Phylotype diversity in a benthic cyanobacterial mat community on King George Island, maritime Antarctica

Callejas, Cecilia; Gill, Paul R.; Catalán, Ana Inés; Azziz, Gastón; Castro‐Sowinski, Susana; Batista, Silvia

doi:10.1007/s11274-010-0578-1

Cited by 15 publications

(8 citation statements)

References 18 publications

(22 reference statements)

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“…not using commercial kits) were used in the majority of studies (e.g. Callejas et al 2011;Barberan & Casamayor 2014;Mao et al 2014) DNA in a number of studies, but only twice since 2014 (Merlin et al 2014;Wasaki et al 2015).…”

Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

“…Pansu et al 2015b) or biofilm samples (Callejas et al 2011;Zimmermann et al 2015; see Table S3 in Supplementary Material). These water column studies targeted a broad range of taxa including prokaryotes (e.g.…”

Section: Study Environmentsmentioning

confidence: 99%

“…Stoeck et al 2010;Thomsen et al 2012a;Calvignac-Spencer et al 2013) and the Promega Wizard SV Gel and PCR Clean-Up system (e.g. Bhadury & Austen 2010;Callejas et al 2011;Keskin 2014). The AMPure XP method was used only in high-throughput sequencing studies and the Promega Wizard system only in Sanger sequencing studies, whereas the Qiagen MinElute method was used for a range of applications.…”

Section: Summary Of Pcr Product Purification Approachesmentioning

confidence: 99%

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Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

Section: Study Environmentsmentioning

confidence: 99%

Section: Summary Of Pcr Product Purification Approachesmentioning

confidence: 99%

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Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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“…, Table S2), the specific organisms present in a mat may vary considerably. Certain groups are regularly detected in Antarctic mats: Cyanobacteria , particularly members of the Oscillatoriales such as Leptolyngbya and Phormidium , and the Nostocales (Taton et al ., ; Jungblut et al ., ; Taton et al ., ; Fernández‐Valiente et al ., ; Sutherland, ; Borghini et al ., ; Verleyen et al ., ; Anderson et al ., ; Callejas et al ., ; Fernandez‐Carazo et al ., ), Proteobacteria , the CFB group, Actinobacteria , and Firmicutes (Brambilla et al ., ; Van Trappen et al ., ; Peeters et al ., ; Antibus et al ., ; Varin et al ., ). Less commonly reported are Deinococcus‐Thermus , Planctomycetes , Verrucomicrobiales , and others (Brambilla et al ., ; Antibus et al ., ; Peeters et al ., ; Varin et al ., ).…”

Section: Antarctic Lakesmentioning

confidence: 99%

Key microbial drivers in Antarctic aquatic environments

et al. 2013

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Antarctica is arguably the world's most important continent for influencing the Earth's climate and ocean ecosystem function. The unique physico-chemical properties of the Southern Ocean enable high levels of microbial primary production to occur. This not only forms the base of a significant fraction of the global oceanic food web, but leads to the sequestration of anthropogenic CO2 and its transport to marine sediments, thereby removing it from the atmosphere; the Southern Ocean accounts for ~ 30% of global ocean uptake of CO2 despite representing ~ 10% of the total surface area of the global ocean. The Antarctic continent itself harbors some liquid water, including a remarkably diverse range of surface and subglacial lakes. Being one of the remaining natural frontiers, Antarctica delivers the paradox of needing to be protected from disturbance while requiring scientific endeavor to discover what is indigenous and learn how best to protect it. Moreover, like many natural environments on Earth, in Antarctica, microorganisms dominate the genetic pool and biomass of the colonizable niches and play the key roles in maintaining proper ecosystem function. This review puts into perspective insight that has been and can be gained about Antarctica's aquatic microbiota using molecular biology, and in particular, metagenomic approaches.

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“…As in the present study, the cyanobacteria genes aligned to freshwater polar strains (Jungblut et al ., 2010). In another study of benthic mat samples from the Antarctic Peninsula, it was also shown that the recovered cyanobacterial diversity matched closely to other Antarctic terrestrial cyanobacteria (Callejas et al ., 2011).…”

Section: Primers Used In This Studymentioning

confidence: 60%

The origin of cyanobacteria in Antarctic sea ice: marine or freshwater?

Koh

Cowie

Simpson

et al. 2012

Environ Microbiol Rep

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Cyanobacteria play an important role in the primary productivity of many ecosystems and are dominant in non-marine polar environments. Apart from detecting low levels of cyanobacteria-like pigments in the Southern Ocean, little effort has been spent in trying to elucidate Cyanobacteria in Antarctic sea ice. Here, we report the first use of culture, microscope, microarray and molecular techniques to show that marine Cyanobacteria are rare or absent in sea ice. Our infrequent positive signals were most closely related to freshwater Cyanobacteria from neighbouring terrestrial sources, which illustrates our techniques were sensitive enough to find sea-ice cyanobacteria if they were present. It is still possible that minute quantity of marine cyanobacteria may exist in sea ice and do not contribute significantly to the polar marine ecosystems.

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Phylotype diversity in a benthic cyanobacterial mat community on King George Island, maritime Antarctica

Cited by 15 publications

References 18 publications

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Key microbial drivers in Antarctic aquatic environments

The origin of cyanobacteria in Antarctic sea ice: marine or freshwater?

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