title: Diversity of benzylsuccinate synthase-like (bssA) genes in hydrocarbon-polluted marine sediments suggests substrate-dependent clustering.
abstract: The potential of hydrocarbon biodegradation in marine sediments was determined through the detection of a functional biomarker, the bssA gene, coding for benzylsuccinate synthase, the key enzyme of anaerobic toluene degradation. Eight bssA clone libraries (409 sequences) were constructed from polluted sediments affected by the Prestige oil spill in the Atlantic Islands National Park and from hydrocarbon-amended sediment microcosms in Mallorca. The amplified products and database-derived bssA-like sequences grouped into four major clusters, as determined by phylogenetic reconstruction, principal coordinate analysis (PCoA), and a subfamily prediction tool. In addition to the classical bssA sequences that were targeted, we were able to detect sequences homologous to the naphthylmethylsuccinate synthase gene (nmsA) and the alkylsuccinate synthase gene (assA), the bssA homologues for anaerobic 2-methylnaphthalene and alkane degradation, respectively. The detection of bssA-like variants was determined by the persistence and level of pollution in the marine samples. The observed level of gene diversity was lower in the Mallorca sediments, which were dominated by assA-like sequences. In contrast, the Atlantic Islands samples, which were highly contaminated with methylnaphthalene-rich crude oil, showed a high proportion of nmsA-like sequences. Some of the detected genes were phylogenetically related to Deltaproteobacteria communities, previously described as the predominant hydrocarbon degraders at these sites. Differences between all detected bssA-like genes described to date indicate separation between marine and terrestrial sequences and further subgrouping according to taxonomic affiliation. Global analysis suggested that bssA homologues appeared to cluster according to substrate specificity. We observed undetected divergent gene lineages of bssA homologues, which evidence the existence of new degrader groups in these environments.
authors.affiliation: Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, Granada, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Acosta-González
authors.forename: Ramon
authors.initials: R
authors.lastname: Rosselló-Móra
authors.forename: Silvia
authors.initials: S
authors.lastname: Marqués
mesh_terms: D001483:Base Sequence; D001673:Biodegradation, Environmental; D019755:Carbon-Carbon Lyases / Q000235:genetics*; D004785:Environmental Pollutants / Q000378:metabolism*; D014644:Genetic Variation; D005843:Geography; D019015:Geologic Sediments / Q000032:analysis / Q000382:microbiology*; D006838:Hydrocarbons / Q000378:metabolism*; D008969:Molecular Sequence Data; D059392:Petroleum Pollution; D010802:Phylogeny; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D013030:Spain
chemical_list: D004785:Environmental Pollutants; D006838:Hydrocarbons; D019755:Carbon-Carbon Lyases; C114354:benzylsuccinate synthase
references.citation: Environ Microbiol. 2008 Feb;10(2):376-85
references.pmid: 17961174
references.citation: J Am Chem Soc. 2011 Sep 21;133(37):14666-74
references.pmid: 21823587
references.citation: J Mol Biol. 2006 Mar 17;357(1):221-35
references.pmid: 16414072
references.citation: J Bacteriol. 1999 Oct;181(20):6403-10
references.pmid: 10515931
references.citation: Appl Environ Microbiol. 2000 Dec;66(12):5393-8
references.pmid: 11097919
references.citation: Appl Environ Microbiol. 2004 Mar;70(3):1385-92
references.pmid: 15006757
references.citation: FEMS Microbiol Ecol. 2011 Oct;78(1):165-75
references.pmid: 21385190
references.citation: Environ Microbiol Rep. 2011 Feb;3(1):125-135
references.pmid: 21837252
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: Appl Environ Microbiol. 2003 Feb;69(2):760-8
references.pmid: 12570993
references.citation: J Bacteriol. 1997 Feb;179(3):670-6
references.pmid: 9006019
references.citation: Biodegradation. 2000;11(2-3):85-105
references.pmid: 11440245
references.citation: FEMS Microbiol Ecol. 2007 Oct;62(1):118-30
references.pmid: 17784862
references.citation: J Chromatogr A. 2004 Jan 30;1025(1):133-8
references.pmid: 14753680
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D123-9
references.pmid: 22086953
references.citation: Appl Environ Microbiol. 2013 Jan;79(2):543-52
references.pmid: 23124238
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W242-8
references.pmid: 22689646
references.citation: Biosci Biotechnol Biochem. 2005 Aug;69(8):1483-91
references.pmid: 16116275
references.citation: Appl Microbiol Biotechnol. 2004 May;64(4):437-46
references.pmid: 14735323
references.citation: Biochemistry. 2004 Apr 27;43(16):4635-45
references.pmid: 15096031
references.citation: Appl Environ Microbiol. 2007 Feb;73(4):1367-9
references.pmid: 17142355
references.citation: Biodegradation. 2002;13(2):149-54
references.pmid: 12449317
references.citation: ISME J. 2010 Jan;4(1):17-27
references.pmid: 19710709
references.citation: Arch Microbiol. 1999 Nov;172(5):287-94
references.pmid: 10550470
references.citation: Environ Microbiol. 2011 Jun;13(6):1488-99
references.pmid: 21414123
references.citation: Environ Sci Technol. 2002 Sep 15;36(18):3977-84
references.pmid: 12269751
references.citation: Environ Microbiol. 2007 Apr;9(4):1035-46
references.pmid: 17359274
references.citation: PLoS One. 2010 Nov 19;5(11):e14072
references.pmid: 21124915
references.citation: Environ Sci Technol. 2008 Aug 15;42(16):6065-72
references.pmid: 18767667
references.citation: FEMS Microbiol Rev. 2000 Dec;24(5):691-710
references.pmid: 11077159
references.citation: J Bacteriol. 2001 Jan;183(2):752-7
references.pmid: 11133971
references.citation: Environ Sci Technol. 2010 Oct 1;44(19):7287-94
references.pmid: 20504044
references.citation: Environ Toxicol Chem. 2005 Sep;24(9):2203-17
references.pmid: 16193747
references.citation: Environ Microbiol. 2011 May;13(5):1216-27
references.pmid: 21281422
references.citation: Environ Microbiol. 2009 Jan;11(1):209-19
references.pmid: 18811643
references.citation: Environ Microbiol. 2013 May;15(5):1334-55
references.pmid: 23088741
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Eur J Biochem. 1996 Jun 15;238(3):661-8
references.pmid: 8706665
references.citation: Nat Struct Biol. 1999 Oct;6(10):969-75
references.pmid: 10504733
references.citation: J Bacteriol. 2001 Dec;183(23):6763-70
references.pmid: 11698363
references.citation: J Bacteriol. 2010 Jan;192(1):295-306
references.pmid: 19854898
references.citation: Appl Environ Microbiol. 1996 Feb;62(2):316-22
references.pmid: 8593035
references.citation: Mol Microbiol. 1998 May;28(3):615-28
references.pmid: 9632263
references.citation: Environ Microbiol. 2013 Jan;15(1):77-92
references.pmid: 22626032
references.citation: Biol Chem. 2005 Oct;386(10):981-8
references.pmid: 16218870
references.citation: Appl Microbiol Biotechnol. 2012 Oct;96(2):531-42
references.pmid: 22249716
references.citation: Arch Microbiol. 2004 Jun;181(6):407-17
references.pmid: 15127183
references.citation: Appl Environ Microbiol. 1997 Dec;63(12):4759-64
references.pmid: 9471963
references.citation: Environ Microbiol Rep. 2009 Dec;1(6):535-44
references.pmid: 23765932
references.citation: Biochem Biophys Res Commun. 2008 Feb 1;366(1):142-8
references.pmid: 18053803
references.citation: J Bacteriol. 2001 Mar;183(5):1707-15
references.pmid: 11160102
references.citation: Environ Sci Technol. 2011 Apr 15;45(8):3407-14
references.pmid: 21438602
references.citation: Curr Opin Chem Biol. 2007 Apr;11(2):188-94
references.pmid: 17349816
references.citation: Environ Microbiol. 2012 Mar;14(3):754-64
references.pmid: 22040260
references.citation: Arch Microbiol. 2004 Mar;181(3):182-94
references.pmid: 14735297
references.citation: Appl Environ Microbiol. 1998 May;64(5):1650-6
references.pmid: 9572931
references.citation: J Mol Biol. 2007 Oct 26;373(3):801-10
references.pmid: 17868687