bacteria were mainly shaped by NO3−-N, while soil conductivity mainly drove the altitude patterns of α-diversity inferred from hyper-rare bacteria. Additionally, the community structures of total, abundant, rare, and hyper-rare bacteria were mainly shaped by NO3−-N, while the altitude patterns of functional redundancy inferred from total, abundant, and rare bacteria were mainly shaped by soil conductivity in natural soils. In disturbed subalpine forest soils, the influences of NO3−-N for the altitude patterns of α-diversity and community structure, and those of soil conductivity for functional redundancy, were relatively weak in total, abundant, rare, and hyper-rare bacteria. This study examined the roles of bacteria with varying predominance levels in maintaining the altitude pattern of bacteria in both natural and disturbed subalpine forest soils, providing novel insights for devising strategies to conserve biodiversity and ecologically restore disturbed soils in subalpine ecosystems. Full article
(This article belongs to the Special Issue Microbiota Diversity in Plants and Forest)
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16 pages, 4923 KiB  
Article
Two New and One First Recorded Species of Xylaria Isolated from Fallen Leaves in Hainan Tropical Rainforest National Park in China
by Xiaoyan Pan, Zongzhu Chen, Jinrui Lei, Xiaohua Chen, Tingtian Wu, Yuanling Li and Yiqing Chen
Diversity 2024, 16(3), 179; https://doi.org/10.3390/d16030179 - 14 Mar 2024
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Abstract
Xylaria is a widely distributed genus in the Ascomycota phylum that can decompose wood. It is an essential decomposer in ecosystems and a source of bioactive secondary metabolites. Based on morphological characteristics and molecular evidence, this article thoroughly describes two new species discovered [...] Read more.
Xylaria is a widely distributed genus in the Ascomycota phylum that can decompose wood. It is an essential decomposer in ecosystems and a source of bioactive secondary metabolites. Based on morphological characteristics and molecular evidence, this article thoroughly describes two new species discovered on the fallen leaves in Hainan Tropical Rainforest National Park, along with illustrations and comparisons with similar species. Xylaria diaoluoshanensis is characterized by filamentous stromata with long infertile apexes, ascospores sometimes with non-cellular appendages. Xylaria fulvotomentosa differentiates itself from other Xylaria species that grow on fallen leaves by its stroma surface, being yellow tomentose. These two new species of the genus Xylaria were found by phylogenetic analysis using the ITS-β-tubulin-RPB2 sequence dataset. Furthermore, a species first discovered in China, X. petchii, is described. Finally, a search table for 44 species related to fallen leaves and petioles in the world is established. Full article
(This article belongs to the Special Issue Microbiota Diversity in Plants and Forest)
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14 pages, 21383 KiB  
Article
Comparative Analysis of Bacteria, Fungi, and Arbuscular Mycorrhizal Fungi in Medicinal Plants Lippia alba and Petiveria alliacea in Colombia
by Glever Alexander Vélez-Martínez, Juan Diego Duque-Zapata, Wendy Lorena Reyes-Ardila, Jaime Eduardo Muñoz Flórez, Sergio Alberto Díaz Gallo, Lucia Ana Díaz Ariza and Diana López-Álvarez
Diversity 2023, 15(12), 1167; https://doi.org/10.3390/d15121167 - 23 Nov 2023
Viewed by 1000
Abstract
Medicinal plants maintain structures and diversities of bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) that can interact to promote growth and therapeutic properties. Therefore, the purpose of this research was to evaluate the microbiome of Lippia alba and Petiveria alliacea, species known [...] Read more.
Medicinal plants maintain structures and diversities of bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) that can interact to promote growth and therapeutic properties. Therefore, the purpose of this research was to evaluate the microbiome of Lippia alba and Petiveria alliacea, species known for their high potential for medicinal benefits in Colombia. To achieve this, rhizosphere soils and roots were sampled from five departments in Colombia: Boyacá, Cundinamarca, Tolima, Putumayo, and Valle del Cauca. The results revealed that the dominant bacterial groups in both plants were primarily Proteobacteria, Acidobacteriota, and Actinobacteriota, with the first phylum showing the highest number of differentially abundant genera between the sampling points. In fungi, Ascomycota tended to dominate in most of the sampled locations, while Mortierellomycota was particularly abundant in roots of P. alliacea in Valle. Furthermore, the study of AMF indicated differentiation in the colonization for both plants, with the genera Glomus and Paraglomus being predominant. Differences in the Shannon diversity index were recorded between sampling types within these sampling points, possibly influenced by local and environmental factors. Our findings reveal that the microbiomes of both medicinal plants exhibit distinct community assemblies, which could be a significant factor for their future therapeutic use. Full article
(This article belongs to the Special Issue Microbiota Diversity in Plants and Forest)
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11 pages, 3104 KiB  
Article
Characterization of the Root Nodule Microbiome of the Exotic Tree Falcataria falcata (Fabaceae) in Guangdong, Southern China
by Siyu Xiang, Shu Yan, Qianxi Lin, Rong Huang, Runhui Wang, Ruping Wei, Guandi Wu and Huiquan Zheng
Diversity 2023, 15(10), 1092; https://doi.org/10.3390/d15101092 - 18 Oct 2023
Viewed by 988
Abstract
Falcataria falcata is an exotic tree species that was imported to southern China around 1940 and has been widely planted in the Guangdong province of China. Using the 16S rRNA amplicon sequencing approach, we investigated the composition of the bacterial endophytes in the [...] Read more.
Falcataria falcata is an exotic tree species that was imported to southern China around 1940 and has been widely planted in the Guangdong province of China. Using the 16S rRNA amplicon sequencing approach, we investigated the composition of the bacterial endophytes in the root nodules of naturally grown F. falcata and elucidated the core bacterial endophyte group. Across all samples, there were 575 bacterial genera and 29 bacterial phyla. Proteobacteria accounted for 42–90% relative abundance in all regions. Notably, Bradyrhizobium, Paucibacter, Rhizobium, and Mesorhizobium were consistently detected in all regions studied. Among these, Bradyrhizobium (13–37%) and Paucibacter (1–34%) were the dominant genera. Despite the differences in endophytic amplicon sequence variants (ASVs) across all regions, our results demonstrate that some ASVs, which have been termed herein as commonly shared core ASVs (c-ASVs), still inhabit F. falcata root nodules across multiple regions simultaneously. More importantly, some c-ASVs dominated in F. falcata root nodules across multiple regions. This study demonstrated the consistency of the bacterial endophyte communities of F. falcata root nodules. Full article
(This article belongs to the Special Issue Microbiota Diversity in Plants and Forest)
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14 pages, 4139 KiB  
Article
Study on the Soil Microbial Diversity of Cymbidium goeringii and Cymbidium faberi in the Qinling Mountains after Introduction and Domestication
by Ruixue Lv, Jing Zhang, Huimin Liao, Jean W. H. Yong and Junyang Song
Diversity 2023, 15(9), 951; https://doi.org/10.3390/d15090951 - 23 Aug 2023
Viewed by 874
Abstract
Rhizosphere microbial communities have abundant species and a large number, and affect the physiology and growth of plants. When studying rhizosphere microbes, the rhizosphere ecosystem function and protection of wild orchids will be facilitated. By using high-throughput sequencing technology, the rhizosphere and non-rhizosphere [...] Read more.
Rhizosphere microbial communities have abundant species and a large number, and affect the physiology and growth of plants. When studying rhizosphere microbes, the rhizosphere ecosystem function and protection of wild orchids will be facilitated. By using high-throughput sequencing technology, the rhizosphere and non-rhizosphere bacteria and fungi of wild Cymbidium goeringii and Cymbidium faberi in the Qinling Mountains were analyzed at phylum, class, order, family, and genus levels to explore the rhizosphere bacterial and fungal community structure and diversity of orchid plants (C. goeringii and C. faberi) under natural conditions. The results showed that at the phylum level Proteobacteria was dominant in rhizosphere and non-rhizosphere soil of C. goeringii and C. faberi, but the proportion was different. The abundance of Proteobacteria in rhizosphere soil of C. faberi was the highest (35.5%), which was about 1.3 times of that in non-rhizosphere soil. Bacteroidetes accounted for 17.2% in rhizosphere soil of C. goeringii, much higher than that of non-rhizosphere soil (7.92%). The dominant groups of fungi in rhizosphere soil of C. goeringii and C. faberi were both Ascomycota. At the genus level, PCoA analysis showed that the community structure of bacteria and fungi in different samples was not only common but also specific, which was manifested in the similar dominant species but different subdominant species. This difference is reflected in the composition and relative abundance of microbial communities between different samples, and will gradually become obvious with the refinement of genera. Full article
(This article belongs to the Special Issue Microbiota Diversity in Plants and Forest)
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