skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes
Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associatedStreptomycesphenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find thatStreptomycesphenotypes varied more between richness plots—with theStreptomycesfrom polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance—than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.  more » « less
Award ID(s):
1831944 2129332
PAR ID:
10556786
Author(s) / Creator(s):
; ; ; ; ; ; ;
Publisher / Repository:
Frontiers Media SA
Date Published:
Journal Name:
Frontiers in Microbiology
Volume:
15
ISSN:
1664-302X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Hui, Dafeng (Ed.)
    Abstract While the relationship between genetic diversity and plant productivity has been established for many species, it is unclear whether environmental conditions and biotic associations alter the nature of the relationship. To address this, we investigated the interactive effects of genotypic diversity, drought and mycorrhizal association on plant productivity and plant traits. Our mesocosm study was set up at the Konza Prairie Biological Research Station, located in the south of Manhattan, Kansas. Andropogon gerardii, the focal species for our study, was planted in two levels of genotypic richness treatment: monoculture or three-genotype polyculture. A rainout shelter was constructed over half of the experimental area to impose a drought and Thiophanate-methyl fungicide was used to suppress arbuscular mycorrhizal fungi in selected pots within each genotypic richness and drought treatment. Genotypic richness and mycorrhizal association did not affect above-ground biomass of A. gerardii. Drought differentially affected the above-ground biomass, the number of flowers and bolts of A. gerardii genotypes, and the biomass and the functional traits also differed for monoculture versus polyculture. Our results suggest that drought and genotypic richness can have variable outcomes for different genotypes of a plant species. 
    more » « less
  2. Abstract Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH4+and decreased NO3availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems. 
    more » « less
  3. Abstract Research suggests that microbiomes play a major role in structuring plant communities and influencing ecosystem processes, however, the relative roles and strength of change of microbial components have not been identified. We measured the response of fungal, arbuscular mycorrhizal fungal (AMF), bacteria, and oomycete composition 4 months after planting of field plots that varied in plant composition and diversity. Plots were planted using 18 prairie plant species from three plant families (Poaceae, Fabaceae, and Asteraceae) in monoculture, 2, 3, or 6 species richness mixtures and either species within multiple families or one family. Soil cores were collected and homogenized per plot and DNA were extracted from soil and roots of each plot. We found that all microbial groups responded to the planting design, indicating rapid microbiome response to plant composition. Fungal pathogen communities were strongly affected by plant diversity. We identified OTUs from genera of putatively pathogenic fungi that increased with plant family, indicating likely pathogen specificity. Bacteria were strongly differentiated by plant family in roots but not soil. Fungal pathogen diversity increased with planted species richness, while oomycete diversity, as well as bacterial diversity in roots, decreased. AMF differentiation in roots was detected with individual plant species, but not plant family or richness. Fungal saprotroph composition differentiated between plant family composition in plots, providing evidence for decomposer home-field advantage. The observed patterns are consistent with rapid microbiome differentiation with plant composition, which could generate rapid feedbacks on plant growth in the field, thereby potentially influencing plant community structure, and influence ecosystem processes. These findings highlight the importance of native microbial inoculation in restoration. 
    more » « less
  4. Agricultural practices have a profound impact on watershed dynamics, water quality, and the well-being of aquatic life. One major concern is agricultural pollution, particularly the excess of nutrients, which can elevate disease risks in various host-pathogen relationships. However, the exact mechanisms driving this effect remain uncertain. Elevated nutrient levels are believed to significantly influence populations of aquatic environmental bacteria, potentially reshaping the microbiomes of aquatic organisms and affecting their vulnerability to disease. Despite this, the impact of nutrient enrichment on host microbiomes as a link to diseases in aquatic organisms has been largely overlooked. In this study, we investigated the impact of nutrient enrichment on the skin-associated microbial communities of the American bullfrogLithobates catesbeianus. We observed a significant shift in bacterial richness and community composition in nutrient-enriched ponds compared with reference ponds. Although the proportion of the community inhibitory towardsBatrachochytrium dendrobatidis(Bd) did not change significantly,Bdloads were markedly higher in nutrient-enriched ponds. Nutrient enrichment significantly altered carbon utilization patterns as measured by Biolog EcoPlates, and antibiotic resistance was prevalent across all ponds and samples, with resistance to trimethoprim, sulfamethazine, and chloramphenicol significantly higher in nutrient-enriched ponds. Our findings indicate that nutrient enrichment affects the structure and function of skin-associated microbial communities in American bullfrogs, influencing bothBdload and antibiotic resistance. 
    more » « less
  5. ABSTRACT Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes. 
    more » « less