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	15.8 Days	CHF 2600
Diversity diversity	2.4	3.1	2009	17.8 Days	CHF 2600
Ecologies ecologies	-	-	2020	19.8 Days	CHF 1000
Microorganisms microorganisms	4.5	6.4	2013	15.1 Days	CHF 2700
Plants plants	4.5	5.4	2012	15.3 Days	CHF 2700

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Published Papers (7 papers)

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All Agronomy Diversity Ecologies Microorganisms Plants

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Open AccessArticle

Stochastic Processes Shape Bacterial Community Diversity Patterns along Plant Niche Gradients

by Zhiyuan Yang, Jiayi Xu, Junlin Li, Lirong He, Hongwei Xu, Xinrong Guo, Sha Xue and Yang Cao

Agronomy 2024, 14(1), 204; https://doi.org/10.3390/agronomy14010204 - 17 Jan 2024

Viewed by 700

Abstract

The ecological niche gradient is an important determinant of microbial community structure. In this paper, we studied variation in rhizosphere bacterial diversity and community composition along an ecological niche gradient. We used the high-throughput sequencing of 16S rRNA genes to study changes in [...] Read more.

The ecological niche gradient is an important determinant of microbial community structure. In this paper, we studied variation in rhizosphere bacterial diversity and community composition along an ecological niche gradient. We used the high-throughput sequencing of 16S rRNA genes to study changes in the rhizosphere soil microbial communities of six grass and four shrub species during the secondary succession of abandoned farmland on the Loess Plateau of China. A structural equation model (SEM) was employed to disentangle the relative contribution of ecological niche and soil properties to bacterial diversity and community composition. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of rhizosphere bacteria in all samples. During the dynamics of the plant niche from low to high, bacterial community composition transitioned from Actinobacteria + Acidobacteria to Proteobacteria + Bacteroidetes higher abundance. Moreover, the bacterial diversity and species richness changed with an increasing niche gradient, showing a clear differentiation in the rhizosphere bacterial community of grassland and shrubland. Further, diversity and species richness decreased from the middle niche of B. ischaemum to the poles, indicating that the succession process had not yet reached the climax community stage. Community assembly analysis suggested that the stochastic process gradually strengthened along the increasing ecological niche gradient, especially the drift effect. Furthermore, SEM analysis showed that the ecological niche had significant negative effects on soil properties and bacterial richness, while the effects on bacterial diversity and the stochastic processes of community assembly were weakened and insignificant. Altogether, our findings suggest that the complex interaction of the ecological niche with bacterial diversity and composition was determined by soil properties. Further, bacterial diversity was not necessarily higher with increasing ecological niche gradients. Full article

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

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14 pages, 946 KiB  

Open AccessArticle

Bacterial Products and Their Effect on the Shrubby Legume Calicotome villosa (Poir.) Link

by María A. Pérez-Fernández, Irene Ariadna De-Lara-Del-Rey and Anathi Magadlela

Diversity 2023, 15(10), 1101; https://doi.org/10.3390/d15101101 - 23 Oct 2023

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Abstract

Calicotome villosa is a eurioic legume with broad distribution in the south of Europe. It can grow in almost any type of soil as well as in humid and dry and nutrient-deficient ecosystems. The broad distribution and eurioic nature of C. villosa may [...] Read more.

Calicotome villosa is a eurioic legume with broad distribution in the south of Europe. It can grow in almost any type of soil as well as in humid and dry and nutrient-deficient ecosystems. The broad distribution and eurioic nature of C. villosa may be attributed to its ability to establish endophytic associations with plant-growth-promoting (PGP) bacteria housed in the nodules and rootlets. This study examined the legume–microbe interaction of C. villosa growing in two contrasting locations: a hilltop with high sun irradiance and drought, and a valley bottom with a low level of radiation and sufficient soil humidity for plant growth. Calicotome villosa adult plants established endophytic interactions with bacteria in six genera: Pseudomonas, Stenotrophomonas, Bacillus, Paenibacillus, Brevicacterium, and Rhizobium. Plants growing on the hilltop had associated lower bacterial richness than those grown on the valley bottom. All strains were drought-tolerant and produced siderophores, IAA, HCN, and NH₃ that stimulated plant performance in C. villosa plants and the other four legumes commonly present in the understory of the shrub communities. The legumes’ capacity to selectively host symbiotic bacteria that enhance plant survival in harsh conditions partly accounts for the diverse partnerships between C. villosa plants and their symbionts, ultimately explaining the wide distribution of this plant species. Full article

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

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15 pages, 2661 KiB  

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

Cited by 1 | Viewed by 946

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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14 pages, 2928 KiB  

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

Cited by 1 | Viewed by 2300

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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19 pages, 1981 KiB  

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

Cited by 3 | Viewed by 1901

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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13 pages, 4220 KiB  

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

Cited by 2 | Viewed by 2070

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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17 pages, 1987 KiB  

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 12 | Viewed by 2710

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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