Metagenomic Functional Shifts to Plant Induced Environmental Changes

Yurgel, Svetlana N.; Nearing, Jacob T.; Douglas, Gavin M.; Langille, Morgan G. I.

doi:10.3389/fmicb.2019.01682

Cited by 35 publications

(20 citation statements)

References 51 publications

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“…The most common approach for profiling communities is to sequence the highly 13 conserved 16S rRNA gene. Functional profiles cannot be directly identified from 16S rRNA 14 gene sequence data due to strain variation and because 16S rRNA genes are not unique among 15 microbes, but several approaches have been developed to infer approximate microbial 16 community functions from taxonomic profiles (and thus amplicon sequences) alone [1][2][3][4][5][6] . 17…”

mentioning

confidence: 99%

PICRUSt2: An improved and customizable approach for metagenome inference

Douglas

Maffei

Zaneveld

et al. 2019

Preprint

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581

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One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2 (https://github.com/picrust/picrust2), which expands the capabilities of the original PICRUSt method1 to predict the functional potential of a community based on marker gene sequencing profiles. This updated method and implementation includes several improvements over the previous algorithm: an expanded database of gene families and reference genomes, a new approach now compatible with any OTU-picking or denoising algorithm, and novel phenotype predictions. Upon evaluation, PICRUSt2 was more accurate than PICRUSt1 and other current approaches overall. PICRUSt2 is also now more flexible and allows the addition of custom reference databases. We highlight these improvements and also important caveats regarding the use of predicted metagenomes, which are related to the inherent challenges of analyzing metagenome data in general.

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mentioning

confidence: 99%

PICRUSt2: An improved and customizable approach for metagenome inference

Douglas

Maffei

Zaneveld

et al. 2019

Preprint

Self Cite

581

463

View full text Add to dashboard Cite

show abstract

“…The generated KO abundance table was subsequently preprocessed following the workflow of the previous study ( Yurgel et al, 2019 ). First, the count matrix was normalized to the Reads Per Kilobase per Genome equivalent (RPKG) method using MicrobeCensus version 1.1.0 ( Nayfach and Pollard, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

et al. 2021

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Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

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“…The rhizosphere is a hotspot of plant-bacteria interplay within the soil environments [15]. It is colonized by diverse bacterial communities, which are functionally and structurally controlled by soil type and texture, environmental factors and plants [16]. Studies have revealed that the plant root exudates and other rhizodeposits lure beneficial bacteria to the rhizosphere, although uninvited ones are also enticed [1].…”

Section: The Rhizosphere Soil As a Treasure Trove For Bacterial Community Concentrationmentioning

confidence: 99%

Elucidating the Rhizosphere Associated Bacteria for Environmental Sustainability

Nwachukwu

Babalola

2021

Agriculture

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The abundance of nutrient accumulation in rhizosphere soils has placed the rhizosphere as an “epicenter” of bacterial concentrations. Nonetheless, over the years, little attention has been given to bacterial inoculants and soil-like substrates. The reason is that many farmers and experiments have focused on chemical fertilizers as an approach to improve plant growth and yield. Therefore, we focused on assessing the application of rhizosphere soil and its associated bacteria for biotechnological applications. This review has been structured into major subunits: rhizosphere soil as a treasure trove for bacterial community concentration, biodegradation of lignocellulose for biofuel production, rhizosphere soil and its bacteria as soil amendments, and the role of rhizosphere soil and its bacteria for bioremediation and biofiltration. Hence, the efficient use of rhizosphere soil and its bacteria in an environmentally friendly way can contribute to healthy and sustainable environments.

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Metagenomic Functional Shifts to Plant Induced Environmental Changes

Cited by 35 publications

References 51 publications

PICRUSt2: An improved and customizable approach for metagenome inference

PICRUSt2: An improved and customizable approach for metagenome inference

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Elucidating the Rhizosphere Associated Bacteria for Environmental Sustainability

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