Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure.

Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.

Insights into bacterial diversity in compost: Core microbiome and prevalence of potential pathogenic bacteria.

Fertilizer-replacement programs by the ministry of agriculture and rural affairs are extraordinary actions for environment protection and sustainable agriculture in China. A national-level survey was performed to acquire consensuses of bio-physiochemical properties for composts. A total of 116 compost samples collected from 16 provinces in China were analyzed by high throughput sequencing of bacterial 16S rRNA gene amplicons. The germination index and bacterial alpha-diversity were lower in composts from poultry manure than others. This large-scale survey revealed that bacterial communities were distinct among different composts and slightly explained by pH, moisture and total nitrogen, but not by raw material or composting process. Nevertheless, 26 OTUs affiliated with Firmicutes (Cerasibacillus, Atopostipes and Bacillus) and Actinobacteria (Thermobifida, Actinomadura and Nocardiopsis) were present in most (>90%) composts and majority of these bacterial species were possibly associated with the biodegradation of organic materials. Surprisingly, 629 potential human or animal bacterial pathogens accounting an average of 1.21% of total 16S rRNA gene were detected and these bacteria were mainly affiliated with Helicobacter, Staphylococcus, Acinotobacter, Streptococcus, Mycobacterium and Enterococcus. In summary, this study provides baseline data for the diversity and abundance of core microbiome and potential pathogens in composts.

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici).

Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of organic, integrated, and conventionally managed soils to pepper blight (Phytophthora capsici) was studied in growth chamber experiments. Disease incidence was 41.3 and 34.1% lower in the soil from an organic farming system than in either the soil from the integrated or from the conventional farming systems, respectively. Beta-diversity of rhizospheric microbial communities differed among treatments, with enrichment of Bacillus, Sporosarcina, Acidobacteria Gp5, Gp6, Gp22, and Ignavibacterium by the organic soil. Cultivation-dependent analysis indicated that 50.3% of in vitro antagonists of P. capsici isolated from the rhizosphere of healthy peppers were affiliated to Bacillus. An integration of in vitro antagonists and bacterial diversity analyses indicated that Bacillus antagonists were higher in the rhizosphere of pepper treated by the organic soil. A microbial consortium of 18 in vitro Bacillus antagonists significantly increased the suppressiveness of soil from the integrated farming system against pepper blight. Overall, the soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly owing to Bacillus antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppression under greenhouse conditions.

Enrichment of phosphate solubilizing bacteria during late developmental stages of eggplant (Solanum melongena L.).

Understanding the ecology of phosphate solubilizing bacteria (PSBs) is critical for developing better strategies to increase crop productivity. In this study, the diversity of PSBs and of the total bacteria in the rhizosphere of eggplant (Solanum melongena L.) cultivated in organic, integrated and conventional farming systems was compared at four developmental stages of its lifecycle. Both selective culture and high-throughput sequencing analysis of 16S rRNA amplicons indicated that Enterobacter with strong or very strong in vivo phosphate solubilization activities was enriched in the rhizosphere during the fruiting stage. The high-throughput sequencing analysis results demonstrated that farming systems explained 23% of total bacterial community variation. Plant development and farming systems synergistically shaped the rhizospheric bacterial community, in which the degree of variation influenced by farming systems decreased over the plant development phase from 56% to 26.3% to 16.3%, and finally to no significant effect as the plant reached at fruiting stage. Pangenome analysis indicated that two-component and transporter systems varied between the rhizosphere and soil PSBs. This study elucidated the complex interactions among farming systems, plant development and rhizosphere microbiomes.