Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant

Abstract

Soil-derived microbiota associated with plant roots are conducive to plant growth and stress resistance. However, the spatio-temporal dynamics of microbiota in response to organochlorine pollution during the unstable vegetative growth phase of rice is not well understood. In this study, we focused on the rice (Oryza sativa L.) microbiota across the bulk soil, rhizosphere and endosphere compartments during the vegetative growth phase in two different soils with and without lindane pollutant. The results showed that the factors of growth time, soil types and rhizo-compartments had significant influence on the microbial communities of rice, while lindane mostly stimulated the construction of endosphere microbiota at the vegetative phase. Active rice root-soil-microbe interactions induced an inhibition effect on lindane removal at the later vegetative growth phase in rice-growth-dependent anaerobic condition, likely due to the root oxygen loss and microbial mediated co-occurring competitive electron-consuming redox processes in soils. Each rhizocompartment owned distinct microbial communities, and therefore, presented specific ecologically functional categories, while the moderate functional differences were also affected by plants species and residual pollution stress. This work revealed the underground micro-ecological process of microbiota and especially their potential linkage to the natural attenuation of residual organochlorine such as lindane.

Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

“…The analyses for bacterial community among four niches were conducted via 16 S rRNA gene amplicon sequencing. The V4 region was amplified using the common primer pairs 515 F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806 R (5′-GGACTACHVGGGT-WTCTAAT-3′) [ 31 ]. All DNA samples were sequenced on the Illumina Nova6000 platform from Guangdong Magigene Biotechnology Co. Ltd. (Guangzhou, China).…”

“…Recently, high-throughput sequencing has been widely used to study the microbiomes of different crops in response to environmental stresses [ 30 , 31 ]. Metagenomic binning can describe the taxonomic composition and functional potential of microbial communities with high taxonomic resolution [ 32 ].…”

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ

“…CH 4 and CO 2 concentrations were analyzed using gas chromatography (GC-2010 Plus SHIMADZU, Japan) . The concentrations of γ-HCH were determined using a method based on accelerated solvent extraction (ASE) with a Dionex ASE 350 (Thermo Fisher; Sunnyvale, CA, USA), followed by solid-phase enrichment and GC–MS analysis. , Cell surface morphologies of M. barkeri were taken at the end of the incubation and were observed through a scanning electron microscope (XL-30 ESEM-TMP, Philips, Amsterdam, Netherlands) equipped with a Phenom mapping energy spectrometer that was operated at 5 kV.…”

Assessment of residual chlorine in soil microbial community using metagenomics

“…Soil microorganisms, especially those colonizing the plant rhizosphere, play an important role in growth yield and disease-resistance of plant (Lu et al, 2018;Qu et al, 2020;Feng et al, 2021), but most soil ecotoxicology experiments have usually focused on big-size model organisms for study but have ignored the soil microbial ecology. The indiscriminate spraying of a large amounts of chlorine-containing disinfectants can directly destroy the community balance and functional diversity of soil microbiome, which may further perturb the health of plants and result in invasion by pathogenic bacteria (Mendes et al, 2013;Qian et al, 2021).…”