isolation-analysis-microbial-communities-soil-rhizosphere-roots

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Plant and soil microbiome studies are becoming increasingly important for understanding the roles microorganisms play in agricultural productivity. The ...

University of Nebraska-Lincoln

Roots play an essential role in the acquisition of water and minerals from soils. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance. In this review, we focus mainly on the molecular genetic advances that have been made in altering root system architecture and function in crop plants, as well as phenotyping methods. The future for the modification of crop plant roots looks promising based on recent advances, but there are also important challenges ahead. 

Challenges of modifying root traits in crops for agriculture.

Zinc deficiency in humans is a serious problem worldwide with an estimated one third of populations at risk for insufficient zinc in diet, which leads to impairment of cognitive abilities and immune system function. The goal of this research was to increase the bioavailable zinc in the edible portion of cassava roots to improve the overall zinc nutrition of populations that rely on cassava as a dietary staple. To increase zinc concentrations, two Arabidopsis thaliana genes coding for ZIP1 and MTP1 were overexpressed with a tuber-specific or constitutive promoter. Eighteen transgenic events from four constructs, out of a total of 73 events generated, showed significantly higher zinc concentrations in the edible portion of the storage root compared to the non-transgenic controls. The zinc content in the transgenic lines ranged from 4 to 73 mg/kg dry weight (DW) as compared to the non-transgenic control which contained 8 mg/kg. Striking changes in whole plant phenotype such as smaller plant size and chlorotic leaves were observed in transgenic lines that over accumulated zinc. In a confined field trial five transgenic events grown for 12 months showed a range of zinc concentrations from 18 to 217 mg/kg DW. Although the overexpression of zinc transporters was successful in increasing the zinc concentrations in 25% of the transgenic lines generated, it also resulted in a decrease in plant and tuber size and overall yield due to what appears to be zinc deficiency in the aerial parts of the plant. 

Overexpression of the transporters AtZIP1 and AtMTP1 in cassava changes zinc accumulation and partitioning.

Potassium is an essential macronutrient that is involved in regulating turgor, in driving plant growth, and in modulating enzyme activation. The changes in root morphology, root function, as well as cellular and molecular responses to low potassium conditions have been studied in the model plant Arabidopsis and in other plant species. In Arabidopsis ethylene plays a key role in roots in the transduction of the low potassium signal, which results in altered root function and growth. The first clues regarding the role of ethylene were detected through transcriptional profiling experiments showing changes in the expression of genes related to ethylene biosynthesis. Later it was shown that ethylene plays a foundational early role in the many responses observed in Arabidopsis. One of the most striking findings is the link between ethylene and reactive oxygen species (ROS) production, which is part of the signal transduction pathway in K(+) deprived plants. This mini-review will summarize what is known about the role ethylene plays in response to low potassium in Arabidopsis and other plant species. 

The Role of Ethylene in Plant Responses to K(+) Deficiency.

Protein transport between organelles is an essential process in all eukaryotic cells and is mediated by the regulation of processes such as vesicle formation, transport, docking, and fusion. In animals, SCY1-LIKE2 (SCYL2) binds to clathrin and has been shown to play roles in trans-Golgi network-mediated clathrin-coated vesicle trafficking. Here, we demonstrate that SCYL2A and SCYL2B, which are Arabidopsis () homologs of animal SCYL2, are vital for plant cell growth and root hair development. Studies of the SCYL2 isoforms using multiple single or double loss-of-function alleles show that SCYL2B is involved in root hair development and that SCYL2A and SCYL2B are essential for plant growth and development and act redundantly in those processes. Quantitative reverse transcription-polymerase chain reaction and a β-glucuronidase-aided promoter assay show that  and  are differentially expressed in various tissues. We also show that SCYL2 proteins localize to the Golgi, trans-Golgi network, and prevacuolar compartment and colocalize with Clathrin Heavy Chain1 (CHC1). Furthermore, bimolecular fluorescence complementation and coimmunoprecipitation data show that SCYL2B interacts with CHC1 and two Soluble NSF Attachment Protein Receptors (SNAREs): Vesicle Transport through t-SNARE Interaction11 (VTI11) and VTI12. Finally, we present evidence that the root hair tip localization of Cellulose Synthase-Like D3 is dependent on SCYL2B. These findings suggest the role of SCYL2 genes in plant cell developmental processes via clathrin-mediated vesicle membrane trafficking.

SCYL2 Genes Are Involved in Clathrin-Mediated Vesicle Trafficking and Essential for Plant Growth.

Rising atmospheric concentrations of CO and O are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO and O (eCO and eO) the endosphere, rhizosphere and soil were sampled from soybeans under eCO and maize under eO. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO and O.

Article	Year
Challenges of modifying root traits in crops for agriculture. Trends in plant science\| PubMed ID: 25239776	2014
Overexpression of the transporters AtZIP1 and AtMTP1 in cassava changes zinc accumulation and partitioning. Frontiers in plant science\| PubMed ID: 26217349	2015
The Role of Ethylene in Plant Responses to K(+) Deficiency. Frontiers in plant science\| PubMed ID: 26734048	2015
SCYL2 Genes Are Involved in Clathrin-Mediated Vesicle Trafficking and Essential for Plant Growth. Plant physiology\| PubMed ID: 28751315	2017
Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO and O. Scientific reports\| PubMed ID: 29101364	2017

Daniel P. Schachtman

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