Rhizosphere Methods 
Archiroot

Archiroot is a web site dedicated to methods in root research. This is my attempt to collects useful tools I have used and developped over the years. I also provide data, image, software and information about approaches to study root system architectures in a quantitative way.

Common Root Phenotyping Methods 

Root observation and phenotyping is often an important and a required part of abiotic stress research, especially in breeding and selection. The available information on methods of root research is very large, scattered and often difficult to resolve towards one’s work. Here, several of the more common and significant methods are described as an entry point.

Handbook of Methods used in Rhizosphere Research

One of the deliverables of COST action 631 was to compile a handbook of methods used in rhizosphere research, and make it available to the broader rhizosphere community. Another objective was to build a bridge between researchers who work experimentally and those who focus on modelling. The result of this effort is a collection of standardized method and model descriptions covering important aspects of rhizosphere research

Plant Imaging Analysis 

Guillaume Lobet (Assistant Professor between the Forschungszentrum Juelichand the Université catholique de Louvain), curates a website of aggregated information about root (and more generally plant) image analysis software. The website was initially only about root software, but in January 2013, it was extend to include all plant image analysis tools.

Rhizosphere Research Labs/Groups
 

Zoe Cardon - The Ecosystem Center - Woods Hole 

Research in the Cardon lab includes several long-term projects, each linking plants, soils, and microbes in a unique way. Overall, they drive to understand how biogeochemical cycles have dramatically affected, and been dramatically affected by, evolutionary changes in the anatomy and physiology of organisms on Earth, and by the ecological interplay of those organisms above- and below-ground in complex mutualisms, symbioses and food webs.

Weixin Cheng's Soil Ecology Lab -  UC Santa Cruz

​Research interest spans from root-soil interactions to the effects of global change factors (e.g., elevated CO2, nitrogen deposition, and global warming) on belowground processes, and to global patterns of social-ecological entanglement (e.g., biospheric carrying capacity and ecological foundation of human societies). The Soil ecology lab group engages in research on ecological processes at varying scales from the rhizosphere to the landscape. These processes are integral components in carbon and nitrogen dynamics (e.g., production, respiration, root exudation, root turnover, decomposition, and nitrogen fixation). Current research projects are taking advantage of recently developed methods such as stable isotope tracing/labeling and minirhizotron root imaging. Please refer to the web page on research for more information about ongoing and previous projects, and see my list of publications for research work.

Dinneny Lab - Carnegie Institution for Science 

While plants are sedentary, their bodies often traverse long distances as they explore their local environment in search of resources necessary for growth.  The biology of root systems is governed by both micro-scale and systemic signaling that allows the plant to integrate these complex variables into growth and branching decisions that ultimately determine the efficiency with which resources are captured.  Research in my lab is aimed at understanding the response of roots to water-limiting conditions and is exploring this process at different organizational scales from the individual cell type to the level of the whole plant. 

Maren Friesen Lab - Michigan State University 

Our research interests lie at the interface of ecology and evolution. How do the molecular and physiological pathways of organisms shape their ecology, and how does selection imposed by interactions with other organisms and the environment ultimately shape their genomes?

Kao-Kniffin Lab - Cornell University 

Below Ground Ecology of Invasive Plants and Weeds - We are broadly interested in three areas of research:

• Selection of rhizosphere microbiomes that modulate plant traits
• Identifying novel biosynthetic compounds from rhizosphere microorganisms contributing to plant growth or inhibition
• Assembly of plant-microbial communities that enhance ecosystem services

Jonathan Lynch's - Roots Lab -  Penn State Univ. ​

​The overall research focus of the Roots Lab at Penn State is understanding the genetic, physiological, and ecological basis of plant adaptation to infertile soils.

M. Luke Mccormick Lab - University of Minnesota 

my overarching goal is to provide insight into how belowground processes connect with and act as part of a larger whole.  These efforts lead me to examine my study systems from multiple spatial and temporal perspectives ranging from a single tree root in an instant to whole landscapes over centuries. ​

Rich Phillips - Indiana University 

Our lab investigates how plants and soil microbes mediate energy flow and nutrient dynamics in forests. We use a complementary suite of approaches that integrate field observations with controlled environmental systems to address questions that intersect plant physiological ecology and soil microbial ecology in an ecosystem context.

VaTech - Rhizosphere and Soil Microbial Ecology and Biogeochemistry

We study microbial communities and how they are impacted by plants and their surrounding soil environment. Using next-gen sequencing, LC and GC- mass spectrometry, we are answering questions about the distribution and function of microbial communities in the root-zone and soil habitats of both native and human-managed ecosystems. We are also interested in how plants and microbes interact to create ecosystems, cycle nutrients, and contribute to the process of soil organic matter formation.

Richard Ferrieri

Building an Integrative Imaging Platform in Plant Science A Grand Challenge in Sustainable Cropping. The Ferrieri labs mission is to establish a multidisciplinary imaging platform that will integrate radiochemical imaging technologies including PET and SPECT with mass spectrometric imaging (MSI) technologies including NanoSIMS, MALDI MS and LA-ICP-MS. When utilized in concert, researchers will be uniquely positioned to examine the exchange of plant resources, including metabolites, hormones and inorganic ions both at the root-soil interface and between the plant root and shoot systems.

Larry M. York Lab - Samuel Roberts Noble Foundation

Research in the York lab addresses fundamental issues in root biology by using integrative theory and techniques. This research has occurred on 4 continents with work in the field, simulation modeling, X-ray computed tomography, and genetic methods. We need to address the concept of phenotype and the gene-to-phene map to understand how form gives rise to function based on microeconomic principles applied to plants, such as cost-benefit analysis and game theory.

Laboratory Resources
West Coast Metabolomics Center (WCMC)

he West Coast Metabolomics Center is a NIH Regional Resource Core designed to expand the availability of metabolomics services to investigators in many diverse fields while simultaneously advancing the state-of-the art in metabolomics research.

Rhizosphere Research Products 

For research in soil science, plant physiology, marine geochemistry and environmental issues, Rhizons are used frequently. For each purpose, for instance field research, green house experiments, core and rhizotron sampling in the laboratory, or subsea floor sediments, there is a specific Rhizon.

Advanced Science Tools 

Micro-ROCs allow the direct observation of: a) root cell structure, b) fluorescent tagged proteins expressed in root cells, c) root symbiont/pathogen interactions, d) root growth etc. in vivo. The chambers are optimized for highest resolution in light- and confocal microscopy. We use exclusively high quality, corrosion resistant cover glass, recommended by leading microscope manufacturers. The root guidance system ensures that roots and root hairs are in contact with their natural soil environment, while they grow along the cover glass.

Metagenomic and Bioinformatic Resources 

Edwards Lab - Sand Diego State University

Rob Edwards’ bioinformatics lab at San Diego State University is all about decoding life’s best kept secrets. These secrets are encoded, as you must have already guessed, in genomes of bacteria, archaea, eukaryotes and the viruses that infect them. They use all kinds of computers, from clusters to cell phones, to solve the most unsolvable computational problems that help us better understand biology.

QIIME

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples

Coordinated Research Networks

EURoots

EURoot objective is to enhance the cereal plant capability to acquire water and nutrients through their roots and maintain growth and performance under stress conditions. 

International Plant Phenotyping Network

International Plant Phenotyping Network is an association representing the major plant phenotyping centers. IPPN aims to provide all relevant information about plant phenotyping. The goal is to increase the visibility and impact of plant phenotyping and enable cooperation by fostering communication between stakeholders in academia, industry, government, and the general public. Through workshops and symposia, IPPN seeks to establish different working groups and distribute all relevant information about plant phenotyping in a web-based platform.

International Society of Root Research

The Society’s aim is to promote cooperation and communication between root researchers around the world. I hope that you will join us in this endeavour.

RhizoNet

Linking roots, the rhizosphere and soil science with aboveground ecosystem ecology--RhizoNet is a network designed to link observations of roots, soil fungi, and belowground processes with whole-plant and ecosystem function.  Beginning with a suite of sites across China and elsewhere, the overarching goal of RhizoNet is to bring the often disparate fields of aboveground and belowground ecology into balance.  To that end, the collaborative framework offered by RhizoNet provides information on methods and approaches to facilitate cross-site and cross-species comparisons.