Synthetic community with six <i>Pseudomonas</i> strains screened from garlic rhizosphere microbiome promotes plant growth

Zhuang, Lubo; Li, Yán; Wang, Zhenshuo; Yu, Yue; Zhang, Nan; Yang, Chang Yeol; Zeng, Qingchao; Wang, Qi

doi:10.1111/1751-7915.13640

Cited by 81 publications

(70 citation statements)

References 54 publications

(58 reference statements)

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“…This is the first comparative analysis of this type to have been performed on arable crop residues, a matrix of major agroecological importance. By focusing on methodological aspects, we have extended a broader experimental work (Kerdraon et al, 2019b;2019c;2020), paving the way for further technical improvements. The isolation approach used here for bacteria was based on a single medium.…”

Section: Resultsmentioning

confidence: 99%

“…Together with the high-throughput isolation, this may partly explain the greater similarity of the results obtained by the two approaches for bacterial profiles than for fungal profiles It appears to be essential to combine the two approaches if we wish to go beyond descriptive aspects and characterize the ecological function of a microbial community. The main advantage of microbial isolation is that the different strains can be preserved and then testedindividually or after the creation of synthetic communities (Großkopf and Soyer, 2014; Sergaki et al 2018) -to decipher these ecological functions and identify positive specific interactions (Durán et al, 2018;Liu et al, 2019;Zhuang et al, 2020). Conversely, metabarcoding limits the biases linked to the cultivable/non-cultivable nature of microbes in the fine characterization of communities, and dedicated statistical analyses, such as linear discriminant analysis or ecological network analysis, are complementary approaches that could be used to identify putative microbial interactions (e.g.…”

Section: Some Methodological Considerationsmentioning

confidence: 99%

“…The impact of plant species, seasonality and crop rotation on the residue microbiome was highlighted for both fungal and bacterial communities, with the replacement of plant-specific taxaincluding pathogens and endophytesby more generalist taxa originating from the soil. The effect of the presence of Zymoseptoria tritici and Leptosphaeria maculanstwo important residue-borne fungal pathogens of wheat and oilseed rape, respectively (Suffert and Sache, 2011;Fitt et al, 2006) on the residue microbiome was then assessed by combining linear discriminant analyses and ecological network analyses (Kerdraon et al, 2019c;2020). The bacterial and fungal communities associated with residues were compared between wheat with and without preliminary Z. tritici inoculation, between wheat in contact with the soil and without soil contact (Kerdraon et al, 2019c) and between two isogenic oilseed rape lines with and without a resistance gene against L. maculans (Kerdraon et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

Laval

Kerdraon

Barret

et al. 2021

Preprint

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This study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the ‘1%’ paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

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Section: Resultsmentioning

confidence: 99%

Section: Some Methodological Considerationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

Laval

Kerdraon

Barret

et al. 2021

Preprint

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“…The bacteria in the stems come from the environmental soil, air, air or water, which are enriched by microorganisms (Doju et al 2018). This may explain the greater richness in the roots compared to the stems (Zhuang et al 2020). Over time, endophytic bacteria from the roots can migrate or be transported to the upper parts of plants (Lamo et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Tomato endophyte bacteria diversity under long-term organic agricultural manipulation systems

Zhang¹,

Zhan²,

Zhang³

et al. 2021

Preprint

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Purpose: Differences were observed in both microbial structure and physicochemical properties were observed in the organic and conventional agricultural systems. However, very little is known about the diversity of endophytic bacterial communities in plants grown in separate manipulation systems. The goal of this work was to get a broader overview of the diversity and dynamics of the tomato endophytic bacteria in the different agricultural manipulation systems.Methods: The structure of endophyte bacterial communities under different growth periods (seeding stage, flowering stage, fruiting stage and harvesting stage), agricultural manipulation practices (organic and conventional systems) and organ-type (root or stem) were explored by using 16Sr RNA gene profiling in this study.Results: A total of 2,014,992 part 16 SRRNA gene sequences were obtained. These sequences revealed large-scale functional taxonomy units (OTUs). That is, there are 648 different OTUS in libraries, and 96 OTUs are common. Tomato endophytes consisted mainly of four phylloxera, of which Proteobacteria was the most represented, followed by Formigiotes, bacteriophages, Actinobacteria, Gamma proteobacteria, the most abundant class of proteobacteria, bacteriobacteria, and so on. Proteobacteria are low. General enterobacteriaceae, Vecella, Bacillus, Mesorizobium and Chrysobacterium were shared by all growth periods. Rich endophytic bacterial diversity was observed at the seedling stage (DI), and endophytic bacterial diversity at the flowering stage and fruiting stage was low. Significant difference in endophytic bacterial communities emerged from roots and different host biographical stages, and tomato exerts greater influence on endophyte bacteria compared to organ type (main) agricultural manipulation methods.Conclusions: Tomato endophyte microbiota have a distinct structure in different growth periods. Bacillus were enriched seeding stage and decreased in the fruiting stage while Mesorhizobium increased during in the fruiting stage. Tomato have distinct endosphere microbiota by comparing beta diversity of microbiota in different growth periods, compared with the manipulation resume and organ type. And a strong correlation was observed between the structure of the microbiota in the whole dataset and soil chemistry which indicated that the soil type and treatment affected the endosphere microbiota of tomato. Organ-type (niche) exert more influence on the tomato microbiota compared with manipulation treatments between organic-farming and conventional farming.

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“…Genus Pseudomonas was proved to be a group of plant growth promoting rhizobacteria (PGPR) [36][37]. For instance, Pseudomonas was found to be a key PGPR in the rhizosphere of garlic regardless of growth periods, soil types and agricultural practices, the constructed six Pseudomonas strains displayed strong plant growth promoting effects [38]. These results indicated that the stronger growth characteristics of A. sinensis in Gansu group may be related to the increased abundance of these antagonistic microorganisms in the rhizosphere.…”

Section: Effect Of Soil Type On the Composition Of Rhizosphere Bactermentioning

confidence: 97%

Insights Into the Mechanism of Rhizosphere Microorganisms Effecting on Quality Formation of Authentic Angelica Sinensis Under Different Soil Microenvironments

Zhu

Yan

Zhou

et al. 2021

Preprint

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Background: Angelica sinensis (Oliv.) Diels (A. sinensis), the commonly used famous-region Chinese herbs, grew in different geographical locations which were crucial to active components accumulation in medicinal plants. Rhizosphere microbiome played a critical role in plant performance, including nutrient acquisition, growth and development and plant diseases resistance etc., there were still few studies on how microbiome effecting on accumulation of active components of A. sinensis. This study aim to illustrate whether the variations of rhizosphere microbial communities and metabolites profilings of A. sinensis were dependant on soil microenvironments. Soils from the two main A. sinensis producing areas, Gansu and Yunnan Province, were selected for a pot experiment, and then divided into two parts, one part was sterilized and the other did not, planting with Gansu danggui 90-01, allowed to grow for 180 days. After the trial radix A. sinensis were collected for analysis of growth targets and chemical compositions, rhizosphere soils for microbial analyses. Results: The metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments showed similar variation. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) group were significantly separated. Specifically, compared with Yunnan soil, antagonistic bacteria such as Sphingomonas, Pseudomonas, Lysobacter, Pseudoxanthomonas, etc. were significantly (p <0.05) enriched in Gansu soil. The characteristic constituents of senkyunolide I and ligustilide dimers enriched in GS group has an extremely positive correlation with Pseudomonas parafulva; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate enriched in YS Group were significantly positively relevant with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. Conclusions: Given that soil microenvironments may contribute to growth and active components accumulation of A. sinensis. Further study aimes at exploring the functional characteristics of quality-related bacterias, and finding the main response genes and the interactions between genes and the environments, to elucidate the main mechanism of genuine A. sinensis quality formation.

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Synthetic community with six Pseudomonas strains screened from garlic rhizosphere microbiome promotes plant growth

Cited by 81 publications

References 54 publications

Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

Tomato endophyte bacteria diversity under long-term organic agricultural manipulation systems

Insights Into the Mechanism of Rhizosphere Microorganisms Effecting on Quality Formation of Authentic Angelica Sinensis Under Different Soil Microenvironments

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