Rhizosphere Metabolomics: Methods and Applications

Reuben, Sheela; Bhinu, V.-S.; Swarup, Sanjay

doi:10.1007/978-3-540-74543-3_3

Cited by 9 publications

(5 citation statements)

References 86 publications

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“…Screening for gene clusters coding for the synthesis of secondary metabolites by means of antiSMASH [40] yielded an extensive array of corresponding clusters in MAG_11. Secondary metabolites are structurally highly diverse compounds that exert various biological effects and have multiple functions in microbial soil communities [82]. Two of ten identified antiSMASH clusters were predicted to encode the biosynthesis of siderophores since they are similar to the Xanthoferrin biosynthesis gene cluster of Xanthomonas oryzae .…”

Section: Resultsmentioning

confidence: 99%

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Nelkner

Henke

Lin

et al. 2019

Genes

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To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

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Section: Resultsmentioning

confidence: 99%

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Nelkner

Henke

Lin

et al. 2019

Genes

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“…Similarly, Rochford et al [ 60 ] observed that growth inhibition against Bacillus subtilis of different soil extracts was strongly correlated with their metabolic profile. Metabolite composition is governed by the extant microbial communities in the substrate and it is well-known that pathogen inhibition may be mediated by the secretion of antibiotics or antimicrobial compounds [ 63 , 64 ]. For instance, over two-thirds of all natural antibiotics are derived from Streptomyces spp.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, over two-thirds of all natural antibiotics are derived from Streptomyces spp. [ 63 ]. Some species within this genus can produce antifungal compounds such as tuberdicidin, phosphalactomycin, and candicidin [ 65 – 67 ].…”

Section: Discussionmentioning

confidence: 99%

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control

Blaya¹,

Marhuenda²,

Pascual³

et al. 2016

PLoS ONE

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Phytophthora root rot caused by Phytophthora nicotianae is an economically important disease in pepper crops. The use of suppressive composts is a low environmental impact method for its control. Although attempts have been made to reveal the relationship between microbiota and compost suppressiveness, little is known about the microorganisms associated with disease suppression. Here, an Ion Torrent platform was used to assess the microbial composition of composts made of different agro-industrial waste and with different levels of suppressiveness against P. nicotianae. Both bacterial and fungal populations responded differently depending on the chemical heterogeneity of materials used during the composting process. High proportions (67–75%) of vineyard pruning waste were used in the most suppressive composts, COM-A and COM-B. This material may have promoted the presence of higher relative abundance of Ascomycota as well as higher microbial activity, which have proved to be essential for controlling the disease. Although no unique fungi or bacteria have been detected in neither suppressive nor conducive composts, relatively high abundance of Fusarium and Zopfiella were found in compost COM-B and COM-A, respectively. To the best of our knowledge, this is the first work that studies compost metabolome. Surprisingly, composts and peat clustered together in principal component analysis of the metabolic data according to their levels of suppressiveness achieved. This study demonstrated the need for combining the information provided by different techniques, including metagenomics and metametabolomics, to better understand the ability of compost to control plant diseases.

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“…By identifying which root metabolites are responsible for the proliferation of specific microbes, root exudates can be purified or synthesized and used to increase the host’s ability to recruit a beneficial microbiome [160] . However, several bottlenecks have been identified by Reuben et al [161] , such as the cost and technical constraints to detect different metabolites, the absence of a well-curated database and chemoinformatics tools to enable analysis and interpretation of collected data. In the future, if limitations related to techniques, analyses, and integration with other mentioned “omics” sciences are overcome, incorporating metabolomics studies into microbiome studies would enable engineering of the native soil microbiome for increased plant growth and performance under bespoke conditions.…”

Section: Gaps - How Far Are We From Achieving a Microbiome-facilitatementioning

confidence: 99%

Defining the wheat microbiome: Towards microbiome-facilitated crop production

Kavamura

Mendes

Bargaz

et al. 2021

Computational and Structural Biotechnology Journal

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Rhizosphere Metabolomics: Methods and Applications

Cited by 9 publications

References 86 publications

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control

Defining the wheat microbiome: Towards microbiome-facilitated crop production

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