Pinned Repositories
banocc
BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`
equSA
HerbivoreDetritivoreInteractions
A repository for experimental data and code associated with the manuscript: Interactions between herbivores and detritivores develop slowly and conspicuously into feedbacks
med_qiime_tutorial
a tutorial for using MED & QIIME to create an OTU table
microbe-networks
Roxanne's thesis project, studying microbe co-occurrence in corn seed
microbiome
microbiome-1
microbiome R package
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.
NWT_MovingUphill2
Analysis of Niwot 2015 18S, 16S, ITS data
R
R - learning
JunqiangZheng's Repositories
JunqiangZheng/HerbivoreDetritivoreInteractions
A repository for experimental data and code associated with the manuscript: Interactions between herbivores and detritivores develop slowly and conspicuously into feedbacks
JunqiangZheng/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.
JunqiangZheng/16S-main
JunqiangZheng/2021_DVRFS_microbiome
Scripts for a manuscript titled "Subsurface Planktonic Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity" (submitted)
JunqiangZheng/blogofxiaoming
小明的数据分析笔记本 推文合集
JunqiangZheng/codyn
:exclamation: This is a read-only mirror of the CRAN R package repository. codyn — Community Dynamics Metrics. Homepage: https://github.com/NCEAS/codyn/ Report bugs for this package: https://github.com/NCEAS/codyn/issues
JunqiangZheng/Consistent-effects-of-independent-domestication-events-on-seed-microbiome
JunqiangZheng/EasyAmplicon
Easy Amplicon data analysis pipeline
JunqiangZheng/ensembleTax
source R package
JunqiangZheng/fungal-competition2020
A place for code and figures associated with the manuscript I hope to publish in 2020 from my fungal competition data.
JunqiangZheng/Grace_2012_Guidelines_for_SEM
JunqiangZheng/iCAMP1
Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis (Version 1)
JunqiangZheng/Intraspecific_Competition
This repository contains data and analysis from my studies looking at the role of intraspecific competition in providing protection from C. difficile Infection.
JunqiangZheng/marcel
(eventually) an R package that calculates nematode community indices
JunqiangZheng/Metagenomics_Analysis
JunqiangZheng/microtrait
JunqiangZheng/MulderVonk2011
nematode bodymasses from 10.1890/11-0546.1
JunqiangZheng/NitrogenWaterMowingGrasslandSoilMicrobial
Long-term nitrogen and water additions with or without mowing altered soil microbial community characteristics in a semi-arid steppe
JunqiangZheng/peptidoglycan_related_genes_in_basal_aphids
Comparative genomics of eight aphid subfamilies reveals variable relationships between host horizontally-transferred genes and symbiont peptidoglycan metabolism
JunqiangZheng/phylo_z_scores
Null modelling of phylogenetic nearest taxon distances for individual taxa
JunqiangZheng/Pycnandra
JunqiangZheng/QIIME2_18Sv9_ASV_protocol
JunqiangZheng/Rare-Taxa-Sequence-Level-Analysis
JunqiangZheng/sheng-xin-xiao-bai-yu
历史文档备份（只包含2019年和2020年）
JunqiangZheng/sheng-xin-xiao-bai-yu-2021
历史文档备份（2021年）
JunqiangZheng/sheng-xin-xiao-bai-yu-2022
历史文档备份（2022年）
JunqiangZheng/Soil-microbiomes-and-functional-genes-along-latitudinal-and-altitudinal-gradients
This project included workflow code for three independent researches which are designed along latitude and altitude.
JunqiangZheng/TraitResolution-Simulations
Simulated impacts of trait resolution on the inferences about ecological processes (Kohli & Jarzyna. 2021. GEB)
JunqiangZheng/traitsyndromes
Code for "Facilitation and the evolution of plant trait-syndromes in Mediterranean vegetation"
JunqiangZheng/waafle
WAAFLE (a Workflow to Annotate Assemblies and Find LGT Events) is a method for finding novel LGT (Lateral Gene Transfer) events in assembled metagenomes, including those from human microbiomes.