Open AccessCommercial DNA extraction kits impact observed microbial community composition in permafrost samples
Author(s) -
Vishnivetskaya Tatiana A.,
Layton Alice C.,
Lau Maggie C. Y.,
Chauhan Archana,
Cheng Karen R.,
Meyers Arthur J.,
Murphy Jasity R.,
Rogers Alexandra W.,
Saarunya Geetha S.,
Williams Daniel E.,
Pfiffner Susan M.,
Biggerstaff John P.,
Stackhouse Brandon T.,
Phelps Tommy J.,
Whyte Lyle,
Sayler Gary S.,
Onstott Tullis C.
Publication year - 2014
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/1574-6941.12219
Subject(s) - biology , permafrost , dna extraction , dna , microbial population biology , extraction (chemistry) , composition (language) , ecology , bacteria , polymerase chain reaction , genetics , chromatography , gene , linguistics , chemistry , philosophy
The total community genomic DNA (g DNA ) from permafrost was extracted using four commercial DNA extraction kits. The g DNA s were compared using quantitative real‐time PCR (q PCR ) targeting 16 S r RNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16 S r RNA ( V 3 region) amplified in single or nested PCR . The F ast DNA ® SPIN ( FDS ) K it provided the highest g DNA yields and 16 S r RNA gene concentrations, followed by M o B io P ower S oil ® ( PS ) and M o B io P ower L yzer™ ( PL ) kits. The lowest g DNA yields and 16 S r RNA gene concentrations were from the M eta‐ G ‐ N ome™ ( MGN ) DNA I solation K it. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by A ctinobacteria , F irmicutes , G emmatimonadetes , P roteobacteria , and A cidobacteria . Weighted U ni F rac and statistical analyses indicated that bacterial community compositions derived from FDS , PS , and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β‐ and γ‐ P roteobacteria and lower proportions of A ctinobacteria and M ethylocystaceae important in carbon cycling. These results indicate that g DNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using g DNA s from the three bead‐beating lysis extraction kits.