title: Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester.
abstract: The applicability of a newly-designed PCR primer pair in examination of methanogenic Archaea in a digester treating plant biomass was evaluated by Ribosmal Intergenic Spacer Analysis (RISA). To find a suitable approach, three variants of RISA were tested: (1) standard, polyacrylamide gel-based, (2) automated, utilized capillary electrophoresis (GA-ARISA), and (3) automated microfluidics-based (MF-ARISA). All three techniques yielded a consistent picture of archaeal community structure changes during anaerobic digestion monitored for more than 6 weeks. While automated variants were more practical for handling and rapid analysis of methanogenic Archaea, the gel-based technique was advantageous when micro-organism identification was required. A DNA-sequence analysis of dominant bands extracted from the gel revealed that the main role in methane synthesis was played by micro-organisms affiliated with Methanosarcina barkeri. The obtained results revealed that RISA is a robust method allowing for detailed analysis of archaeal community structure during organic biomass conversion into biogas. In addition, our results showed that GA-ARISA has a higher resolution and reproducibility than other variants of RISA and could be used as a technique for tracking changes in methanogenic Archaea in an anaerobic digester.
authors.affiliation: Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland. slavcm@uwm.edu.pl
authors.forename: Slawomir
authors.initials: S
authors.lastname: Ciesielski
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Bułkowska
authors.forename: Dorota
authors.initials: D
authors.lastname: Dabrowska
authors.forename: Dariusz
authors.initials: D
authors.lastname: Kaczmarczyk
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Kowal
authors.forename: Justyna
authors.initials: J
authors.lastname: Możejko
mesh_terms: D000693:Anaerobiosis; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D019149:Bioreactors; D017931:DNA Primers / Q000235:genetics; D019641:DNA, Archaeal / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D000455:Medicago sativa / Q000378:metabolism / Q000382:microbiology; D008697:Methane / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S; D003313:Zea mays / Q000378:metabolism / Q000382:microbiology
chemical_list: D017931:DNA Primers; D019641:DNA, Archaeal; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S; D008697:Methane