Halomonas and Marinobacter ecotypes from hydrothermal vent, subseafloor and deep-sea environments

FEMS Microbiology Ecology

Volumn 75, Issue 1, 2011, Pages 123-133

  Kaye, Jonathan Z ^a   Sylvan, Jason B ^b   Edwards, Katrina J ^b   Baross, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Biogeography; Ecophysiology; Metal cycling

Indexed keywords

BACTERIAL DNA; RNA 16S; SEA WATER;

ADAPTIVE RADIATION; BACTERIUM; BIOGEOGRAPHY; CHEMOAUTOTROPHY; CLADISTICS; COLD TOLERANCE; DEEP SEA; DEPOSITION; ECOPHYSIOLOGY; ECOTYPE; GENETIC ANALYSIS; HABITAT TYPE; HYDROTHERMAL VENT; ION; PHENOTYPIC PLASTICITY; POPULATION DISTRIBUTION; SEAFLOOR; SEAMOUNT; SPECIES DIVERSITY; SULFIDE;

ARTICLE; BIODIVERSITY; CLASSIFICATION; COLD; ECOSYSTEM; GENE LIBRARY; GENETICS; GEOGRAPHY; HALOMONAS; ISOLATION AND PURIFICATION; MARINOBACTER; MICROBIOLOGY; PACIFIC OCEAN; PHYLOGENY;

BIODIVERSITY; COLD TEMPERATURE; DNA, BACTERIAL; ECOSYSTEM; GENE LIBRARY; GEOGRAPHY; HALOMONAS; MARINOBACTER; PACIFIC OCEAN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; WATER MICROBIOLOGY;

JUAN DE FUCA RIDGE; PACIFIC OCEAN;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; HALOMONAS; MARINOBACTER;

EID: 78650003333     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.00984.x     Document Type: Article

References (49)

1. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL & Polz MF (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
2. Alain K & Querellou J (2009) Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13: 583-594.
3. Arahal DR, Ludwig W, Schleifer KH & Ventosa A (2002) Phylogeny of the family Halomonadaceae based on 23S and 16S rDNA sequence analyses. Int J Syst Evol Micr 52: 241-249.
4. Butterfield DA, Jonasson IR, Massoth GJ, Feely RA, Roe KK, Embley RE, Holden JF, McDuff RE, Lilley MD & Delaney JR (1997) Seafloor eruptions and evolution of hydrothermal fluid chemistry. Philos T Roy Soc A 355: 369-386.
5. Campbell BJ, Engel AS, Porter ML & Takai K (2006) The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4: 458-468.
6. Cole JR, Chai B, Marsh TL et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
7. Cowen JP (2004) The microbial biosphere of sediment-buried oceanic basement. Res Microbiol 155: 497-506.
8. De La Haba RR, Arahal DR, Márquez MC & Ventosa A (2010) Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis. Int J Syst Evol Micr 60: 737-748.
9. DeSantis TZ, Hugenholtz P, Larsen N et al. (2006) Greengenes, a Chimera-Checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb 72: 5069-5072.
10. Edwards KJ (2004) Formation and degradation of seafloor hydrothermal sulfide deposits. Sulfur Biogeochemistry: Past and Present (Amend JA, Edwards KJ & Lyons T, eds), pp. 83-96. GSA Publications, Washington, DC.
11. Edwards KJ, Rogers DR, Wirsen CO & McCollom TM (2003) Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α- and γ-Proteobacteria from the deep sea. Appl Environ Microb 69: 2906-2913.
12. Fendrich C (1988) Halovibrio variabilis gen. nov. sp. nov., Pseudomonas halophila sp. nov. and a new halophilic aerobic coccoid Eubacterium from Great Salt Lake, Utah, USA. Syst Appl Microbiol 11: 36-43.
13. Giovannoni S & Stingl U (2007) The importance of culturing bacterioplankton in the 'omics' age. Nat Rev Microbiol 5: 820-826.
14. Hickford SJH, Küpper FC, Zhang G et al. (2004) Petrobactin sulfonate, a new siderophore produced by the marine bacterium Marinobacter hydrocarbonoclasticus. J Nat Prod 67: 1897-1899.
15. Homann VV, Edwards KJ, Webb EA & Butler A (2009a) Siderophores of Marinobacter aquaeolei: petrobactin and its sulfonated derivatives. Biometals 22: 565-571.
16. Homann VV, Sandy M, Tincu JA, Templeton A, Tebo BM & Butler A (2009b) Loihichelins A-F, a suite of amphiphilic siderophores produced by the marine bacterium Halomonas LOB-5. J Nat Prod 72: 884-888.
17. Huber JA, Butterfield DA & Baross JA (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microb 68: 1585-1594.
18. Huber JA, Butterfield DA & Baross JA (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol 43: 393-409.
19. Huber JA, Johnson HP, Butterfield DA & Baross JA (2006) Microbial life in ridge flank crustal fluids. Environ Microbiol 8: 88-99.
20. Huber JA, Welch DBM, Morrison HG et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
21. Hugenholtz P & Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Micr 53: 289-293.
22. James SR, Dobson SJ, Franzmann PD & McMeekin TA (1990) Halomonas meridiana, a new species of extremely halotolerant bacteria isolated from Antarctic saline lakes. Syst Appl Microbiol 13: 270-278.
23. Kaye JZ & Baross JA (2000) High incidence of halotolerant bacteria in Pacific hydrothermal-vent and pelagic environments. FEMS Microbiol Ecol 32: 249-260.
24. Kaye JZ & Baross JA (2004) Synchronous effects of temperature, hydrostatic pressure and salinity on growth, phospholipid profiles and protein patterns of four Halomonas species isolated from deep-sea hydrothermal-vent and sea-surface environments. Appl Environ Microb 70: 6220-6229.
25. Kaye JZ, Márquez MC, Ventosa A & Baross JA (2004) Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov., and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int J Syst Evol Micr 54: 499-511.
26. Kelley DS, Delaney JR & Yoerger DR (2001) Geology and venting characteristics of the Mothra hydrothermal field, Endeavour Segment, Juan de Fuca Ridge. Geology 29: 959-962.
27. Koeppel A, Perry EB, Sikorski J et al. (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. P Natl Acad Sci USA 105: 2504-2509.
28. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E & Goodfellow M, eds), pp. 115-175. John Wiley & Sons, New York.
29. Ludwig W, Strunk O, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
30. Martinez JS, Zhang GP, Holt PD, Jung H-T, Carrano CJ, Haygood MG & Butler A (2000) Self-assembling amphiphilic siderophores from marine bacteria. Science 287: 1245-1247.
31. Mata JA, Martínez-Cánovas J, Quesada E & Béjar V (2002) A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 25: 360-375.
32. Mehta MP, Butterfield DA & Baross JA (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microb 69: 960-970.
33. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA & Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
34. Okamoto T, Fujioka K & Naganuma T (2001) Phylogenetic similarity of aerobic gram-negative halophilic bacteria from a deep-sea hydrothermal mound and Antarctic habitats. Polar Biosci 14: 1-9.
35. Polz MF & Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microb 64: 3724-3730.
36. Porter KG & Feig YS (1980) The use of DAPI for identifying and counting microflora. Limnol Oceanogr 25: 943-948.
37. Rappé MS & Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
38. Rappé MS, Connon SA, Vergin KL & Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
39. Reddy GSN, Raghavan PUM, Sarita NB, Prakash JSS, Nagesh N, Delille D & Shivaji S (2003) Halomonas glaciei sp. nov. isolated from fast ice of Adelie Land, Antarctica. Extremophiles 7: 55-61.
40. Rogers DR, Santelli CM & Edwards KJ (2003) Geomicrobiology of deep-sea deposits: estimating community diversity from low-temperature seafloor rocks and minerals. Geobiology 1: 109-117.
41. Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL, Staudigel H & Edwards KJ (2008) Abundance and diversity of microbial life in ocean crust. Nature 453: 653-657.
42. Schrenk MO, Kelley DS, Delaney JR & Baross JA (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microb 69: 3580-3592.
43. Suzuki MT & Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microb 62: 625-630.
44. 4 production by a hyperthermophilic methanogen under high-pressure cultivation. P Natl Acad Sci USA 105: 10949-10954.
45. Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
46. Templeton AS, Staudigel H & Tebo BM (2005) Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi seamount. Geomicrobiol J 22: 127-139.
47. Thompson JR, Marcelino LA & Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
48. Yayanos AA & DeLong EF (1987) Deep-sea bacterial fitness to environmental temperatures and pressures. Current Perspectives in High Pressure Biology (Jannasch HW, Marquis RE & Zimmerman AM, eds), pp. 17-32. Academic Press, London.
49. ZoBell CE & Upham HC (1944) A list of marine bacteria including descriptions of sixty new species. Bull Scripps Inst Oceanogr 5: 239-292.