Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi.
Ontology highlight
ABSTRACT:
SUBMITTER: Liao HL
PROVIDER: S-EPMC8601753 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Root-associated entomopathogenic fungi (R-AEF) indirectly influence herbivorous insect performance. However, host plant-R-AEF interactions and R-AEF as biological control agents have been studied independently and without much attention to the potential synergy between these functional traits. In this study, we evaluated behavioral responses of cabbage root flies [Delia radicum L. (Diptera: Anthomyiidae)] to a host plant (white cabbage cabbage Brassica oleracea var. capitata f. alba cv. Castello L.) with and without the R-AEF Metarhizium brunneum (Petch). We performed experiments on leaf reflectance, phytohormonal composition and host plant location behavior (behavioral processes that contribute to locating and selecting an adequate host plant in the environment). Compared to control host plants, R-AEF inoculation caused, on one hand, a decrease in reflectance of host plant leaves in the near-infrared portion of the radiometric spectrum and, on the other, an increase in the production of jasmonic, (+)-7-iso-jasmonoyl-L-isoleucine and salicylic acid in certain parts of the host plant. Under both greenhouse and field settings, landing and oviposition by cabbage root fly females were positively affected by R-AEF inoculation of host plants. The fungal-induced change in leaf reflectance may have altered visual cues used by the cabbage root flies in their host plant selection. This is the first study providing evidence for the hypothesis that R-AEF manipulate the suitability of their host plant to attract herbivorous insects.
| S-EPMC7773740 | biostudies-literature
Project description:Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.
| S-EPMC6328596 | biostudies-literature
Project description:Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.
| S-EPMC5432656 | biostudies-literature
Project description:BackgroundThe role of anaerobic organisms in the cystic fibrosis (CF) lung microbiome is unclear. Our objectives were to investigate the effect of broad (BS) versus narrow (NS) spectrum antianaerobic antibiotic activity on lung microbiome diversity and pulmonary function, hypothesizing that BS antibiotics would cause greater change in microbiome diversity without a significant improvement in lung function.MethodsPulmonary function tests and respiratory samples were collected prospectively in persons with CF before and after treatment for pulmonary exacerbations. Treatment antibiotics were classified as BS or NS. Gene sequencing data from 16S rRNA were used for diversity analysis and bacterial genera classification. We compared the effects of BS versus NS on diversity indices, lung function and anaerobic/aerobic ratios. Statistical significance was determined by multilevel mixed-effects generalized linear models and mixed-effects regression models.ResultsTwenty patients, 6-20 years of age, experienced 30 exacerbations. BS therapy had a greater effect on beta diversity than NS therapy when comparing time points before antibiotics to after and at recovery. After antibiotics, the NS therapy group had a greater return toward baseline forced expiratory volume at 1 second and forced expiratory flow 25%-75% values than the BS group. The ratio of anaerobic/aerobic organisms showed a predominance of anaerobes in the NS group with aerobes dominating in the BS group.ConclusionsBS antianaerobic therapy had a greater and possibly longer lasting effect on the lung microbiome of persons with CF, without achieving the recovery of pulmonary function seen with the NS therapy. Specific antibiotic therapies may affect disease progression by changing the airway microbiome.
| S-EPMC8511214 | biostudies-literature
Project description:Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs.IMPORTANCE We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions.
| S-EPMC7762793 | biostudies-literature
Project description:Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes - collectively termed the root microbiome - are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.
| S-EPMC6792034 | biostudies-literature
Project description:This study investigated ericoid mycorrhizal fungi (EMF) diversity in Vaccinium uliginosum across its main wild distribution range in China. Fungal communities in hair roots of V. uliginosum were analyzed using Illumina MiSeq sequencing. Only 22 OTUs were assigned to putative EMF genera. Rhizoscyphus and Meliniomyces dominated EMF communities, followed by Clavaria, Oidiodendron, Lachnum, Acephala, and Phialocephala. There were more dark septate endophytes (DSE) reads from the Greater Khingan Mountains than from other study areas, similar to the results of the percent colonization of DSE by the magnified intersections method. Overall, high-throughput sequencing data provided a rough community-scale sketch of root-associated fungi of V. uliginosum. Two hundred and eighty slow-growing isolates were isolated from root pieces of V. uliginosum, and the isolates matched 16 fungal genera on the basis of morphological and internal transcribed spacer sequence comparison. The isolates of Cryptosporiopsis ericae, Oidiodendron maius, Lachnum sp., Sordariomycetes sp., and Pleosporales sp., formed ericoid hyphal coils via resynthesis trails. The co-existence between EMF and DSE in hair roots was observed via trypan blue staining. A putative model for the co-existence between EMF and DSE in the hair roots of V. uliginosum was proposed. We suggest that under certain environmental stresses, such as low temperature and poor available nutrients, ericoid plants may favor co-colonization by both DSE and EMF.
| S-EPMC6191440 | biostudies-literature
Project description:BackgroundOne method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.MethodsHere, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.ResultsThe 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.ConclusionsFungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
| S-EPMC5863371 | biostudies-literature
Project description:BackgroundPlants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.ResultsIntegration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.ConclusionCollectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.
| S-EPMC10401788 | biostudies-literature
Project description:Potassium (K) reduces the deleterious effects of drought stress on plants. However, this mitigation has been studied mainly in the aboveground plant pathways, while the effect of K on root-soil interactions in the underground part is still underexplored. Here, we conducted the experiments to investigate how K enhances plant resistance and tolerance to drought by controlling rhizosphere processes. Three culture methods (sand, water, and soil) evaluated two rapeseed cultivars' root morphology, root exudates, soil nutrients, and microbial community structure under different K supply levels and water conditions to construct a defensive network of the underground part. We found that K supply increased the root length and density and the organic acids secretion. The organic acids were significantly associated with the available potassium decomposition, in order of formic acid > malonic acid > lactic acid > oxalic acid > citric acid. However, the mitigation had the hormesis effect, as the appropriate range of K facilitated the morphological characteristic and physiological function of the root system with increases of supply levels, while the excessive input of K could hinder the plant growth. The positive effect of K-fertilizer on soil pH, available phosphorus and available potassium content, and microbial diversity index was more significant under the water stress. The rhizosphere nutrients and pH further promoted the microbial community development by the structural equation modeling, while the non-rhizosphere nutrients had an indirect negative effect on microbes. In short, K application could alleviate drought stress on the growth and development of plants by regulating the morphology and secretion of roots and soil ecosystems.
| S-EPMC7996290 | biostudies-literature