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 4060

Special Issue Editor


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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

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Keywords

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

Published Papers (4 papers)

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Research

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
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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
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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
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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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