The structure and function of the global citrus rhizosphere microbiome

Xu, Jin; Zhang, Yunzeng; Zhang, Pengfan; Trivedi, Pankaj; Riera, Nadia; Wang, Yayu; Liu, Xin; Fan, Guangyi; Tang, Ji‐Liang; Coletta-Filho, Helvécio Della; Cubero, Jaime; Deng, Xiaoling; Ancona, Veronica; Lu, Zhanjun; Zhong, Balian; Roper, M. Caroline; Capote, Nieves; Catara, Vittoria; Pietersen, Gerhard; Vernière, Christian; Al-Sadi, Abdullah M.; Lei, Li; Yang, Fan; Xu, Xun; Jian, Wang; Yang, Huanming; Jin, Tao; Wang, Nian

doi:10.1038/s41467-018-07343-2

Cited by 382 publications

(313 citation statements)

References 77 publications

(143 reference statements)

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“…Rhizoplane, one of the root-associated layers, serves as a critical gate that regulates microbial entry into roots 49 . A comprehensive analysis indicated that no difference existed in the microbial community structure of rhizosphere and associated bulk soil samples collected from twelve citrus varieties which distributed on six continents 50 . In this study, the microbial community structure in roots was also similar to that in soil, suggesting that root-associated microbes were mainly derived from the soil biome 35 .…”

Section: Discussionmentioning

confidence: 99%

“…Alternatively, the exudates containing sugars, organic acids and amino acids secreted by plant roots have strongly affected the composition of microbes in surrounding soil. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes have been reported as the primary consumers of plant exudates and the predominant taxa of citrus 50,51 . Other reports supported the above results and the microbial community of other plants including maize, arabidopsis and tamarix consists of a few dominant phyla, such as Proteobacteria, Actinobacteria, and Bacteroidetes 16,52,53 .…”

Section: Discussionmentioning

confidence: 99%

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Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

et al. 2020

Sci Rep

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Plant microbiota colonize all organs of a plant and play crucial roles including supplying nutrients to plants, stimulating seed germination, promoting plant growth, and defending plants against biotic and abiotic stress. Because of the economic importance, interactions between citrus and microbes have been studied relatively extensively, especially citrus-pathogen interactions. However, the spatial distribution of microbial taxa in citrus trees remains under-studied. In this study, Citrus reticulata cv. Chachiensis was examined for the spatial distribution of microbes by sequencing 16S rRNA genes. More than 2.5 million sequences were obtained from 60 samples collected from soil, roots, leaves, and phloem. The dominant microbial phyla from all samples were Proteobacteria, Actinobacteria and Acidobacteria. The composition and structure of microbial communities in different samples were analyzed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial species between samples were analyzed and the indicator microbes of each sample group were identified. Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.www.nature.com/scientificreports www.nature.com/scientificreports/ trees 23 . Most previous investigation on citrus-associated microbiomes are analyses on huanglongbing-infected, or specially-treated samples [24][25][26][27][28][29] .Citrus reticulata cv. Chachiensis is an important citrus variety widely cultivated around the world and the orange peel of the fruit was regarded as the valuable material which could be processed as food, tea drinks, and seasoning 30 . Besides, the orange peel owned antioxidant properties and extremely high medicinal value was also used as herb-medicine 31 . In China, C. reticulata cv. Chachiensis has grown in Xinhui District, Jiangmen City, Guangdong Province was considered as one of the most important cash crops for locals and the orange peel named genuine Pericarpium Citri Reticulatae (Guang Chen Pi) was admired as the best Chen pi which possesses the excellent clinical efficacy 32 . Plant-related microorganisms could protect the host from pathogens and pests, help plants use nutrients, and improve plant stress resistance 33 , while the microbial community of C. reticulata cv. Chachiensis remains unknown. In this study, endosphere microbiomes in soils, roots, leaves, and phloem of C. reticulata cv. Chachiensis were systematically investigated by sequencing 16S rRNA genes. The composition and structure of the microbial community in different tissues were performed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial compositions among citrus tissues were analyzed and indicator microbes for different samples were identified. Our results suggested that the microbial community from different tissues of C. reticulata cv. Chachiensis in south china varied significantly. Our results laid a foundation for future studies on microbial comm...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

et al. 2020

Sci Rep

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“…Using MetaBAT2 [14], an unsupervised MAG extraction tool, we recovered a high-quality MAG affiliated with the Cellvibrio genus, supported by both CheckM and AMPHORA2 results [15,16]. Cellvibrio is a crucial member of the citrus rhizosphere microbiome, as revealed by our global-scale citrus microbiome analysis, and is further enriched to the rhizoplane niche [6,13]. Therefore, we further refined this Cellvibrio MAG to assemble a high-quality genome [40] to investigate the strategies used for rhizoplane niche adaptation.…”

Section: Recovery and Curation Of The Almost Complete Metagenome-assementioning

confidence: 73%

Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Zhang

Wang

et al. 2020

Microorganisms

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Maintaining integrity of the plant cell walls is critical for plant health, however, our previous study showed that Cellvibrio, which is recognized by its robust ability to degrade plant cell walls, was enriched from the citrus rhizosphere to the rhizoplane (i.e., the root surface). Here we investigated the mechanisms underlying the rhizosphere-to-rhizoplane enrichment of Cellvibrio through genome-centric metagenomics and metatranscriptomics analyses. We recovered a near-complete metagenome-assembled genome representing a potentially novel species of Cellvibrio, herein designated Bin79, with genome size of 5.71 Mb across 11 scaffolds. Differential gene expression analysis demonstrated that plant cell wall degradation genes were repressed, whereas genes encoding chitin-degrading enzymes were induced in the rhizoplane compared with the rhizosphere. Enhanced expression of multi-drug efflux genes and iron acquisition- and storage-associated genes in the rhizoplane indicated mechanisms by which Bin79 competes with other microbes. In addition, genes involved in repelling plant immune responses were significantly activated in the rhizoplane. Comparative genomics analyses with five related Cellvibrio strains showed the importance of gene gain events for the rhizoplane adaptation of Bin79. Overall, this study characterizes a novel Cellvibrio strain and indicates the mechanisms involved in its adaptation to the rhizoplane from meta-omics data without cultivation.

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“…Citrus rhizosphere microbiome are the microorganism closely attached to the rhizosphere, which plays an important role in promoting citrus growth and development. Xu et al suggested that plant-microbe interactions are very likely to be important factors that influence the assembly of rhizosphere microbiomes, such as bacterial secretion systems [40]. The enrichment of rhizosphere microbes can be attributed to their lifestyles [41][42].…”

Section: Discussionmentioning

confidence: 99%

“…Delgado-Baquerizo et al reported that only 2% of bacterial taxa made up nearly half of the soil bacteria at various sites around the world [43]. Meanwhile, Xu et al also found that there are only a few bacterial taxa, such as Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes, which are abundant in the citrus rhizosphere [40]. Similarly, we found that the dominant bacterial groups were Proteobacteria, Acidobacteria, and Actinobacteria in the citrus-cultivated rhizosphere soil, while the other bacterial groups were non-dominant bacteria.…”

Section: Discussionmentioning

confidence: 99%

Effects of Mancozeb on Citrus Rhizosphere Bacterial Community

Huang

Wang

et al. 2020

Preprint

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Mancozeb is extensively used fungicide to prevent citrus melanose in most Asian countries, especially in China. So far, however, there have been no reports of thet effect of Mancozeb on the citrus rhizosphere bacterial community. Therefore, this comparative experiment defined the genomic and functional related to community and soil health of 2-years old Citrus unshiu Marc. rhizosphere through amplicon sequencing and chemical analysis. This study evaluated the effect of mancozeb on the chemical properties of citrus-cultivated soil and the richness and diversity of rhizosphere bacterial community. We also investigated the abundance response of rhizosphere bacterial groups to 0, 2, 4, 6 and 8 times application of 2 g mancozeb (active ingredient content, ai.) 600 times diluted with water. Our data revealed that the abundance of rhizosphere-associated bacterial species increased significantly after planting citrus. The relative abundance of Candidatus, Saccharibacteria, Parcubacteria, and Proteobacteria increased with the increase in mancozeb watering times. Meanwhile, the abundance of Nitrospirae decreased with the increase in mancozeb application times. The findings indicated that the chemical properties of the soil and the richness and diversity of rhizosphere bacterial community did not significantly differ across the mancozeb gradients in soil.

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The structure and function of the global citrus rhizosphere microbiome

Cited by 382 publications

References 77 publications

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Effects of Mancozeb on Citrus Rhizosphere Bacterial Community

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