The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis

FEMS Microbiology Ecology

Volumn 89, Issue 2, 2014, Pages 376-387

  Bowman, Jeff S ^a,b   Berthiaume, Chris T ^a,b   Armbrust, E Virginia ^a,b   Deming, Jody W ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Frost flower; Metagenomics; Rhizobiales

Indexed keywords

RHIZOBIALES;

BACTERIAL PROTEIN; ICE; RNA 16S;

ALPHAPROTEOBACTERIA; ARCTIC; ARTICLE; BACTERIAL CHROMOSOME; ECOSYSTEM; ENZYMOLOGY; FROST FLOWER; GENETICS; ICE COVER; METABOLISM; METAGENOME; METAGENOMICS; MICROBIOLOGY; MOLECULAR GENETICS; MOLECULAR TYPING; PHYLOGENY; PLASMID; RHIZOBIALES;

FROST FLOWER; METAGENOMICS; RHIZOBIALES;

ALPHAPROTEOBACTERIA; ARCTIC REGIONS; BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; ECOSYSTEM; ICE; ICE COVER; METAGENOME; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; PHYLOGENY; PLASMIDS; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY;

EID: 84905369553     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12331     Document Type: Article

References (48)

1. Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Alvarez-Aviles L, Simpson WR, Douglas TA, Sturm M, Perovich D & Domine F (2008) Frost flower chemical composition during growth and its implications for aerosol production and bromine activation. J Geophys Res 113: D21304.
3. Amachi S, Kamagata Y, Kanagawa T & Muramatsu Y (2001) Bacteria mediate methylation of iodine in marine and terrestrial environments. Appl Environ Microbiol 67: 2718-2722.
4. Aslam S, Underwood G, Kaartokallio H et al. (2012) Dissolved extracellular polymeric substances (dEPS) dynamics and bacterial growth during sea ice formation in an ice tank study. Polar Biol 35: 661-676.
5. Bairoch A, Bougueleret L, Altairac S et al. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37: D169-D174.
6. Beine H, Anastasio C, Domine F et al. (2012) Soluble chromophores in marine snow, seawater, sea ice and frost flowers near Barrow, Alaska. J Geophys Res 117: D00R15.
7. Bengtson P, Bastviken D & Öberg G (2012) Possible roles of reactive chlorine II: assessing biotic chlorination as a way for organisms to handle oxygen stress. Environ Microbiol 15: 991-1000.
8. Bidle KD & Azam F (2001) Bacterial control of silicon regeneration from diatom detritus: significance of bacterial ectohydrolases and species identity. Limnol Oceanogr 46: 1606-1623.
9. Boratyn GM, Schaffer A, Agarwala R, Altschul SF, Lipman DJ & Madden TL (2012) Domain enhanced lookup time accelerated BLAST. Biol Direct 7: 12.
10. Bordeleau L & Prévost D (1994) Nodulation and nitrogen fixation in extreme environments. Plant Soil 161: 115-125.
11. Bowman JS & Deming JW (2010) Elevated bacterial abundance and exopolymers in saline frost flowers with implications for atmospheric chemistry and microbial dispersal. Geophys Res Lett 37: L13501.
12. Bowman JS, Larose C, Vogel TM & Deming JW (2013) Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere. Environ Microbiol Rep 5: 575-582.
13. Douglas TA, Sturm M, Simpson WR, Brooks S, Lindberg SE & Perovich DK (2005) Elevated mercury measured in snow and frost flowers near Arctic sea ice leads. Geophys Res Lett 32: L04502.
14. Douglas TA, Domine F, Barret M et al. (2012) Frost flowers growing in the Arctic ocean-atmosphere-sea ice-snow interface: 1. Chemical composition. J Geophys Res 117: D00R09.
15. Downie JA (1998) Functions of rhizobial nodulation genes. The Rhizobiaceae (Spaink HP, Kondorosi A & Hooykaas PJJ, eds), pp. 387-402. Springer, the Netherlands.
16. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
17. Eicken H, Gradinger R, Gaylord A, Mahoney A, Rigor I & Melling H (2005) Sediment transport by sea ice in the Chukchi and Beaufort Seas: increasing importance due to changing ice conditions? Deep Sea Res Part II 52: 3281-3302.
18. Ewert M, Carpenter S, Colangelo-Lillis J & Deming J (2013) Bacterial and extracellular polysaccharide content of brine-wetted snow over Arctic winter first-year sea ice. J Geophys Res Oceans 18: 726-735.
19. Granfors A, Andersson M, Chierici M et al. (2013) Biogenic halocarbons in young Arctic sea ice and frost flowers. Mar Chem 155: 124-134.
20. Grossmann S & Dieckmann GS (1994) Bacterial standing stock, activity, and carbon production during formation and growth of sea ice in the Weddell Sea, Antarctica. Appl Environ Microbiol 60: 2746-2753.
21. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL & Armbrust EV (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335: 587-590.
22. Jasti S, Sieracki ME, Poulton NJ, Giewat MW & Rooney-Varga JN (2005) Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol 71: 3483-3494.
23. Kaczmarska I, Ehrman JM, Bates SS, Green DH, Léger C & Harris J (2005) Diversity and distribution of epibiotic bacteria on Pseudonitzschia multiseries (Bacillariophyceae) in culture, and comparison with those on diatoms in native seawater. Harmful Algae 4: 725-741.
24. Kazamia E, Czesnick H, Nguyen TTV et al. (2012) Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation. Environ Microbiol 14: 1466-1476.
25. Kempema E, Reimnitz E & Barnes PW (1989) Sea ice sediment entrainment and rafting in the Arctic. J Sediment Res 59: 308-317.
26. Li H & Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
27. López-Lara IM & Geiger O (2001) The nodulation protein NodG shows the enzymatic activity of an 3-oxoacyl-acyl carrier protein reductase. Mol Plant Microbe Interact 14: 349-357.
28. Makk J, Beszteri B, Ács É, Márialigeti K & Szabó K (2003) Investigations on diatom-associated bacterial communities colonizing an artificial substratum in the River Danube. Arch Hydrobiol 14: 249-265.
29. Matsen F, Kodner R & Armbrust EV (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538.
30. Meyer F, Paarmann D, D'Souza M et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
31. Møller A, Barkay T, Hansen M et al. (2013) Mercuric reductase genes (merA) and mercury resistance plasmids in High Arctic snow, freshwater and sea-ice brine. FEMS Microbiol Ecol 73: 2230-2238.
32. Moosvi AS, Mcdonald IR, Pearce DA, Kelly DP & Wood AP (2005) Molecular detection and isolation from Antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds. Syst Appl Microbiol 28: 541-554.
33. Nadalig T, Farhan M, Haque U, Roselli S & Schaller H (2011) Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. FEMS Microbiol Ecol 77: 438-448.
34. Patten CL & Glick BR (1996) Bacterial biosynthesis of indole-3-acetic acid. Can J Microbiol 42: 207-220.
35. Perovich DK & Richter-Menge JA (1994) Surface characteristics of lead ice. J Geophys Res 99: 16341-16350.
36. Poulain AJ, Ni Chadhain SM, Ariya PA et al. (2007) Potential for mercury reduction by microbes in the high Arctic. Appl Environ Microbiol 73: 2230-2238.
37. Price M, Dehal P & Arkin A (2010) FastTree 2 - Approximate maximum likelihood trees for large alignments. PLoS One 5: e9490.
38. Punta M, Coggill PC, Eberhardt RY et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301.
39. Rankin AM, Wolff EW & Martin S (2002) Frost flowers: implications for tropospheric chemistry and ice core interpretation. J Geophys Res 107: 4683-4695.
40. Rusch DB, Halpern AL, Sutton G et al. (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
41. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
42. Sievers F, Wilm A, Dineen D et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
43. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
44. Stevenson BS & Waterbury JB (2006) Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells. Biol Bull 210: 73-77.
45. Style RW & Worster MG (2009) Frost flower formation on sea ice and lake ice. Geophys Res Lett 36: L11501.
46. Welsh DT (2000) Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate. FEMS Microbiol Rev 24: 263-290.
47. Wilhelm L, Tripp HJ, Givan S, Smith D & Giovannoni S (2007) Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol Direct 2: 27.
48. Zerbino DR (2010) Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 31: 11.5.1-11.5.12.