Response of Rhizosphere Bacterial Communities to Near-Natural Forest Management and Tree Species within Chinese Fir Plantations

Lei, Jie; Wu, Hanbin; Li, Xiaoyan; Wen-fu, Guo; Duan, Aiguo; Jian-guo, Zhang

doi:10.1128/spectrum.02328-22

Cited by 11 publications

(8 citation statements)

References 106 publications

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“…The results of this study showed that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla in the microbiomes of P. lactiflora cultivars, among which the relative abundance of Actinobacteria, Proteobacteria and Acidobacteria was much higher than that of other phyla. This finding has also been confirmed in Cathaya argyrophylla and Chinese fir [48,49]. We also noted that the rhizosphere bacterial communities associated with P. lactiflora exhibited high diversity and abundance.…”

Section: Discussionsupporting

confidence: 83%

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar

Yang,

Wan,

Zhou

et al. 2023

Biology

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The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora—a perennial herb species of the family Paeoniaceae—includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars “Sheng Tao Hua” and “Zi Lou Xian Jin” exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between “Lian Tai” and “Zi Hong Zheng Hui”, as well as between “Sheng Tao Hua” and “Tao Hua Fei Xue”, and the maximum similarity between “Duo Ye Zi” and “Xue Feng”. Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.

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Section: Discussionsupporting

confidence: 83%

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar

Yang,

Wan,

Zhou

et al. 2023

Biology

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“…In addition to aspects related to the host plant, data reported in the scientific literature converge in identifying the soil type as another key parameter that greatly influences rhizosphere microbial communities. Rhizomicrobiota composition and diversity are significantly affected by soil organic matter and pH, with lower pH values associated with less diversified communities [33,92,93,99].…”

Section: Rhizosphere Microbial Communitiesmentioning

confidence: 99%

“…Despite the differences related to the plant genotype and environmental factors, similarities in rhizomicrobiota composition and the presence of shared taxa selected from the surrounding bulk soil can be observed for all plants. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Verrucomicrobia are the main bacterial phyla generally found in the rhizosphere, whereas Ascomycota and Basidiomycota are among the dominant fungal groups [92,94,[99][100][101][102]. Recent work on an intercontinental scale and based on comparisons between microbial communities of the rhizosphere and bulk soils revealed that some bacterial groups, including Bacteroidetes and Proteobacteria, were consistently enriched in the rhizosphere, whereas other phyla (such as Acidobacteria, Chloroflexi, and Nitrospirae) were significantly less abundant in rhizosphere soils than in root-free soils [103].…”

Section: Rhizosphere Microbial Communitiesmentioning

confidence: 99%

Impact of Plant–Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems—A Review

Monaco,

Baldoni,

Naclerio

et al. 2024

Microorganisms

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The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and “omics” analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant–microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.

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“…Metagenomic data indicated the ubiquity of Planctomycetes in diverse ecosystems (Wiegand et al, 2018), encompassing soil (Stackebrandt et al, 1993; Wang et al, 2002; Buckley et al, 2006; Ivanova et al, 2016;), plant rhizosphere (Lei et al, 2023; Ravinath et al, 2022), seawater (Schlesner, 1994; Wiegand et al, 2020), freshwater (Schlesner, 1994; Wang et al, 2002; Dedysh et al, 2020), chlorinated water (Aghnatios and Drancourt, 2015), the human gastrointestinal tract (Cayrou et al, 2013), and very frequently in association with several algae (Bengtsson and Øvreås, 2010; Lage and Bondoso, 2011, 2012; Wiegand et al, 2020). However, the cultivation of Planctomycetes in pure axenic cultures has proven to be challenging, primarily attributed to their recalcitrance to grow on synthetic media and their inherently slow growth kinetics (Kaboré et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Specificities and commonalities of the Planctomycetes plasmidome

Coronel,

Devos,

Garcillán-Barcia

2024

Preprint

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Although plasmids play a crucial role in antibiotic resistance and contemporary biotechnology, our comprehension of their natural ecological dynamics remains restricted to a few bacterial groups. Planctomycetes is a bacterial phylum with unusual molecular and cellular biology for which little is known about its plasmidome. This study provides the first comprehensive description of the diversity of the endogenous plasmids found in Planctomycetes, which may be used as starting points to generate different genetic tools for research on this phylum. Plasmids from Planctomycetes encode a wide variety of biological functions, although for a large portion of the encoded genes a function cannot be assigned, which is usual in Planctomycetes. They seemed to have largely coevolved with the genome of their hosts, with which they share many homologs. We also detected recent transfer events of insertion sequences between co-habiting chromosomes and plasmids. 60% of the plasmid genes are distantly related to chromosomally-encoded genes and 40% have homologs in plasmids from other bacterial groups, while 36% of the proteins composing the planctomycetal plasmidome are exclusive. Most planctomycetal plasmids encode a replication initiation protein of the RPA family in the proximity of a putative iteron-containing replication origin, as well as active type I partition systems. One conjugative and three mobilizable plasmids were identified, suggesting horizontal gene transfer via conjugation in this phylum.

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Response of Rhizosphere Bacterial Communities to Near-Natural Forest Management and Tree Species within Chinese Fir Plantations

Cited by 11 publications

References 106 publications

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar

Impact of Plant–Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems—A Review

Specificities and commonalities of the Planctomycetes plasmidome

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