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Comparison of Two 16S rRNA Primers (V3-V4 and V4-V5) for Studies of Arctic Microbial Communities.

https://arctichealth.org/en/permalink/ahliterature306495
Source
Front Microbiol. 2021; 12:637526
Publication Type
Journal Article
Date
2021
Author
Eduard Fadeev
Magda G Cardozo-Mino
Josephine Z Rapp
Christina Bienhold
Ian Salter
Verena Salman-Carvalho
Massimiliano Molari
Halina E Tegetmeyer
Pier Luigi Buttigieg
Antje Boetius
Author Affiliation
Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
Source
Front Microbiol. 2021; 12:637526
Date
2021
Language
English
Publication Type
Journal Article
Abstract
Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3-V4 and V4-V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3-V4, and the phylum Planctomycetes by V4-V5). However, the V4-V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10-20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4-V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment.
PubMed ID
33664723 View in PubMed
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Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean.

https://arctichealth.org/en/permalink/ahliterature292161
Source
Front Microbiol. 2018; 9:1035
Publication Type
Journal Article
Date
2018
Author
Josephine Z Rapp
Mar Fernández-Méndez
Christina Bienhold
Antje Boetius
Author Affiliation
HGF-MPG Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
Source
Front Microbiol. 2018; 9:1035
Date
2018
Language
English
Publication Type
Journal Article
Abstract
In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (~400-500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (~1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future.
Notes
Cites: Bioinformatics. 2012 Jul 15;28(14):1823-9 PMID 22556368
Cites: Genome. 2003 Feb;46(1):48-50 PMID 12669795
Cites: Ann Rev Mar Sci. 2014;6:439-67 PMID 24015900
Cites: Appl Environ Microbiol. 2006 Apr;72(4):2637-43 PMID 16597968
Cites: Front Microbiol. 2017 Jan 19;8:27 PMID 28154558
Cites: Environ Microbiol. 2012 Jan;14(1):4-12 PMID 22004523
Cites: Appl Environ Microbiol. 2015 Mar;81(6):2137-48 PMID 25595764
Cites: Int J Syst Evol Microbiol. 2001 Jul;51(Pt 4):1235-43 PMID 11491319
Cites: ISME J. 2010 Apr;4(4):564-76 PMID 20010630
Cites: Biotechnol Adv. 2016 Jan-Feb;34(1):14-29 PMID 26657897
Cites: Environ Microbiol. 2013 May;15(5):1262-74 PMID 23419081
Cites: Bioinformatics. 2014 Mar 1;30(5):614-20 PMID 24142950
Cites: Int J Syst Evol Microbiol. 2015 Mar;65(Pt 3):915-9 PMID 25563909
Cites: Science. 2012 May 4;336(6081):608-11 PMID 22556258
Cites: Microb Ecol. 2002 Apr;43(3):315-28 PMID 12037610
Cites: PLoS One. 2013 Oct 16;8(10):e76599 PMID 24204642
Cites: Nucleic Acids Res. 2013 Jan 7;41(1):e1 PMID 22933715
Cites: FEMS Microbiol Ecol. 2014 Oct;90(1):115-25 PMID 25041280
Cites: Environ Microbiol. 2016 May;18(5):1403-14 PMID 26271760
Cites: ISME J. 2009 Jul;3(7):860-9 PMID 19322244
Cites: Appl Environ Microbiol. 2002 Jan;68(1):316-25 PMID 11772641
Cites: Polar Biol. 2015;38(5):719-731 PMID 26257467
Cites: Appl Environ Microbiol. 2000 Jul;66(7):2888-97 PMID 10877783
Cites: PLoS One. 2014 Jan 31;9(1):e86887 PMID 24497990
Cites: PLoS One. 2011;6(11):e27492 PMID 22096583
Cites: Nat Biotechnol. 2011 May;29(5):415-20 PMID 21552244
Cites: PLoS One. 2014 Sep 10;9(9):e107452 PMID 25208058
Cites: Nat Rev Microbiol. 2014 Oct;12(10):686-98 PMID 25134618
Cites: J Phycol. 2013 Apr;49(2):229-40 PMID 27008512
Cites: Bioinformatics. 2014 Aug 1;30(15):2114-20 PMID 24695404
Cites: Appl Environ Microbiol. 2003 Nov;69(11):6610-9 PMID 14602620
Cites: Science. 2013 Mar 22;339(6126):1430-2 PMID 23413190
Cites: Environ Microbiol. 2008 Sep;10(9):2444-54 PMID 18557769
Cites: Mol Ecol. 2010 Mar;19 Suppl 1:21-31 PMID 20331767
Cites: Nucleic Acids Res. 2010 Aug;38(15):e155 PMID 20547594
Cites: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6 PMID 23193283
Cites: FEMS Microbiol Ecol. 2006 Sep;57(3):442-51 PMID 16907758
Cites: Front Microbiol. 2015 Aug 04;6:771 PMID 26300854
Cites: ISME J. 2016 Apr;10 (4):979-89 PMID 26430855
Cites: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-8 PMID 16043709
Cites: Environ Microbiol. 2015 Oct;17(10):3466-80 PMID 24612402
Cites: Front Microbiol. 2017 Sep 08;8:1696 PMID 28943866
Cites: Science. 2015 May 22;348(6237):1262073 PMID 25999517
Cites: FEMS Microbiol Ecol. 2005 Mar 1;52(1):79-92 PMID 16329895
Cites: Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17633-8 PMID 23045668
Cites: Appl Environ Microbiol. 2004 Nov;70(11):6753-66 PMID 15528542
Cites: Appl Environ Microbiol. 2003 May;69(5):2463-83 PMID 12732511
Cites: Appl Environ Microbiol. 2004 Feb;70(2):781-9 PMID 14766555
Cites: Appl Environ Microbiol. 1998 Jul 1;64(7):2691-6 PMID 9647850
Cites: ISME J. 2011 Jan;5(1):8-19 PMID 20596072
Cites: PLoS One. 2011;6(9):e24570 PMID 21931760
Cites: Nat Rev Microbiol. 2015 Nov;13(11):677-90 PMID 26344407
Cites: Appl Environ Microbiol. 1999 Jan;65(1):251-9 PMID 9872786
Cites: Int J Syst Bacteriol. 1997 Jul;47(3):670-7 PMID 9226898
Cites: Science. 2016 Nov 11;354(6313):747-750 PMID 27811286
Cites: ISME J. 2016 Oct;10 (10 ):2543-52 PMID 26882269
Cites: J Food Prot. 2002 Aug;65(8):1240-7 PMID 12182474
Cites: Int J Syst Evol Microbiol. 2010 Aug;60(Pt 8):1958-61 PMID 19801396
Cites: FEMS Microbiol Ecol. 2007 Dec;62(3):242-57 PMID 17991018
Cites: ISME J. 2012 Jan;6(1):11-20 PMID 21716307
Cites: Environ Microbiol. 2010 May;12(5):1132-43 PMID 20132284
Cites: ISME J. 2017 Feb;11(2):362-373 PMID 27648811
Cites: ISME J. 2016 Sep;10 (9):2158-73 PMID 26953597
Cites: Environ Microbiol. 2005 Jun;7(6):860-73 PMID 15892705
Cites: Environ Microbiol. 2007 May;9(5):1219-32 PMID 17472636
Cites: PeerJ. 2015 Dec 10;3:e1420 PMID 26713226
Cites: Environ Microbiol. 2013 May;15(5):1302-17 PMID 23126454
Cites: Science. 2009 Oct 23;326(5952):539 PMID 19900890
Cites: ISME J. 2013 Apr;7(4):685-96 PMID 23190727
Cites: Appl Environ Microbiol. 2001 Feb;67(2):632-45 PMID 11157226
Cites: Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):866-71 PMID 18398184
PubMed ID
29875749 View in PubMed
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Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments.

https://arctichealth.org/en/permalink/ahliterature280896
Source
Front Microbiol. 2017;8:266
Publication Type
Article
Date
2017
Author
Katy Hoffmann
Christiane Hassenrück
Verena Salman-Carvalho
Moritz Holtappels
Christina Bienhold
Source
Front Microbiol. 2017;8:266
Date
2017
Language
English
Publication Type
Article
Abstract
Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.
Notes
Cites: Front Microbiol. 2016 Mar 23;7:28427047451
Cites: Bioinformatics. 2012 Jul 15;28(14):1823-922556368
Cites: Nat Rev Microbiol. 2007 Oct;5(10):770-8117828281
Cites: Appl Environ Microbiol. 1985 Oct;50(4):1002-616346897
Cites: FEMS Microbiol Ecol. 2004 Jun 1;48(3):357-6719712305
Cites: PLoS One. 2013 Sep 02;8(9):e7277924023770
Cites: ISME J. 2012 Apr;6(4):724-3222071347
Cites: ISME J. 2012 Sep;6(9):1740-822378534
Cites: Environ Microbiol. 2011 May;13(5):1138-5221176054
Cites: Biophys Chem. 2013 Dec 15;183:30-4123891571
Cites: Annu Rev Microbiol. 2000;54:49-7911018124
Cites: Antonie Van Leeuwenhoek. 2011 Oct;100(3):421-3521671195
Cites: Appl Microbiol Biotechnol. 2012 Mar;93(5):1805-1522290643
Cites: Bioinformatics. 2014 Mar 1;30(5):614-2024142950
Cites: J Bacteriol. 1998 Apr;180(7):1750-89537371
Cites: Science. 2012 May 4;336(6081):608-1122556258
Cites: J Ind Microbiol Biotechnol. 1999 Oct;23(4-5):268-27211423943
Cites: Int J Syst Evol Microbiol. 2004 Sep;54(Pt 5):1773-8815388743
Cites: Appl Environ Microbiol. 2004 Jun;70(6):3321-815184127
Cites: FEMS Microbiol Ecol. 2005 Feb 1;51(3):341-5216329882
Cites: Nucleic Acids Res. 2013 Jan 7;41(1):e122933715
Cites: Int J Syst Evol Microbiol. 2002 May;52(Pt 3):901-1112054256
Cites: Environ Microbiol. 2009 Dec;11(12):3140-5319694787
Cites: ISME J. 2015 Jun;9(6):1410-2225478683
Cites: PeerJ. 2014 Sep 25;2:e59325276506
Cites: Biotechnol Prog. 2011 May-Jun;27(3):597-61321452192
Cites: Appl Environ Microbiol. 1982 May;43(5):1116-2416346008
Cites: Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):33-716403863
Cites: Appl Environ Microbiol. 1999 Aug;65(8):3721-610427073
Cites: PLoS One. 2010 Feb 08;5(2):e910920174598
Cites: BMC Genomics. 2016 Feb 04;17 :9326847793
Cites: Bioinformatics. 2014 Aug 1;30(15):2114-2024695404
Cites: Stand Genomic Sci. 2011 Apr 29;4(2):221-3221677859
Cites: Appl Environ Microbiol. 1990 Feb;56(2):352-62306088
Cites: Science. 2013 Mar 22;339(6126):1430-223413190
Cites: Biom J. 2008 Jun;50(3):346-6318481363
Cites: Int J Syst Evol Microbiol. 2004 Sep;54(Pt 5):1627-3115388720
Cites: Biofouling. 2012;28(6):593-60422703021
Cites: Ann Rev Mar Sci. 2011;3:401-2521329211
Cites: Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):183-825316694
Cites: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-816043709
Cites: Microbiome. 2014 May 05;2:1524910773
Cites: Genome Res. 2005 Oct;15(10):1325-3516169927
Cites: Int J Syst Evol Microbiol. 2005 Jul;55(Pt 4):1511-2016014474
Cites: Can J Microbiol. 1962 Apr;8:229-3913902807
Cites: Microb Cell Fact. 2011 Nov 01;10:8822040376
Cites: Int J Syst Evol Microbiol. 2003 Mar;53(Pt 2):539-4512710624
Cites: J Bacteriol. 2012 Oct;194(19):5452-322965082
Cites: PLoS One. 2011;6(9):e2457021931760
Cites: Proc Natl Acad Sci U S A. 1986 Dec;83(24):9542-616593790
Cites: BMC Genomics. 2008 May 06;9:21018460197
Cites: Environ Microbiol. 2000 Aug;2(4):383-811234926
Cites: PLoS Genet. 2008 May 30;4(5):e100008718516288
Cites: Int J Syst Evol Microbiol. 2006 May;56(Pt 5):1001-716627645
Cites: FEMS Microbiol Lett. 1999 Jan 1;170(1):271-99919678
Cites: Extremophiles. 2016 Mar;20(2):227-3426847199
Cites: Elife. 2016 Apr 07;5:e1188827054497
Cites: Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2185-9015545456
Cites: Ecology. 2007 Jun;88(6):1354-6417601128
Cites: PLoS One. 2016 Jan 27;11(1):e014801626814838
Cites: Nature. 2003 Aug 14;424(6950):763-612917681
Cites: Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):821-923633591
Cites: Microb Ecol. 1994 Sep;28(2):209-2124186448
Cites: Appl Environ Microbiol. 2011 Aug 15;77(16):5697-70621705522
PubMed ID
28286496 View in PubMed
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