Literature DB >> 27403572

Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside.

Robyn A Barbato1, Natàlia Garcia-Reyero2, Karen Foley3, Robert Jones3, Zoe Courville4, Thomas Douglas5, Edward Perkins2, Charles M Reynolds5.   

Abstract

The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect conditions over vast time periods and investigation of biological materials harbored inside could provide insight of ancient environments. To appropriately analyze these ecosystems and extract meaningful biological information from frozen soils and ice, proper collection and processing of the frozen samples is necessary. This is especially critical for microbial and DNA analyses since the communities present may be so uniquely different from modern ones. Here, a protocol is presented to successfully collect and decontaminate frozen cores. Both the absence of the colonies used to dope the outer surface and exogenous DNA suggest that we successfully decontaminated the frozen cores and that the microorganisms detected were from the material, rather than contamination from drilling or processing the cores.

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Year:  2016        PMID: 27403572      PMCID: PMC4993323          DOI: 10.3791/54091

Source DB:  PubMed          Journal:  J Vis Exp        ISSN: 1940-087X            Impact factor:   1.355


  22 in total

1.  Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes.

Authors:  K Takai; K Horikoshi
Journal:  Appl Environ Microbiol       Date:  2000-11       Impact factor: 4.792

2.  Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.

Authors:  Mangala A Nadkarni; F Elizabeth Martin; Nicholas A Jacques; Neil Hunter
Journal:  Microbiology       Date:  2002-01       Impact factor: 2.777

3.  Life at the wedge: the activity and diversity of arctic ice wedge microbial communities.

Authors:  Roland C Wilhelm; Kristin J Radtke; Nadia C S Mykytczuk; Charles W Greer; Lyle G Whyte
Journal:  Astrobiology       Date:  2012-04       Impact factor: 4.335

4.  Phylogenetic analysis of bacteria preserved in a permafrost ice wedge for 25,000 years.

Authors:  Taiki Katayama; Michiko Tanaka; Jun Moriizumi; Toshio Nakamura; Anatoli Brouchkov; Thomas A Douglas; Masami Fukuda; Fusao Tomita; Kozo Asano
Journal:  Appl Environ Microbiol       Date:  2007-02-09       Impact factor: 4.792

5.  Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia.

Authors:  Dirk Wagner; Svenja Kobabe; Susanne Liebner
Journal:  Can J Microbiol       Date:  2009-01       Impact factor: 2.419

6.  Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.

Authors:  Eva Bellemain; Marie L Davey; Håvard Kauserud; Laura S Epp; Sanne Boessenkool; Eric Coissac; Jozsef Geml; Mary Edwards; Eske Willerslev; Galina Gussarova; Pierre Taberlet; James Haile; Christian Brochmann
Journal:  Environ Microbiol       Date:  2012-11-22       Impact factor: 5.491

7.  Biogeochemistry of methane and methanogenic archaea in permafrost.

Authors:  Elizaveta Rivkina; Viktoria Shcherbakova; Kestas Laurinavichius; Lada Petrovskaya; Kirill Krivushin; Gleb Kraev; Svetlana Pecheritsina; David Gilichinsky
Journal:  FEMS Microbiol Ecol       Date:  2007-04-11       Impact factor: 4.194

8.  Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge.

Authors:  Taiki Katayama; Tomoko Kato; Michiko Tanaka; Thomas A Douglas; Anatoli Brouchkov; Masami Fukuda; Fusao Tomita; Kozo Asano
Journal:  Int J Syst Evol Microbiol       Date:  2009-03       Impact factor: 2.747

9.  Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic.

Authors:  Blaire Steven; Wayne H Pollard; Charles W Greer; Lyle G Whyte
Journal:  Environ Microbiol       Date:  2008-12       Impact factor: 5.491

10.  Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas.

Authors:  Josselin Bodilis; Sandrine Nsigue-Meilo; Ludovic Besaury; Laurent Quillet
Journal:  PLoS One       Date:  2012-04-24       Impact factor: 3.240

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  4 in total

1.  Potential microbial contamination during sampling of permafrost soil assessed by tracers.

Authors:  Toke Bang-Andreasen; Morten Schostag; Anders Priemé; Bo Elberling; Carsten S Jacobsen
Journal:  Sci Rep       Date:  2017-02-23       Impact factor: 4.379

2.  A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.

Authors:  Vilma Pérez; Yichen Liu; Martha B Hengst; Laura S Weyrich
Journal:  Microorganisms       Date:  2022-08-10

3.  Meeting report of the third annual Tri-Service Microbiome Consortium symposium.

Authors:  J Philip Karl; Robyn A Barbato; Laurel A Doherty; Aarti Gautam; Sarah M Glaven; Robert J Kokoska; Dagmar Leary; Rebecca L Mickol; Matthew A Perisin; Andrew J Hoisington; Edward J Van Opstal; Vanessa Varaljay; Nancy Kelley-Loughnane; Camilla A Mauzy; Michael S Goodson; Jason W Soares
Journal:  Environ Microbiome       Date:  2020-07-13

4.  Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples.

Authors:  Alireza Saidi-Mehrabad; Patrick Neuberger; Maria Cavaco; Duane Froese; Brian Lanoil
Journal:  Sci Rep       Date:  2020-08-31       Impact factor: 4.379

  4 in total

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