Plant-Associated Microbiota: From the Assembly to the Function

Topic Information

Dear Colleagues,

Like all the other living organisms, plants also possess their own microbiota. The plant-associated microbial communities are diverse depending on the plant type/genotype, the considered district (phyllosphere, carposphere, rhizosphere…), and are also influenced by the plant developmental stage. In addition, the whole plant-microbiota holobiont is exposed to a plethora of environmental factors, both of natural and anthropic origin. Scientific advances in this study field have started to demonstrate that plants can actively shape their associated microbial communities, and the other way around. Plants can in fact influence the presence and the activity of rhizosphere-inhabiting microorganisms under specific environmental conditions. In turn, some microbiota members display important plant-growth promoting traits, influencing plant physiological functions and eventually improving plant nutrition, yield and performance. Given the importance of plant–microbe interactions for plant growth and protection against stresses, there is a need for a deeper knowledge of the mechanisms underlying these associations. This is crucial from an ecological and agronomical point of view, since it will lead towards a better exploitation of the plant microbiota to increase plants/crops performance and to improve their resilience under the current global climate change scenario. Within this Topic we aim to collect contributions that analyse plant-microbiota associations under functional aspects of agronomical and/or ecological relevance. We encourage the submission of research papers and reviews dealing with all the aspects related with plant-microbe interactions, from those aimed at elucidating the mechanisms of functioning and/or the resulting beneficial effect, to those focused on formulation/application of microbial biostimulants to crop plants.

Dr. Alessandra Salvioli Di Fossalunga
Dr. Vincenza Cozzolino
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agronomy agronomy	3.7	5.2	2011	17.3 Days	CHF 2600	Submit
Diversity diversity	2.4	3.1	2009	18.4 Days	CHF 2600	Submit
Ecologies ecologies	-	-	2020	20.6 Days	CHF 1000	Submit
Microorganisms microorganisms	4.5	6.4	2013	14.5 Days	CHF 2700	Submit
Plants plants	4.5	5.4	2012	15.3 Days	CHF 2700	Submit

Published Papers (5 papers)

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All Agronomy Diversity Ecologies Microorganisms Plants

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Open AccessArticle

Comparative Analysis of Rhizospheric Fungi Using High-Throughput Sequencing between Wild, Ex Situ, and Reintroduced Pinus squamata, a Plant Species with Extremely Small Populations in Yunnan Province, China

by

Fengrong Li

and

Weibang Sun

Diversity 2023, 15(7), 868; https://doi.org/10.3390/d15070868 - 18 Jul 2023

Viewed by 434

Abstract

Pinus squamata is a rare and endangered tree endemic to northeastern Yunnan Province, China, and it is listed as a Plant Species with Extremely Small Populations (PSESP) in China for requiring urgent conservation. Furthermore, the actions of ex situ conservation and reintroduction based [...] Read more.

Pinus squamata is a rare and endangered tree endemic to northeastern Yunnan Province, China, and it is listed as a Plant Species with Extremely Small Populations (PSESP) in China for requiring urgent conservation. Furthermore, the actions of ex situ conservation and reintroduction based on artificial propagation have been carried out since some 15 years ago. The rhizosphere microbiome plays an important role in soil quality and plant health. However, how the fungal communities of the rhizosphere differ between wild, ex situ, and reintroduced examples of Pinus squamata remains unclear. Illumina sequencing of the internal transcribed spacer 2 (ITS2) region was used to investigate fungal communities in the P. squamata rhizosphere soil. Rhizospheric fungal community composition, structure, diversity, and ecological function in the soil surrounding wild, ex situ, and reintroduced P. squamata individuals were elucidated. The ex situ site Kunming (EK) had the highest fungal community richness and diversity. The samples collected from six different sites were well separated (R = 0.95, p = 0.001), suggesting significant differences between the sites. Soil total potassium (TK), available phosphorus (AP), and pH were the main factors driving fungal community (0.01 < p ≤ 0.05). Prediction of fungal functional guild in the P. squamata rhizosphere demonstrated that the fungi could be classified as ectomycorrhizal, endophyte, and plant pathogenic fungi. Our research will provide a basis to guide the further selection of conservation sites for P. squamata based on fungal diversity and offer guidance on the antagonistic fungi and plant pathogenic fungi that may be of relevance to the conservation of this rare plant. Full article

(This article belongs to the Topic Plant-Associated Microbiota: From the Assembly to the Function)

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Open AccessArticle

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

by

Dario X. Ramirez-Villacis

,

Andrea Pinos-Leon

,

Pamela Vega-Polo

,

Isai Salas-González

,

Corbin D. Jones

and

Maria de Lourdes Torres

Microorganisms 2023, 11(2), 399; https://doi.org/10.3390/microorganisms11020399 - 04 Feb 2023

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Abstract

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, [...] Read more.

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant–microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes. Full article

(This article belongs to the Topic Plant-Associated Microbiota: From the Assembly to the Function)

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Open AccessArticle

A Nitrate-Transforming Bacterial Community Dominates in the Miscanthus Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima

by

Ahmad Arsyadi

,

Yong Guo

,

Akiko Ebihara

,

Nobuo Sakagami

,

Midori Sakoda

,

Kanako Tago

,

Takashi Kamijo

,

Hiroyuki Ohta

and

Tomoyasu Nishizawa

Microorganisms 2023, 11(2), 260; https://doi.org/10.3390/microorganisms11020260 - 19 Jan 2023

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Abstract

The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable [...] Read more.

The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the M. condensatus rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses. Our results showed a large number of functional genes related to denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in the rhizosphere, indicating that nitrate-transforming bacteria dominated the rhizosphere biome. Furthermore, nitrite reductase genes (i.e., nirK and nirS) related to the denitrification and those genes related to DNRA (i.e., nirB and nrfA) were mainly annotated to the classes Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. A total of 304 nitrate-succinate-stimulated isolates were obtained from the M. condensatus rhizosphere and were classified into 34 operational taxonomic units according to amplified 16S rRNA gene restriction fragment pattern analysis. Additionally, two strains belonging to the genus Cupriavidus in the class Beta-proteobacteria showed a high in vitro denitrifying activity; however, metagenomic results indicated that the DNRA-related rhizobacteria appeared to take a major role in the nitrogen cycle of the M. condensatus rhizosphere in recent Miyake-jima volcanic deposits. This study elucidates the association between the Miscanthus rhizosphere and the nitrate-reducing bacterial community on newly placed volcanic deposits, which furthers our understanding of the transformation of nitrogen nutrition involved in the early development of vegetation. Full article

(This article belongs to the Topic Plant-Associated Microbiota: From the Assembly to the Function)

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Open AccessArticle

Isolation, Identification and Pollution Prevention of Bacteria and Fungi during the Tissue Culture of Dwarf Hygro (Hygrophila polysperma) Explants

by

Weijie Li

,

Guanglong Cao

,

Mengqian Zhu

,

Yilin Zhang

,

Rong Zhou

,

Zhenyang Zhao

,

Yaning Guo

,

Wanli Yang

,

Bo Zheng

,

Jiabo Tan

and

Yanling Sun

Microorganisms 2022, 10(12), 2476; https://doi.org/10.3390/microorganisms10122476 - 15 Dec 2022

Viewed by 1073

Abstract

Microbial contamination causes serious damage in plant tissue culture, and attention is always being paid regarding how to control and prevent the unwanted pollution. Dwarf hygro (Hygrophila polysperma) is a popular ornamental aquatic plant and its tissue culture has been reported, [...] Read more.

Microbial contamination causes serious damage in plant tissue culture, and attention is always being paid regarding how to control and prevent the unwanted pollution. Dwarf hygro (Hygrophila polysperma) is a popular ornamental aquatic plant and its tissue culture has been reported, but the microbial pollution and the cure of microbial pollution was unknown. In this study, a number of bacteria and fungi were isolated from contaminants in MS culture media. Based on the 16S rDNA and ITS sequencing, it was identified that fifteen bacteria belong to Bacillus, Enterobacter, Pantoea, Kosakonia, Ensifer and Klebsiella, and three fungi belong to Plectosphaerella, Cladosporium and Peniophora, respectively. In addition, some drugs were further tested to be free of the bacteria and fungi pollution. The results revealed that 10 μg/mL of kanamycin, 5 μg/mL of chloramphenicol, and 0.015625% potassium sorbate could be applied jointly in MS media to prevent the microbial pollution, and the survival rate of H. polysperma explants was highly improved. This study reveals the bacteria and fungi species from the culture pollution of H. polysperma and provides a practical reference for optimizing the tissue culture media for other aquatic plants. Full article

(This article belongs to the Topic Plant-Associated Microbiota: From the Assembly to the Function)

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Open AccessReview

The Suppressive Effects of Biochar on Above- and Belowground Plant Pathogens and Pests: A Review

by

Giuseppina Iacomino

,

Mohamed Idbella

,

Stefania Laudonia

,

Francesco Vinale

and

Giuliano Bonanomi

Plants 2022, 11(22), 3144; https://doi.org/10.3390/plants11223144 - 17 Nov 2022

Cited by 3 | Viewed by 1759

Abstract

Soilborne pathogens and pests in agroecosystems are serious problems that limit crop yields. In line with the development of more ecologically sustainable agriculture, the possibility of using biochar to control pests has been increasingly investigated in recent years. This work provides a general [...] Read more.

Soilborne pathogens and pests in agroecosystems are serious problems that limit crop yields. In line with the development of more ecologically sustainable agriculture, the possibility of using biochar to control pests has been increasingly investigated in recent years. This work provides a general overview of disease and pest suppression using biochar. We present an updated view of the literature from 2015 to 2022 based on 61 articles, including 117 experimental case studies. We evaluated how different biochar production feedstocks, pyrolysis temperatures, application rates, and the pathosystems studied affected disease and pest incidence. Fungal pathogens accounted for 55% of the case studies, followed by bacteria (15%), insects and nematodes (8%), oomycetes and viruses (6%), and only 2% parasitic plants. The most commonly studied belowground pathogen species were Fusarium oxysporum f. sp. radicis lycopersici in fungi, Ralstonia solanacearum in bacteria, and Phytophthora capisci in oomycetes, while the most commonly studied pest species were Meloidogyne incognita in nematodes, Epitrix fuscula in insects, and both Phelipanche aegyptiaca and Orobanche crenata in parasitic plants. Biochar showed suppression efficiencies of 86% for fungi, 100% for oomycetes, 100% for viruses, 96% for bacteria, and 50% for nematodes. Biochar was able to potentially control 20 fungal, 8 bacterial, and 2 viral plant pathogens covered by our review. Most studies used an application rate between 1% and 3%, a pyrolysis temperature between 500 °C and 600 °C, and a feedstock based on sawdust and wood waste. Several mechanisms have been proposed to explain disease suppression by biochar, including induction of systemic resistance, enhancement of rhizosphere competence of the microbial community, and sorption of phytotoxic compounds of plant and/or microbial origin. Overall, it is important to standardize biochar feedstock and the rate of application to improve the beneficial effects on plants in terms of disease control. Full article

(This article belongs to the Topic Plant-Associated Microbiota: From the Assembly to the Function)

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