Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure

• Published in: FEMS microbiology ecology Vol. 70; no. 3; pp. 540 - 552
• Main Authors: Talbot, Guylaine, Roy, Caroline S., Topp, Edward, Beaulieu, Carole, Palin, Marie-France, Massé, Daniel I.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.12.2009; Blackwell; Oxford University Press
• Subjects: Animal, plant and microbial ecology; Animals; Archaea; Archaea - classification; Archaea - genetics; Bacteria; Bacteria - classification; Bacteria - genetics; Biological and medical sciences; Cluster Analysis; Clustering; Communities; Community structure; DNA Fingerprinting; DNA, Archaeal - genetics; DNA, Bacterial - genetics; Ecology; Fingerprinting; Fingerprints; Fundamental and applied biological sciences. Psychology; Heterogeneity; Hogs; Indicator species; length heterogeneity PCR (LH‐PCR); Manure - microbiology; Manures; Microbial activity; Microbial ecology; Microbiology; Microbiomes; Microorganisms; Multivariate Analysis; multivariate statistics; Permutations; Pig manure; Polymerase Chain Reaction; Polymorphism; Polymorphism, Restriction Fragment Length; Populations; Principal Component Analysis; Principal components analysis; Restriction fragment length polymorphism; Reverse transcription; RNA, Archaeal - genetics; RNA, Bacterial - genetics; rRNA; Samples; Sequence Analysis, DNA; Slurries; Species diversity; Statistical analysis; Statistical methods; Statistics; Swine; Swine - microbiology; swine manure microbial population; terminal restriction fragment length polymorphism (T‐RFLP); Various environments (extraatmospheric space, air, water); length heterogeneity PCR (LH-PCR); swine manure microbial population; terminal restriction fragment length polymorphism (T-RFLP); multivariate statistics; Statistical analysis; Ribosomal DNA; Genotype; Gonadotropin; Multivariate analysis; Polymerase chain reaction; Pig manure; Heterogeneity; Restriction fragment length polymorphism; Adenohypophyseal hormone; Ribosomal RNA; Fingerprint method; Luteinizing hormone; Microorganism; Microbial community
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/j.1574-6941.2009.00749.x

Abstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and finishing pigs were characterized using a combination of amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP), using PCR primers targeting Bacteria and Archaea, respectively. Unweighted pair group method with arithmetic mean clustering, principal components analysis (PCA), indicator species analysis (ISA), and diversity analyses showed that rRNA-based fingerprinting methods [reverse transcription (RT)-LH-PCR and RT-T-RFLP] were more effective than rDNA-based fingerprinting methods for distinguishing the manure samples. Multiresponse permutation procedure from fingerprint data showed that all manure samples had distinct microbial communities. PCA and ISA showed that the major phylotypes differentiating the LH-PCR or the RT-LH-PCR profiles were distributed differently between manures, suggesting that the bacterial community structure was different from the metabolically active bacterial community. The detection of minor archaeal populations was greater using RT-T-RFLP instead of T-RFLP. The findings indicated that the analysis of microbial community rRNAs could differentiate each manure sample from the others and would be appropriate for the monitoring of metabolically active populations.