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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Bibliographic Details
Published in:Journal of applied microbiology Vol. 116; no. 5; pp. 1181 - 1194
Main Authors: Tkachuk, V.L, Krause, D.O, Knox, N.C, Hamm, A.C, Zvomuya, F, Ominski, K.H, McAllister, T.A
Format: Journal Article
Language:English
Published: Oxford Published for the Society for Applied Bacteriology by Blackwell Science 01.05.2014
Blackwell
Oxford University Press
Subjects:
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
Online Access:Get full text
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Summary: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.
Bibliography:http://dx.doi.org/10.1111/jam.12449
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ISSN:1364-5072
1365-2672
1365-2672
DOI:10.1111/jam.12449