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Keywords:

  • Ushuaia;
  • sub-Antarctica;
  • bacterial biodiversity;
  • 16S rRNA gene clones;
  • psychrophiles

Abstract

Bacterial diversity in sub-Antarctic seawater, collected off Ushuaia, Argentina, was examined using a culture independent approach. The composition of the 16S rRNA gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (P value 0.001). In both libraries, clones representing the Alphaproteobacteria, Gammaproteobacteria, the Cytophaga–Flavobacterium–Bacteroidetes group and unculturable bacteria were dominant. Clones associated with the genera Roseobacter, Sulfitobacter, Staleya, Glaciecola, Colwellia, Marinomonas, Cytophaga and Cellulophaga were common to both the libraries. However, clones associated with Psychrobacter, Arcobacter, Formosa algae, Polaribacter, Ulvibacter and Tenacibaculum were found only in seawater contaminated with hydrocarbons (Table 1). Further, the percentage of clones of Roseobacter, Sulfitobacter and Glaceicola was high in seawater (43%, 90% and 12% respectively) compared to seawater contaminated with hydrocarbons (35%, 4% and 9% respectively). One of the clones F2C63 showed 100% similarity with Marinomonas ushuaiensis a bacterium identified by us from the same site.

Table 1.   Comparison of 16S rRNA gene clones of seawater and seawater contaminated with the water-soluble fraction (WSF) of crude oil collected off Ushuaia, Argentina, Sub-Antarctica
Phylogenetic neighbour and nucleotide accession numberClone number and nucleotide accession number
Seawater (120)Seawater contaminated with WSF of crude oil (104)
  1. The nucleotide accession numbers of the clones are given in round brackets. The percentage values within square brackets represent the percentage similarity of the 16S rRNA gene sequence of the clones with the nearest phylogenetic neighbour. The bold numericals in columns two and three indicate the number of clones in the particular class or genus. The clones which are in bold font represent unidentified and unculturable bacteria which have been assigned to the nearest phylogenetic neighbour based on their affiliations in the phylogenetic trees (Figs 1 and 2). The remaining clones which did not identify with any known phylogenetic neighbour are listed at the end of the table.

Class: Alphaproteobacteria6744
Roseobacter5136
Roseobacter sp. ANT909 (AY167254)F2C03A (AY794091), F2C05A (AY794093) F2C09A (AY794097), F2C14A (AY794099) F2C01 (AY794100), F2C14 (AY794117), F2C16 (AY794119), F2C17 (AY794120), F2C36 (AY794125), F2C31(AY794123), F2C37 (AY794126), F2C43 (AY697883), F2C67(AY794137), F2C74 (AY794144), F2C77 (AY794143), F2C81(AY794146), F2C86 (AY794147), F2C95 (AY697887), F2C97 (AY794148), F2C98 (AY697888), F4C21(AY794194), F4C14(AY697911), F4C28 (AY794199), F4C85 (AY697924), F4C31 (AY794202), F4C31S (AY936201), F4C31 (AY794202) and F4C70 (AY697920). [96–99%]F1C14 (AY794061), F1C69T (AY794083), F1C27S (AY794068), F1C79 (AY794086), F1C98 (AY697874), F3C01A (AY794150), F3C05 (AY697890), F3C28 (AY697897), F3C44 (AY697902) and F3C50 (AY697904). [94–99%]
Roseobacter sp. ANT9274 (AY167261) F1C69T (AY794083). [97%]
Roseobacter sp. ANT9276a (AY167262) F1C75 (AY794085). [94%]
Roseobacter sp. ANT9270 (AY167260)F2C32 (AY694124). [99%] 
Roseobacter sp. ARCTIC-P4 (AY573044) F1C74S (AY936184). [96%]
Uncultured Roseobacter
Roseobacter sp. clone (AY627365)F4C01 (AY936200), F2C06A (AY79494) and F4C03 (AY697909). [98–99%] 
Roseobacter NAC11-6 (AF245634) F1C74T (AY936185). [97%]
Roseobacter NAC11-7 (AF245635)F2C02 (AY936186) and F4C13 (AY794188). [96–99%] 
Roseobacter sp. EB080-L11F12 (AY627365)F4C02D (AY794181), F2C04 (AY936187), F4C44 (AY697913) and F4C74 (AY697922). [98–99%] 
Roseobacter sp. (AY167254)F2C99 (AY794149). [99%] 
Roseobacter sp. DG1132 (AY258102) F1C10 (AY794059). [95%]
Unidentified and uncultured RoseobacterF2C08A (AY794096), F2C18 (AY697878), F2C35 (AY697881), F2C78 (AY794144), F2C79 (AY794145), F2C92 (AY697886), F2C100 (AY936189), F2C102 (AY794106). F2C107 (AY794111), F2C110 (AY794114), F4C04 (AY697910) and F4C59 (AY697917). [92–99%].F1C18 (AY697871), F1C28 (AY697872), F1C58M (AY794078), F1C60 (AY936180), F1C69S (AY794082), F1C69 (AY794084), F3C07 (AY697891), F3C17B (AY794155), F3C24 (AY794157), F3C48 (AY697903), F3C56 (AY794164), F3C59 (AY794165), F3C60 (AY794166), F3C65 (AY794167), F3C68 (AY697905), F3C73 (AY794169), F3C86 (AY794172), F3C91 (AY794174), F3C94 (AY794176), F3C96 (AY794177) and F3C99 (AY794179). [94–100%].
Sulfitobacter114
Sulfitobacter mediterraneus (Y17387)F2C25 (AY697879). [97%] 
Sulfitobacter sp. (AJ534236)F2C44 (AY794129). [94%] 
Sulfitobacter sp. GAI-21 (AF007257)F2C47 (AY697884), F2C84 (AY697885), F4C57 (AY794211) and F4C56 (AY697915). [95–99%]F3C23 (AY936196). [99%]
Sulfitobacter sp. DFL-41 (AJ534222)F2C07A (AY794095). [95%] 
Sulfitobacter sp. ANT9282b (AY167263)F2C10 (AY794105), F2C42 (AY794128) and F2C103 (AY794107). [96–97%]F1C67 (AY794080), F1C68D (AY794081) and F3C110 (AY697908). [96–98%]
Sulfitobacter sp. ANT9115 (AY167322)F2C52 (AY794132). [96%] 
Staleya11
Staleya guttiformis EL-38T (Y16427)F4C15 (AY697912) [98%].F1CA9 (AY697867). [98%]
UnculturedAlphaproteobacteria43
Alphaproteobacterium Shippagan (AF100168) F1C27T (AY794069). [97–98%]
Alphaproteobacterium OM42 (U70680)F4C02E (AY794180). [98%] 
Marine Alphaproteobacterium (AJ391182)F4C42 (AY794207). [96%]F1C26D (AY794066). [97%]
Marine Alphaproteobacterium (AF365990) F1A08 (AY936173). [92%]
‘Candidatus pelagibacter’ ubiqueF2CB3 (AY697875) and F2CB7 (AY697876). [96%] 
Gammaproteobacteria2525
Glaciecola149
Glaciecola mesophila (AJ548479) F3C55 (AY794163). [93%]
Glaciecola sp. EL-110 (AJ308105)F2C26 (AY794121). [96%]F1C08 (AY936188). [96%]
Glaciecola sp. HA02 (AB049729)F2C105 (AY794109). [95%] 
Glaciecola pallidula ACAM 615T (AJ308105) F1C16 (AY794062). [97%]
Glaciecola pallidula ACAM 615T (AJ308105)F2C04A (AY794092), F2C21 (AY794120), F2C28 (AY697880), F2C38 (AY697882), F2C53 (AY794133), F2C48 (AY794130), F2C60 (AY794134), F4C18 (AY794191), F4C19 (AY794192), F4C48 (AY794210), F4C63 (AY697918) and F4C71 (AY697921). [95–97%]F3C08 (AY697892), F3C14 (AY697894), F3C16 (AY697895), F3C20 (AY936194), and F3C90 (AY794173). [95–97%]
Glaciecola punicea ACAM 611T (U85853) F3C95 (AY936198). [98%]
Psychromonas20
Psychromonasprofunda (AJ416756)F2C08 (AY936188) and F2C72 (AY794140). [97–99%] 
Colwellia11
Colwellia piezophila (AB094412) F1C89T (AY794088). [98%]
Colwellia psychrerythraea IC064 (U85842)F4C86 (AY794216). [97%] 
Marinomonas22
Marinomonas ushuaiensis (AJ627909)F2C63 (AY794136) and F2C68 (AY794138). [97–100%]F3C93 (AY794175). [96%]
Marinomonas primoryensisAJ238597) F3C32 (AY697898). [99%]
Psychrobacter06
Psychrobacter psychrophilus (AJ748270) F3C17A (AY794154). [98%]
Psychrobacter sp. DY9-2 (AY383045) F3C12 (AY794152), F3C15 (AY794153), F3C39 (AY794160), F3C54 (AY794162) and F3C46 (AY936197). [98–99%}
Vibrio10
Vibrio sp. LnSQ6 (AY158028)F4C73 (AY794214). [97%] 
Oleispira01
Oleispira Antarctica RB-8T (AJ426420) F3C18 (AY697896). [93%]
Pseudomonas10
Pseudomonas balearica SP1402T (U26418)F4C67 (AY697919). [99%] 
Uncultured and unidentified Gammaproteobacteria46
Gammaproteobacterium SUR (AF114620)F4C06 (AY794184). [97%] 
Gammaproteobacterium UMB8H (AF505737) F3C103B (AY936199) and F3C10 (AY697906). [98%]
Gammaproteobacterium Arctic96B (AF354595)F4C87 (AY794217). [96%] 
Gammaproteobacterium UMB10B (AF505738) F3C102 (AY936191) and F3C102B (AY936192). [98%]
Gammaproteobacterium UMB10B (AF469279) F3C21 (AY936195). [99%]
Uncultured and unidentified GammaproteobacteriaF4C93 (AY794218) and F4C87 (AY794217). [93–96%]F3C13 (AY697893). [97%]
Epsilonproteobacteria01
Arcobacter01
Arcobacter sp. KT0913 (AF235110) F3C43 (AY697901). [97%]
Uncultured Proteobacteria33
Uncultured Proteobacterium (AY644707)F2C09 (AY794105), F2C104 (AY794107), and F2C108 (AY794112). [92–99%]F3C25 (AY794158), F3C78 (AY794107), F3C97 (AY794178). [94–100%]
Cytophaga–Flexibacter–Bacteriodetes group1520
Cytophaga (Stanierella)10
Cytophaga sp. (AB015532)F2C76 (AY794142). [96%] 
Cellulophaga12
Cellulophaga lytica (AB032510)F4C20 (AY794193). [93%] 
Cellulophaga sp. (AF497997) F1C36 (AY794073). [92%]
Cellulophaga sp. (AY035869) F1C48 (AY936178). [98%]
Formosa algae02
Formosa algae KMM 3553 (AY228461) F3C41 (AY697899) and F3C42 (AY697900). [92%]
Maribacter10
Maribacter orientalis (AY271624)F4C50 (AY697914). [96%] 
Flexibacter11
Flexibacter sp. IUB42 (AB058905)F4C94 (AY697925). [95%]F1C61 (AY697873). [96%]
Polaribacter02
Polaribacter franzmannii ANT9260 (AY167319) F1A13D (AY794060). [93%]
Polaribacter sp. HLE (AY198117) F3C72 (AY794168). [98%]
Ulvibacter01
Ulvibacter litoralis (AY243096) F1C73 (AY936183). [94%]
Tenacibaculum01
Tenacibaculum maritum (92%) (AF359539) F1C24F (AY936177). [92%]
Uncultured Cytophaga–Flexibacter–Bacteroidetes Group1111
CFB bacterium MERTZ (AF424351)F4C47 (AY794209). [88%] 
CFB bacterium MERTZ (AF424352)F4C05 (AY794182). [90%]F1C38 (AY794075). [90%]
CFB bacterium MERTZ_0CM_184 (AF424353)F2C49 (AY794131). [98%] 
Bacteroidetes bacterium (AY274847) F1C29S (AY794070). [98%]
Bacteroidetes bacterium 1D10 (AY274838)F4C17 (AY794190) [96%]F3C79 (AY794171) and F1C08T (AY936176). [94–98%]
Bacteroidetes bacterium (AY580719)F2C106 (AY794110). [97%] 
Bacteroidetes bacterium (AY225660)F4C37 (AY794204). [89%] 
Flexibacterium (AJ297467) F3C16A (AY936193). [98%]
CFBF4C34 (AY794203), F4C41 (AY794206), F4C78 (AY697923) and F2C29 (AY794122). [90–99%]F1C37 (AY794074), F1C12 (AY697870), F1CA7 (AY697866), F1CA12 (AY697868) and F1C07 (AY697869). [92–98%]
Flavobacteriaceae bacterium G1112S4A (AY353814)F4C43 (AY794208). [94%] 
Flavobacteriaceae bacterium (AY285946) F1C17 (AY794063). [97%]
Unidentified and Uncultured organisms1011
Uncultured Antarctic sea ice bacterium (AY165570) F1C34 (AY794072) and F3C19 (AY794156). [97%]
Antarctic sea ice bacterium (AY165576)F2C12 (AY794116) and F4C29 (AY794200). [97–98%] 
Arctic sea ice bacterium ARK10076 (AF468411)F2C61 (AY794135). [95%] 
Uncultured marine bacterium ZD0409 (AJ400350) F1C49 (AY794076). [96%]
Uncultured marine bacterium (AJ400343) F1C30S (AY794071). [98%]
Uncultured marine bacterium (AJ298381) F1C66D (AY936181). [90%]
Uncultured marine bacterium ZD0207 (AJ400341)F2C06 (AY794103). [97%] 
Uncultured bacterium clone 223 (AY172247)F2C101 (AY936190), F4C61D (AY794212) and F4C61E (AY794213). [95–97%] 
Uncultured bacterium clone (AY133378) F1C53F (AY794077) and F1C53S (AY936179). [98%]
Uncultured bacterium GR-Sh1-209 (AJ296579)F2C11A (AY794098). [90%] 
Uncultured bacterium clone OB3 (AY133410)F4C23 (AY794196). [98%] 
Unidentified bacterium DNA (Z88574) F1C22 (AY794064) and F3C31 (AY794154). [96–98%]
Bacterium DG890 small subunit (AY258122) F1C66E (AY936182). [89%]
Gas vacuolate str. 206 (U73723) F1C83S (AY794087). [97%]
Ophiopholis aculeata symbiont (U63548)F2C41 (AY794127). [97%]