Targeted 16S rRNA high‐throughput sequencing to characterize microbial communities during composting of livestock mortalities

AIM: A comprehensive understanding of the microbial community is necessary to ensure a significant reduction in pathogens during the composting process. METHODS AND RESULTS: Two biosecure, static composting systems containing cattle mortalities were constructed at subzero temperatures. Temperature a...

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Veröffentlicht in:	Journal of applied microbiology Jg. 116; H. 5; S. 1181 - 1194
Hauptverfasser:	Tkachuk, V.L, Krause, D.O, Knox, N.C, Hamm, A.C, Zvomuya, F, Ominski, K.H, McAllister, T.A
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Oxford Published for the Society for Applied Bacteriology by Blackwell Science 01.05.2014 Blackwell Oxford University Press
Schlagworte:	16S rRNA Actinomycetales Animals Bacteria - classification Bacteria - genetics Bacteria - isolation & purification bacterial communities Biological and medical sciences Cattle Clostridiaceae Clostridiales Clostridium compost Composting Composts Environmental Microbiology Firmicutes Fundamental and applied biological sciences. Psychology High-Throughput Nucleotide Sequencing Inactivation Livestock Microbial activity microbial community Microbiology Microenvironments mortalities Pathogens Pathology pyrosequencing Ribonucleic acid ribosomal RNA RNA RNA, Ribosomal, 16S - genetics Sequence Analysis, RNA Soil spatial variability spores Temperature Thermobifida thermophilic thermophilic Compost 16S rRNA mortalities Targeting Applied microbiology Mortality Thermophily cattle Spatial variation Target Composting High throughput sequencing Ribosomal RNA spatial variability Pyrosequencing 16S-RNA Livestock Microbial community microbial community compost pyrosequencing
ISSN:	1364-5072, 1365-2672, 1365-2672
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Zusammenfassung:	AIM: A comprehensive understanding of the microbial community is necessary to ensure a significant reduction in pathogens during the composting process. METHODS AND RESULTS: Two biosecure, static composting systems containing cattle mortalities were constructed at subzero temperatures. Temperature at each sampling site was measured continuously and samples were grouped as either ≤50 or ≥55°C, based on temperature exposure required for effective pathogen inactivation during composting. High‐throughput 454 sequencing was used to characterize the bacterial communities within each sample. Clustering of bacterial communities was observed according to temperature. However, neither richness nor diversity differed between temperature groups. Firmicutes was the most abundant phylum within both temperature groups but was more pronounced (63·6%) in samples ≥55°C (P < 0·05). Similarly, members of Clostridia, Clostridium sensu stricto (3·64%), Clostridium XI (0·59%), UF (Clostridiaceae 1) (5·29%) and UF (Clostridiales Incertae Sedis XI) (6·20%), were prominent at ≥55°C (P < 0·05), likely a reflection of spore survival and/or anaerobic microenvironments within passively aerated compost piles. Members of Thermobifida (3·54%), UO (Actinomycetales) (12·29%) and UO (Bacillales) (19·49%) were also prominent at ≥55°C (P < 0·05). CONCLUSION: Substantial spatial diversity exists within bacterial communities in field‐scale compost piles. Localized temperature at the site of sampling may be one of the factors contributing to this phenomenon. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to describe the microbial community profile with the use of targeted 16S rRNA high‐throughput sequencing in passively aerated composted livestock mortalities.
Bibliographie:	http://dx.doi.org/10.1111/jam.12449 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1364-5072 1365-2672 1365-2672
DOI:	10.1111/jam.12449