The rhizosphere, defined as the soil environment that surrounds the plant roots, is a rich and diverse habitat for microbes. Some members of the rhizosphere microbiome (or collection of microbes), are good, others bad while many are just there and don’t provide any benefits or harm to the host. One function of the good microbes in the rhizosphere is to help facilitate the availability and assimilation of nutrients and water from the rhizosphere. Just like the human gut, the plant rhizosphere conveys key nutritional functions and the analogy was made that “plants wear their gut on the outside”. One example is the symbiotic relationship between legumes (peas, beans) and rhizobia. Those bacteria help the plant fix atmospheric nitrogen in exchange for carbon supply. Another example is the symbiotic relationship between the plant and mycorrhizal fungi, whereby the mycorrhizae receive carbon from the plant in exchange for increased nutrient uptake (principally phosphorus and nitrogen). There is undeniable evidence that plants have developed a mechanism for recruiting good microbes to cope with environmental stress such as protection against opportunistic pathogens or drought. The rise of ‘omics’ technologies have helped profile entire microbial communities associated with plants and shed light in their biological functions. This research has fueled the development of novel commercial bioproducts to address the increasing consumer’s demand of environmentally-friendly products. As a result, there has been several commercial ‘probiotics’ and ‘prebiotics’ that have been marketed for agricultural use including many biocontrol agents such as fungal- (e.g., Trichoderma) and bacterial- based (e.g., Bacillus, Streptomyces, or Pseudomonas) bioproducts.
One goal of my research program is to identify beneficial microbes for tree and vines crops, promote practices that support the presence and abundance of beneficial microbes and figure out how good microbes help combat pathogens and support plant health. As part of a collaborative project (UC Riverside, University of Florida, USDA-ARS) funded by the California Citrus Research Board and the USDA-NIFA, we profiled the microbiome of citrus trees in the context of Huanglongbing disease (or HLB). HLB is a highly destructive and lethal disease to all commercial citrus cultivars making it a threat to citrus production globally. Finding strategies that do not only rely exclusively on management of the insect vector of the bacterium (the Asian Citrus Psyllid), is a priority to the citrus industry. In our research, we found that there were significant tissue-specific microbial shifts occurring within the citrus microbiome as trees get sicker, especially in the root compartment. As HLB progressed, there were depletions of beneficial species in roots, such as mycorrhizal fungi, and enrichments of parasitic microorganisms, such as Fusarium and Phytophthora (see Figure). HLB-affected trees decline because of the clogging the phloem sieve tubes, which limit movement of sap and translocation of sugar to the roots, hence leading to feeder root collapse. Once tree is weakened, it becomes more susceptible to pathogens such as Phytophthora which further weakens the trees and exacerbate above ground HLB symptoms. In addition, several studies from Florida suggested that cultural practices that supported root health and rhizosphere microbiome richness and diversity limited root collapse.
Figure: Citrus decline caused by HLB (https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-04-20-0027- R – Ginnan et al. 2020. Phytobiomes); canopy thinning, wood dieback, feeder roots decline, collapse of beneficial microbes and enrichment of pathogens in roots.
Our group was recently awarded another research funding by the USDA-NIFA Emergency Citrus Disease Research and Extension program (project director, M.C. Roper, Microbiology and Plant Pathology, UC Riverside). This research effort in collaboration with UC Agricultural and Natural Resources, UC Davis, University of Florida, and the USDA-ARS aims at investigating the root collapse associated with HLB- impacted trees and finding ways to mitigate it by promoting root health. In the proposed work, we will test how different sectors of the root microbiome contribute to or lessen fibrous root loss and if soil amendments (e.g., humic acid treatment, mulching) and planting of HLB tolerant rootstocks (Poncirus trifoliata and P. trifoliata hybrids) can be used to mitigate root loss associated with HLB in Florida, and how tree respond to those practices under a HLB free environment in California. While these approaches will not cure trees from HLB, it will provide a science-based information for strategies that support root and tree health and sustain orchard longevity until remedies are discovered. — By Philippe Rolsausen, Professor in Cooperative Extension, UC Riverside