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Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane.

ABSTRACT: Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum. Using a metabarcoding approach, bacterial communities were assessed in bulk composts and cress rhizoplanes. Six and nine composts showed significant disease suppression or growth promotion, respectively, but these traits did not correlate. Growth promotion correlated positively with nitrate content of composts, whereas disease suppression correlated negatively with factors representing compost age. Growth promotion and disease suppression explained significant portions of variation in bacterial community structures, i.e. 11.5% and 14.7%, respectively. Among the sequence variants (SVs) associated with growth promotion, Microvirga, Acinetobacter, Streptomyces, Bradyrhizobium and Bacillus were highly promising, while in suppressive composts, Ureibacillus,Thermogutta and Sphingopyxis were most promising. Associated SVs represent the basis for developing prediction tools for growth promotion and disease suppression, a highly desired goal for targeted compost production and application.

SUBMITTER: Mayerhofer J

PROVIDER: S-EPMC8478479 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:AimsRecent foodborne disease outbreaks have caused farmers to re-evaluate their practices. In particular, concern that soil amendments could introduce foodborne pathogens onto farms and promote their survival in soils has led farmers to reduce or eliminate the application of animal-based composts. However, organic amendments (such as composts and cover crops) could bolster food safety by increasing soil microbial diversity and activity, which can act as competitors or antagonists and reduce pathogen survival.Methods and resultsLeveraging a study of a 27-year experiment comparing organic and conventional soil management, we evaluate the impacts of composted poultry litter and cover crops on soil chemistry, bacterial communities and survival of Salmonella enterica and Listeria monocytogenes. We found that bacterial community composition strongly affected pathogen survival in soils. Specifically, organic soils managed with cover crops and composts hosted more macronutrients and bacterial communities that were better able to suppress Salmonella and Listeria. For example, after incubating soils for 10 days at 20°C, soils without composts retained fourfold to fivefold more Salmonella compared to compost-amended soils. However, treatment effects dissipated as bacterial communities converged over the growing season.ConclusionsOur results suggest that composts and cover crops may be used to build healthy soils without increasing foodborne pathogen survival.Significance and impact of the studyOur work suggests that animal-based composts do not promote pathogen survival and may even promote bacterial communities that suppress pathogens. Critically, proper composting techniques are known to reduce pathogen populations in biological soil amendments of animal origin, which can reduce the risks of introducing pathogens to farm fields in soil amendments. Thus, animal-based composts and cover crops may be a safe alternative to conventional fertilizers, both because of the known benefits of composts for soil health and because it may be possible to apply amendments in such a way that food-safety risks are mitigated rather than exacerbated.

Project description:Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of O. officinalis were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from O. officinalis tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including Desulfomonile and Ruminiclostridium for roots; Lactobacillus, Acinetobacter, Cutibacterium and Dechloromonas for stems; and Stenotrophomonas, Chryseobacterium, Achromobacter and Methylobacterium for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from O. officinalis. Among them, 11 strains identified as Enterobacter mori, E. ludwigii, E. cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae and Kosakonia oryzae were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of O. officinalis and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.

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Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane.

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