Metatranscriptomic Studies of the Plant Rhizosphere for Finding Biological Agents

Kothari, Vishal; Kothari, Charmy; Rank, Jalpa; Joshi, Anjali; Singh, Ravindra; Kothari, Ramesh

doi:10.1007/978-981-10-5050-3_16

Cited by 4 publications

(1 citation statement)

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“…Among the most widely used sequencing approaches is metabarcoding (or amplicon sequencing), which involves the sequencing of variable regions of ribosomal marker genes previously amplified by PCR (amplicons). This method, used throughout this study, enables the identification of members within soil microbial communities and their dynamics in response to various environmental conditions, all in a time-and cost-efficient manner (Kothari et al, 2017).…”

Section: Methodological Insights For Microbiome Analysismentioning

confidence: 99%

Nurturing belowground life: the role of cover crops in shaping soil microbial communities in agroecosystems

Cazzaniga

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Cover crops are used in agriculture to minimise soil erosion, prevent nutrient leaching and increase soil organic matter content. Cover crops can also be grown to stimulate the soil microbial community to improve soil biological conditions. Despite their widespread use, little is known about the impact of different cover crop species on the composition and activity of the soil microbiome. Here we investigate the effect of distinct cover crop species on the rhizosphere microbiome and characterise both the resident (ribosomal (r)DNA-based) and the potentially active (rRNA-based) fractions of the bacterial, fungal, protist and metazoan communities in the cover crops rhizosphere. We conducted a field experiment using 70-litre bottomless containers in which we grew ten monocultures of commonly used cover crop species belonging to five plant families, and an unplanted control treatment (fallow). The total DNA and RNA were extracted from soil and the bacterial, fungal, protistan and metazoan communities were characterized using Illumina MiSeq sequencing. We found that all cover crop species significantly impacted the resident and the potentially active microbial communities in their rhizospheres. Cover crops exerted distinct selection strengths on the native microbial communities. For individual cover crops, the impacts on the resident and the potentially active microbial communities differed while showing similar overall tendencies. Oilseed radish (Brassicaceae) was shown to provoke the strongest microbial shifts, in part attributable to a promotion of the bacterial family Pseudomonadaceae and a repression of Microascaceae in the rhizosphere. Lentil (Fabaceae) induced a widespread stimulation of fungal taxa, including Trichocomaceae and fungal members of the Glomerales order, whereas black oat and hybrid ryegrass (both Poaceae) gave rise to relatively mild changes in the soil microbial communities. Analyses of rRNA-based rhizobiome data revealed that, except for phacelia, all cover crops induced an increase in microbial network complexity as compared to the fallow control. Data presented here provide a broad baseline for the effects of cover crops on four organismal groups, which may facilitate future cover crop selection to advance soil health.

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Section: Methodological Insights For Microbiome Analysismentioning

confidence: 99%