Niche differentiation shapes the bacterial diversity and composition of apple

Huang, Yimei; Chai, Xiaofen; Wang, Xiaona; Gao, Beibei; Li, Hui; Han, Zhenhai; Xu, Xuefeng; Zhang, Xinzhong; Wu, Ting; Wang, Yi

doi:10.1016/j.hpj.2022.03.005

Cited by 9 publications

(5 citation statements)

References 49 publications

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“…Our data further highlights the significant role of plant host genotype in structuring the root-associated microbial community, despite being generally weak, relative to microhabitats (i.e., plant compartments) and environmental stressors (e.g., water stress) ( Naylor et al, 2017 ; Wang et al, 2020 ; Huang et al, 2022 ). We demonstrated that both bacteria and fungi were clustered mainly by microhabitats.…”

Section: Discussionmentioning

confidence: 60%

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

Miller

Shi

2023

Front. Microbiol.

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The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.

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Section: Discussionmentioning

confidence: 60%

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

Miller

Shi

2023

Front. Microbiol.

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“…Molecular identification revealed that all three strains belonged to the genus Pseudomonas. Coincidentally, our previous study found that Pseudomonas was significantly enriched in the rhizosphere of M. xiaojinensis compared to Fe-inefficient rootstocks of M. baccata, with a relative abundance 16.28 times higher than that of M. baccata (Huang et al, 2022). Pseudomonas is widely distributed, has diverse metabolic pathways (Jain & Pandey, 2016;Moreno & Rojo, 2014), and plays an important role in promoting plant growth and disease resistance (Zhuang et al, 2021).…”

Section: Discussionmentioning

confidence: 98%

Siderophore production in pseudomonas SP. strain SP3 enhances iron acquisition in apple rootstock

Gao

Chai

Huang

et al. 2022

Journal of Applied Microbiology

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Aims:The purpose of this study was to analyse the effects of siderophore-producing bacteria and bacterial siderophore on the iron nutrition of apple rootstocks under iron-deficient conditions. Methods and Results:We isolated three Pseudomonas strains, SP1, SP2 and SP3 from the rhizosphere of the Fe-efficient apple rootstocks using the chrome azurol S agar plate assay. We found that all three strains had the ability to secrete indole acetic acid-like compounds and siderophores, especially SP3. When Fe-inefficient rootstocks treated with SP3 were grown in alkaline soil, an increase in the biomass, root development, and Fe concentration was observed in the plants. In addition, SP3 secreted pyoverdine, a siderophore that can chelate Fe 3+ to enhance the bioavailability of Fe for plants. We purified the pyoverdine from the SP3 culture supernatant.Hydroponic experiments were conducted with a Fe-deficient solution supplemented with pyoverdine, resulting in a reduction in the chlorosis caused by Fe deficiency and marked improvement in Fe uptake.Conclusions: Under iron-deficient conditions, Pseudomonas sp. strain SP3 can effectively promote apple rootstock growth and improve plant iron nutrition by secreting siderophores that enhance Fe availability. Significance and Impact of the Study:This study showed that plant growthpromoting rhizobacteria from Fe-efficient plants have the potential to improve iron nutrition in Fe-inefficient plants, and Fe-siderophore chelates can be used as an effective source of iron for apple plants. Based on these findings, it may be possible to develop biological agents such as siderophore-producing bacteria for sustainable agricultural and horticultural production.

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“…This is because the rhizosphere soil-root interface acts as a selective barrier, and only a limited number of bacteria can adapt to the endogenous lifestyle and dominate the endogenous combination, thus forming a unique, highly rich, and diverse microbial community ( 37 ). Some studies have found that niche differentiation, especially between soil and plant tissue, can lead to changes in bacterial community structure ( 38 , 39 ). In this study, there are significant differences in the bacterial community structure in different niches of Camellia oleifera , especially between bulk soil and plant tissues ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera

Zhang,

Ding,

Jiang

et al. 2023

Microbiol Spectr

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Understanding the changes in bacterial community structure in different microenvironments of Camellia oleifera is essential to better explore the benign interaction between beneficial microorganisms and plants. Using Camellia oleifera trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla ( Proteobacteria , Acidobacteria , Actinobacteria , Bacteroidetes , Firmicutes , Chloroflexi , and Verrucomicrobia ) of Camellia oleifera show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria ( Hymenobacter , Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium , Mesorhizobium , Bradyrhizobium , Bacillus , Ochrobactrum , Pantoea , Pseudomonas , etc.) with nitrogen-fixed potentials are enriched in Camellia oleifera tissue. In addition, the hub bacterial groups of Camellia oleifera are Nitrospira , Haemophilus , Staphylococcus , Ruminiclostridium , and Ochrobactrum . They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of Camellia oleifera . These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants. IMPORTANCE Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria , Acidobacteria , Actinobacteria , Bacteroidetes , Firmicutes , Chloroflexi , and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

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Niche differentiation shapes the bacterial diversity and composition of apple

Cited by 9 publications

References 49 publications

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

Siderophore production in pseudomonas SP. strain SP3 enhances iron acquisition in apple rootstock

Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera

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