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my-phd

mycorrhizal-symbiosis-modulates-the-rhizosphere-microbiota-to-promote-rhizobia-legume-symbiosis

Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. The plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula, by quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that the AM symbiosis impacts Rhizobiales-hubs among the plant microbiota and benefit the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction, whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.

mzh_microbiome

Repository for methods or scripts of mine

pcap_2018

pigargs

Codes related to the manuscript "Characteristics and host bacteria of resistome in pigs raised in farms with different management patterns".

pigc

The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.

probiotics-relieve-human-stress-and-anxiety-project

Probiotic consumption relieved human stress and anxiety symptoms via modulating the gut microbiota and neuroactive potential

psp-omics

This directory contains intermediate data files for the 16S amplicon data, metabolomic, and transcriptomic profiles of rats from three groups, as well as all the code used for the analysis in the paper.

ptb

rep-cookbook

Replication Cookbook for FGFP GWAS

rgmgc

This repository contains custom script and pipeline used in RGMGC data mining project.

rmvp

:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

rothschulze_pregnancy-gut-microbiome-t1d

Data, metadata and analyses performed in microbiome whole metagenomics sequencing data of women with and without T1D during pregnancy.

r_bilibili

sars-cov-2-vaccination

scher_et_al_2013

Intermediate data and analysis tools from Scher et al., eLife, 2013

spatiotemporal_analysis

This GitHub repository documents the findings of a spatiotemporal RNA-seq study on mouse brain aging, including 1,076 samples from 15 regions spanning 7 ages and two rejuvenating interventions.

tormes

Making whole bacterial genome sequencing data analysis easy

uc-severity-multiomics

vitamin-d

notebooks for MrOS Vitamin D manuscript

warming-network-complexity-stability

Computer code for the manuscript "Climate Warming Enhances Microbial Network Complexity and Stability"

zhang2018scls

Rice (Oryza Sative) root microbiome time-course analysis. (Zhang2018SCLS)