Dataset Information

High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment.

ABSTRACT: The genetic and predicted functional diversity of bacterial communities in 12 commercial biofertiliser products were evaluated using high-throughput sequencing of the 16S rRNA gene. Proteobacteria, Firmicutes and Bacteroides dominated the bacterial communities, with the genera Pseudomonas, Lactobacillus, Bacillus, Bradyrhizobium and Rhizobium being prevalent. The manufacturer-specified species were detected in relatively high abundance in two of the products while a few or none of the specified species were detected in some products. A number of unspecified microbes were detected, including potential human and crop pathogens such as Alcaligenes, Clostridium, Escherichia-Shigella and Proteus. The functional prediction unravelled high prevalence of enzyme-coding genes such as nitrogenase, NifT, alkaline phosphatase and reductases of nitric oxide, nitrate and nitrite which contribute to nitrogen-fixation, phosphorus solubilisation and degradation of nitrates and nitrites. In addition, toxins such as leukocidin/hemolysin and colicin V protein that cause product quality damage were highly predicted in over 67% of the products. Overall, high-throughput sequence analysis of bacterial communities in biofertiliser products revealed that majority of the products were of poor quality. This result justifies the need for regular quality assessment and improvement in quality control systems during biofertiliser formulation.

SUBMITTER: Raimi AR

PROVIDER: S-EPMC6391514 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment.

Raimi Adekunle R AR Ezeokoli Obinna T OT Adeleke Rasheed A RA

3 Biotech 20190227 3

The genetic and predicted functional diversity of bacterial communities in 12 commercial biofertiliser products were evaluated using high-throughput sequencing of the 16S rRNA gene. Proteobacteria, Firmicutes and Bacteroides dominated the bacterial communities, with the genera <i>Pseudomonas, Lactobacillus, Bacillus, Bradyrhizobium</i> and <i>Rhizobium</i> being prevalent. The manufacturer-specified species were detected in relatively high abundance in two of the products while a few or none of ...[more]

PMID: 30863692

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Project description:BACKGROUND: Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. RESULTS: Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional culture-dependent methods. CONCLUSIONS: The use of pyrosequencing allowed for the identification of low abundance bacteria in leaf salad vegetables not detected by culture-dependent methods. The presence of a range of bacterial populations as endophytes presents an interesting phenomenon as these microorganisms cannot be removed by washing and are thus ingested during salad consumption.

Project description:The importance of microbiota in the health and diseases of farm animals has been well-documented for diverse animal species. However, studies on microbiotas in turkey and turkey farms are relatively limited as compared to other farm animal species. In this study, we performed a comprehensive survey of the litter microbiotas in 5 commercial turkey farms in the Northwest Arkansas (H, M, V, K, and R farms) including one farm with positive incidence of cellulitis (R farm). Altogether 246 boot swabs were used for 16S rRNA gene profiling of bacterial communities. At phylum level, 11 major bacterial phyla (?0.01%) were recovered. At genus level, 13 major bacterial genera were found whose relative abundance were ?2%. The microbial composition at both phylum and genus levels as well as their diversities varied across different farms, which were further affected by different flocks within the same farms and the ages of turkeys. Generally, the Firmicutes were higher in the flocks of younger birds, while the Actinobacteria and Bacteroidetes were higher in the flocks of the older birds. The Proteobacteria were highly enriched (47.97%) in K farm housing 56-day-old turkeys (K-56), but Bacteroidetes were found the highest in the flock C of M farm housing 63-day-old turkeys (M-C-63; 22.38%), followed by K-84 group (17.26%). Four core bacterial genera (Staphylococcus, Brevibacterium, Brachybacterium, and Lactobacillus) were identified in all samples except for those from R farm. In contrast, 24 core bacterial genera were found based in all cellulitis-associated samples (R farm), including Corynebacterium, an unknown genus of family Bacillaceae, Clostridium sensu stricto 1 (>97% similarity with C. septicum), and Ignatzschineria among others, suggesting their possible roles in etiopathogenesis of cellulitis in turkeys. Overall results of this study may provide valuable foundation for future studies focusing on the role of microbiota in the health and diseases of turkeys.

Dataset Information

High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment.

Publications

High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment.

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