publication . Article . 2010

16S rRNA gene-based molecular analysis of mat-forming and accompanying bacteria covering organically-enriched marine sediments underlying a salmon farm in Southern Chile (Calbuco Island)

Aranda, Carlos; Paredes, Javier; Valenzuela, Cristian; Phyllis Lam; Guillou, Laure;
  • Published: 01 Jan 2010
Abstract
The mat forming bacteria covering organic matter-enriched and anoxic marine sediments underlying a salmon farm in Southern Chile, were examined using 16S rRNA gene phylogenies. This mat was absent in the sea bed outside the direct influence of the farm (360 m outside fish cages). Based on nearly complete 16S rRNA gene sequences (-1500 bp), mat-forming filamentous cells were settled as the sulphur-oxidizing and putatively dissimilative nitrate-reducing Beggiatoa spp., being closely related (up to 97% sequence identity) to Beggiatoa spp. identified in eutrophic shallow sediments in northern Europe (Danish Limfjorden and German Dangast inlets). Their phylogenetic a...
Subjects
free text keywords: Ciclo de azufre, genes 16S rARN, salmonicultura, sedimentos, tapete de Beggiatoa, Beggiatoa mat, salmon farming sediments, sulphur cycle, 16S rRNA genes, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, Animal Science and Zoology, Aquatic Science, Anoxic waters, Botany, 16S ribosomal RNA, Phylogenetics, Aquatic animal, Beggiatoa, biology.organism_classification, biology, Aquaculture, business.industry, business, Ribosomal RNA, Fish farming
Related Organizations
41 references, page 1 of 3

a hmad , a, J. p . b yar J.p . & d. C. n Elson . 1999. Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Applied and Environmental Microbiolgy 65: 270-277.

a sami , h., m a ida & k. w anbEta . 2005. Accelerated Sulfur Cycle in Coastal Marine Sediment beneath Areas of Intensive Shellfish Aquaculture. Applied and Environmental Microbiology 71: 2925-2933.

BEnso , d. a., i. k arsCh -m izraChi , d. J. l ipman , J. o stEl , b. a. r ap & l. w hEElEr . 2000. GenBank. Nucleic Acid Research 28: 15-18.

b isEt , a., J. b owman & C. b urkE . 2006. Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiology Ecology 5: 48-56.

b roks , k. m., a. r. s tiErns , C. v . w . m ahnkEn , d. b. b laCkburn . 2003. Chemical and biological remediation of the benthos near Atlantic salmon farms. Aquaculture 219: 355-377.

b usChman , a. h., m. C. h ErnadEz -g onzalEz , C. a rand , t . Chopin , a. n Eori , C. h aling , m. t roEl . 2008. Mariculture Waste Management. In: S.E. Jørgensen, B.D. Fath (Eds), Ecological Engineering, Elsevier, Oxford, Vol. 3 of Encyclopedia of Ecology. pp. 2211-2217.

ChristEsnEn , p . b., s. r ysgard , n. p . s loth , t . d Elsgard & s. s CtEhwärr . 2000. Sediment mineralization, nutrient lfuxes, denitrification and dissimilatory nitrate reduction, to ammonium in an estuarine fjord with sea cage trout farms. Aquatic Microbial Ecology 21: 73-84.

ColE , J. r., b. C hai , t . l. m arsh , r. J. F aris , q. w ang , s. a. k ulam , s. C handr , d. m. m Cg arEl , t . m. s Chmidt , g. m. g arity & J. m. t iEdJE . 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31: 442-443.

FinstEr , k., w . l iEsaCk & b. t hamdrup . 1998. Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment. Applied and Environmental Microbiology 64: 119-125.

g raCo , m., l. F arís , v . m olina , d. g utiérEz & l. p . n ElsEn . 2001. Massive developments of microbial mats following phytoplankton blooms in a naturally eutrophic bay: Implications for nitrogen cycling. Limnology and Oceanography 46: 821-832.

h v Eaman , s.a., E. a. g rEEnE & g. v orduw . 2005. Gene expression analysis of the mechanism of inhibition of Desulfovibrio vulgaris Hildenborough by nitrate-reducing, sulfide-oxidizing bacteria. Environmental Microbiology 7: 1461-1465.

h ubEr , t ., g. F aulknEr & p . h ugEtznhol . 2004. Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.

i nagki , F., k. t aki , k. h. n Ealson & k. h oriksh . 2004. Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilonProteobacteriaisolatedfromOkinawaTroughhydrothermal sediments. International Journal of Systematic and Evolutionary Microbiology 54: 1477-1482.

JansEn , p .h., a. s Chuman , F. b ak & w . l iEsaCk . 1996. Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen. nov., sp. nov. Archives of Microbiology 166: 184- 192.

JEsn En , a . & k . Ftsni Er . 2005. Isolation and characterization of Sulfurospirillum carboxydovorans sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium. Antonie Van Leeuwenhoek. 87: 339-353.

41 references, page 1 of 3
Abstract
The mat forming bacteria covering organic matter-enriched and anoxic marine sediments underlying a salmon farm in Southern Chile, were examined using 16S rRNA gene phylogenies. This mat was absent in the sea bed outside the direct influence of the farm (360 m outside fish cages). Based on nearly complete 16S rRNA gene sequences (-1500 bp), mat-forming filamentous cells were settled as the sulphur-oxidizing and putatively dissimilative nitrate-reducing Beggiatoa spp., being closely related (up to 97% sequence identity) to Beggiatoa spp. identified in eutrophic shallow sediments in northern Europe (Danish Limfjorden and German Dangast inlets). Their phylogenetic a...
Subjects
free text keywords: Ciclo de azufre, genes 16S rARN, salmonicultura, sedimentos, tapete de Beggiatoa, Beggiatoa mat, salmon farming sediments, sulphur cycle, 16S rRNA genes, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, Animal Science and Zoology, Aquatic Science, Anoxic waters, Botany, 16S ribosomal RNA, Phylogenetics, Aquatic animal, Beggiatoa, biology.organism_classification, biology, Aquaculture, business.industry, business, Ribosomal RNA, Fish farming
Related Organizations
41 references, page 1 of 3

a hmad , a, J. p . b yar J.p . & d. C. n Elson . 1999. Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Applied and Environmental Microbiolgy 65: 270-277.

a sami , h., m a ida & k. w anbEta . 2005. Accelerated Sulfur Cycle in Coastal Marine Sediment beneath Areas of Intensive Shellfish Aquaculture. Applied and Environmental Microbiology 71: 2925-2933.

BEnso , d. a., i. k arsCh -m izraChi , d. J. l ipman , J. o stEl , b. a. r ap & l. w hEElEr . 2000. GenBank. Nucleic Acid Research 28: 15-18.

b isEt , a., J. b owman & C. b urkE . 2006. Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiology Ecology 5: 48-56.

b roks , k. m., a. r. s tiErns , C. v . w . m ahnkEn , d. b. b laCkburn . 2003. Chemical and biological remediation of the benthos near Atlantic salmon farms. Aquaculture 219: 355-377.

b usChman , a. h., m. C. h ErnadEz -g onzalEz , C. a rand , t . Chopin , a. n Eori , C. h aling , m. t roEl . 2008. Mariculture Waste Management. In: S.E. Jørgensen, B.D. Fath (Eds), Ecological Engineering, Elsevier, Oxford, Vol. 3 of Encyclopedia of Ecology. pp. 2211-2217.

ChristEsnEn , p . b., s. r ysgard , n. p . s loth , t . d Elsgard & s. s CtEhwärr . 2000. Sediment mineralization, nutrient lfuxes, denitrification and dissimilatory nitrate reduction, to ammonium in an estuarine fjord with sea cage trout farms. Aquatic Microbial Ecology 21: 73-84.

ColE , J. r., b. C hai , t . l. m arsh , r. J. F aris , q. w ang , s. a. k ulam , s. C handr , d. m. m Cg arEl , t . m. s Chmidt , g. m. g arity & J. m. t iEdJE . 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31: 442-443.

FinstEr , k., w . l iEsaCk & b. t hamdrup . 1998. Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment. Applied and Environmental Microbiology 64: 119-125.

g raCo , m., l. F arís , v . m olina , d. g utiérEz & l. p . n ElsEn . 2001. Massive developments of microbial mats following phytoplankton blooms in a naturally eutrophic bay: Implications for nitrogen cycling. Limnology and Oceanography 46: 821-832.

h v Eaman , s.a., E. a. g rEEnE & g. v orduw . 2005. Gene expression analysis of the mechanism of inhibition of Desulfovibrio vulgaris Hildenborough by nitrate-reducing, sulfide-oxidizing bacteria. Environmental Microbiology 7: 1461-1465.

h ubEr , t ., g. F aulknEr & p . h ugEtznhol . 2004. Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.

i nagki , F., k. t aki , k. h. n Ealson & k. h oriksh . 2004. Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilonProteobacteriaisolatedfromOkinawaTroughhydrothermal sediments. International Journal of Systematic and Evolutionary Microbiology 54: 1477-1482.

JansEn , p .h., a. s Chuman , F. b ak & w . l iEsaCk . 1996. Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen. nov., sp. nov. Archives of Microbiology 166: 184- 192.

JEsn En , a . & k . Ftsni Er . 2005. Isolation and characterization of Sulfurospirillum carboxydovorans sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium. Antonie Van Leeuwenhoek. 87: 339-353.

41 references, page 1 of 3
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publication . Article . 2010

16S rRNA gene-based molecular analysis of mat-forming and accompanying bacteria covering organically-enriched marine sediments underlying a salmon farm in Southern Chile (Calbuco Island)

Aranda, Carlos; Paredes, Javier; Valenzuela, Cristian; Phyllis Lam; Guillou, Laure;