Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L.

Latif, Sadia; Bibi, Sameeda; Kouser, Rabia; Fatimah, Hina; Farooq, Saba; Naseer, Samar; Kousar, Rizwana

doi:10.1016/j.ygeno.2020.07.031

Cited by 20 publications

(19 citation statements)

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“…The metagenomic analyses characterizing the wheat rhizosphere revealed that Proteobacteria , Actinobacteria , Chloroflexi , Bacteroidetes , and Firmicutes were the dominant phyla residing in this rhizosphere in the three different soil samples. A similar phylum profile was previously described in the wheat rhizosphere microbiome grown in different regions of the world ( 37 , 39 – 41 ). Abundant classes observed in this study were Alphaproteobacteria , Deltaproteobacteria , Actinobacteria , Betaproteobacteria , Gammaproteobacteria , and Bacilli , which is consistent with other studies that described the rhizosphere communities of different wheat varieties cultivated in Poland ( 37 ) and Pakistan ( 40 ).…”

Section: Discussionsupporting

confidence: 69%

“…A similar phylum profile was previously described in the wheat rhizosphere microbiome grown in different regions of the world ( 37 , 39 – 41 ). Abundant classes observed in this study were Alphaproteobacteria , Deltaproteobacteria , Actinobacteria , Betaproteobacteria , Gammaproteobacteria , and Bacilli , which is consistent with other studies that described the rhizosphere communities of different wheat varieties cultivated in Poland ( 37 ) and Pakistan ( 40 ). These results supported earlier conclusions that wheat plants recruit a core microbiome that is consistent across locations with different soil and environmental characteristics ( 2 ).…”

Section: Discussionsupporting

confidence: 69%

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Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

et al. 2021

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Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored.

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Section: Discussionsupporting

confidence: 69%

Section: Discussionsupporting

confidence: 69%

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

et al. 2021

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“…Indeed, amoA genes appear to be more represented in maize-peanut intercropping than in maize monocropping. Among Chloroflexi, Thermomicrobia are dominant taxa in wheat rhizosphere ( Latif et al, 2020 ) and key taxa in microbial network associated with tall wheat cultivars ( Kavamura et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping

et al. 2021

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Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.

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“…Operational taxonomic units (OTUs) were clustered using UPARSE version 7.1 1 , and chimeric sequences were identified and removed using UCHIME ( Osman et al, 2020 ). High-quality filtered tags with ≥97% similarity in nucleotide identity were clustered into same operational taxonomic units by OTU cluster analysis ( Latif et al, 2020 ). The taxonomy of each 16S rRNA gene sequence was analyzed by the RDP Classifier algorithm 2 against the Silva (SSU123) 16S rRNA database with a confidence threshold of 70%.…”

Section: Methodsmentioning

confidence: 99%

“…The alpha diversity of bacterial community was analyzed using Shannon, Simpson’s, and Ace indices, based on the assigned OTUs ( Latif et al, 2020 ; Osman et al, 2020 ). The beta diversity of bacterial community among different samples was assessed using a hierarchical cluster tree and principal coordinates analysis (PCoA) based on Bray–Curtis similarity.…”

Section: Methodsmentioning

confidence: 99%

Bacterial Communities Associated With Healthy and Bleached Crustose Coralline Alga Porolithon onkodes

et al. 2021

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Crustose coralline algae (CCA) play vital roles in producing and stabilizing reef structures and inducing the settlement and metamorphosis of invertebrate larvae in coral reef ecosystems. However, little is known about the bacterial communities associated with healthy and bleached CCA and their interactions with coral larval settlement. We collected samples of healthy, middle semi-bleached, and bleached CCA Porolithon onkodes from Sanya Bay in the South China Sea and investigated their influences on the larval settlement and metamorphosis of the reef-building coral Pocillopora damicornis. The larval settlement/metamorphosis rates all exceeded 70% when exposed to healthy, middle semi-bleached, and bleached algae. Furthermore, the compositions of bacterial community using amplicon pyrosequencing of the V3–V4 region of 16S rRNA were investigated. There were no obvious changes in bacterial community structure among healthy, middle semi-bleached, and bleached algae. Alphaproteobacteria, Bacteroidetes, and Gammaproteobacteria were dominant in all samples, which may contribute to coral larval settlement. However, the relative abundances of several bacterial communities varied among groups. The relative abundances of Mesoflavibacter, Ruegeria, Nautella, and Alteromonas in bleached samples were more than double those in the healthy samples, whereas Fodinicurvata and unclassified Rhodobacteraceae were significantly lower in the bleached samples. Additionally, others at the genus level increased significantly from 8.5% in the healthy samples to 22.93% in the bleached samples, which may be related to algal bleaching. These results revealed that the microbial community structure associated with P. onkodes generally displayed a degree of stability. Furthermore, bleached alga was still able to induce larval settlement and metamorphosis.

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Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L.

Cited by 20 publications

References 69 publications

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping

Bacterial Communities Associated With Healthy and Bleached Crustose Coralline Alga Porolithon onkodes

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