How Does Climate Change Affect Endophytic Fungi?

Plant-associated microorganisms can have major effects on plant health, but climate change can affect plant microbiomes. While it is unknown how climate change will affect aboveground plant-associated microorganisms, such as foliar endophytic fungi, we hypothesize that increased CO2 concentrations will increase species richness and diversity in endophytic fungal communities, because increased plant photosynthesis under elevated CO2 will increase the resources available to the fungi

Fungal Endophytes Interact with Endophytic Yeast Isolated from Soybean Leaves

Endophytes (endo = inside and phyte=plant) are microscopic fungi that live inside of the leaves of all species of plants and can have beneficial effects on their hosts. Previous work in our lab has shown a significant decrease of Sporobolomyces sp., an endophytic yeast, within soybean hosts exposed to elevated levels of CO₂. Sporobolomyces sp. has certain properties to enable them to act as natural biocontrol agents. This pink yeast may have untapped potential to protect crops from pathogenic organisms. If Sporobolomyces sp. interacts with fungal pathogens, it may have strong effects on other fungal endophytes in the community. The aim of this experiment was to examine how Sporobolomyces sp. interacts with endophytes isolated from soy leaves both in terms of fungal growth and phenotypic changes

Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G) that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G). Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution

Bioinformatics Protocol for Assessing Contamination Level and Quality on Genomics Data of Ensifer meliloti

Nitrogen (N) fixing bacteria have a symbiotic relationship with host plants. The legume plants provide sugar, a product of its photosynthesis, to rhizobacteria. Rhizobacteria, one of the various N fixing bacteria, utilize the sugar for its energy source needed for conversion of N2into NH4+. The rhizobacteria would provide fixed nitrogen to legume plant for its growth in exchange of energy source. There are various symbiotic relationships between microbes and plants, and the Heath Lab is especially interested in relationship between rhizobacteria and legume plants. Various genomic methods to study rhizobacteria require sequence data in Heath Lab. However, there is high possibility of contamination in the sequence data, which may lead to false result in research. Possible non-rhizobacteria that reside within the legume nodules, which don’t participate in N fixation but in survival of the legume plant, could affect the research as well. It was recently found that rhizobacteria other than Ensifer meliloti reside within the legume nodules. Due to the existence of other rhizobacteria, we need a protocol to differentiate between these bacteria. Here, we designed a protocol based on comparing the sequences of E.meliloti from the Heath Lab against public database to determine the level of contamination

Confirming Presence and Mobilization of Partner Quality Genes in Sinorhizobium meliloti

Mutualism is an interaction in which two organisms benefit from each other. The symbiotic relationship between the bacterium Sinorhizobium meliloti and the plant Medicago truncatula is dictated by the bacterial plasmids. The Heath lab has a collection of 191 Sinorhizobium meliloti strains with different symbiotic plasmids that vary across populations (Riley et al., 2022). Each strain can be a better or worse partner for its plant host in symbiosis with the variation in fitness being called partner quality (Fig. 1) These traits can be traced back to the genetic elements that underlie this effect (Batstone et al., These genetic elements can be found in gene clusters that are gained or loss across strains (Fig. 1; Riaz, Sosa Marquez, in prep.). We need assurances of these important and variable clusters presence to understand their mechanism of gene movemen

Plant–environment interactions from the lens of plant stress, reproduction, and mutualisms

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154416/1/ajb21437.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154416/2/ajb21437_am.pd

Discordant Population Structure Among Rhizobium Divided Genomes and Their Legume Hosts

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization

Conventional management has a greater negative impact on Phaseolus vulgaris L. rhizobia diversity and abundance than water scarcity

IntroductionDrought is one of the biggest problems for crop production and also affects the survival and persistence of soil rhizobia, which limits the establishment of efficient symbiosis and endangers the productivity of legumes, the main source of plant protein worldwide.AimSince the biodiversity can be altered by several factors including abiotic stresses or cultural practices, the objective of this research was to evaluate the effect of water availability, plant genotype and agricultural management on the presence, nodulation capacity and genotypic diversity of rhizobia.MethodA field experiment was conducted with twelve common bean genotypes under irrigation and rain-fed conditions, both in conventional and organic management. Estimation of the number of viable rhizobia present in soils was performed before the crop establishment, whereas the crop yield, nodule number and the strain diversity of bacteria present in nodules were determined at postharvest.ResultsRainfed conditions reduced the number of nodules and of isolated bacteria and their genetic diversity, although to a lesser extent than the agrochemical inputs related to conventional management. In addition, the effect of water scarcity on the conventional management soil was greater than observed under organic conditions.ConclusionsThe preservation of diversity will be a key factor to maintain crop production in the future, as problems caused by drought will be exacerbated by climate change and organic management can help to maintain the biodiversity of soil microbiota, a fundamental aspect for soil health and quality

Combining GWAS and Population Genomic Analyses to Characterize Coevolution in a Legume-rhizobia Symbiosis

The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts

Depression-related stigma among primary care providers

Introduction: Depression is one of the most common mental illnesses in the United States and is often treated in primary care settings. Despite its prevalence, depression remains underdiagnosed and undertreated for a variety of reasons, including stigma. This may result in suboptimal management of depression. Studies evaluating stigma in US primary care providers (PCP) are scarce. The main objective of this study was to describe stigma in a cohort of PCPs. Methods: We utilized a validated questionnaire to measure stigma (score range 15 to 75 with lower scores indicating lower stigma levels). PCPs in 2 academic internal medicine clinics were sent an electronic questionnaire and received a small monetary incentive for responding. In addition to the stigma survey, we collected demographic data, including age, provider type, gender, and other data related to social proximity to mental illness. To describe stigma, differences in stigma between provider characteristics were evaluated using t tests and ANOVA tests as appropriate. Results: Of 107 PCPs, 71 responded (66.4% response rate). Male responders displayed higher stigma scores than females (31.8 vs 27.4, P=.0021). Medical residents displayed higher stigma scores than nonresidents (31.3 vs 27.2, P=.0045). Providers with personal exposure to mental illness and those who reported they frequently treated depression had less stigma. Discussion: Overall, a range of stigma was present among PCPs surveyed. Higher levels of stigma were found in men, medical residents, those without personal exposure to mental illness, younger PCPs, and those who reported treating depression less frequently. Future studies should utilize larger sample sizes and focus on the impact of stigma on quality of care