PMID- 29071172 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20200930 IS - 2190-572X (Print) IS - 2190-5738 (Electronic) IS - 2190-5738 (Linking) VI - 7 IP - 6 DP - 2017 Dec TI - Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples. PG - 375 LID - 10.1007/s13205-017-1009-x [doi] LID - 375 AB - The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods. In spite of the non-kit based method (cetyltrimethylammonium bromide) yielding the largest quantity of DNA (approximately 44 microg DNA per gram dry weight), the extracted DNA contained PCR inhibitors. Furthermore, the quantity of extracted DNA was not proportional to species diversity. Diversity, determined using denaturing gradient gel electrophoresis (DGGE), was strongly linked to the type of extraction method used. The spin-column filter-based kit that incorporated mechanical and chemical lysis (Macherey-Nagel kit) gave the best results in terms of bacterial and archaeal diversity (Shannon-Wiener indices: average 2.5 and 2.6, respectively). Furthermore, this kit was the most effective at lysing hard-to-lyse bacterial and archaeal cells. The choice of DNA extraction method significantly influences the reliability and comparability of results obtained during AD microbial ecology investigations. Moreover, the careful selection of the DNA extraction method is of particular importance when analysing AD samples since these samples are rich in PCR inhibitors and hard-to-lyse cells such as archaea and gram-positive bacteria. FAU - Roopnarain, Ashira AU - Roopnarain A AD - Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil Climate and Water, Arcadia, Pretoria, 0001 South Africa. ISNI: 0000 0004 0367 7367. GRID: grid.463098.0 FAU - Mukhuba, Mashudu AU - Mukhuba M AD - Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil Climate and Water, Arcadia, Pretoria, 0001 South Africa. ISNI: 0000 0004 0367 7367. GRID: grid.463098.0 AD - Department of Life and Consumer Sciences, College of Agriculture and Environmental Science, UNISA, P. O. Box 329, Pretoria, South Africa. ISNI: 0000 0004 0610 3238. GRID: grid.412801.e FAU - Adeleke, Rasheed AU - Adeleke R AUID- ORCID: 0000-0002-8974-422X AD - Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil Climate and Water, Arcadia, Pretoria, 0001 South Africa. ISNI: 0000 0004 0367 7367. GRID: grid.463098.0 AD - Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, Potchefstroom, 2520 South Africa. ISNI: 0000 0000 9769 2525. GRID: grid.25881.36 FAU - Moeletsi, Mokhele AU - Moeletsi M AD - Agricultural Research Council-Institute for Soil, Climate and Water, 600, Belvedere Street, Arcadia, Pretoria, 0083 South Africa. ISNI: 0000 0004 0367 7367. GRID: grid.463098.0 LA - eng PT - Journal Article DEP - 20171023 PL - Germany TA - 3 Biotech JT - 3 Biotech JID - 101565857 PMC - PMC5653670 OTO - NOTNLM OT - Anaerobic digestion OT - Archaea OT - Bacteria OT - DNA extraction OT - Diversity EDAT- 2017/10/27 06:00 MHDA- 2017/10/27 06:01 PMCR- 2018/12/01 CRDT- 2017/10/27 06:00 PHST- 2017/03/25 00:00 [received] PHST- 2017/10/09 00:00 [accepted] PHST- 2017/10/27 06:00 [entrez] PHST- 2017/10/27 06:00 [pubmed] PHST- 2017/10/27 06:01 [medline] PHST- 2018/12/01 00:00 [pmc-release] AID - 1009 [pii] AID - 10.1007/s13205-017-1009-x [doi] PST - ppublish SO - 3 Biotech. 2017 Dec;7(6):375. doi: 10.1007/s13205-017-1009-x. Epub 2017 Oct 23.