Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis

FEMS Microbiology Ecology

Volumn 88, Issue 3, 2014, Pages 538-549

  Tourna, Maria ^a   Maclean, Paul ^a   Condron, Leo ^b   O'Callaghan, Maureen ^c   Wakelin, Steven A ^c  

^a RUAKURA RESEARCH CENTRE   (New Zealand)

^b LINCOLN UNIVERSITY   (New Zealand)

^c AGRESEARCH LTD   (New Zealand)

Author keywords

Real time PCR; Soil microcosms; SoxB; Sulphur oxidation; Sulphur oxidising bacteria; Thiobacillus

Indexed keywords

BACTERIUM; BIOGEOCHEMICAL CYCLE; BIOGEOCHEMISTRY; ECOPHYSIOLOGY; HABITAT SELECTION; MICROCOSM; OXIDATION; POLYMERASE CHAIN REACTION; REAL TIME; SOIL AMENDMENT; SOIL MICROORGANISM; SULFUR;

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; THIOBACILLUS;

PRIMER DNA; SULFUR;

ARTICLE; BACTERIAL GENE; BACTERIUM; BETAPROTEOBACTERIA; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PHYLOGENY; POLYMERASE CHAIN REACTION; REAL-TIME PCR; SOIL MICROCOSMS; SOXB; SULPHUR OXIDATION; SULPHUR-OXIDISING BACTERIA; THIOBACILLUS;

REAL-TIME PCR; SOIL MICROCOSMS; SOXB; SULPHUR OXIDATION; SULPHUR-OXIDISING BACTERIA; THIOBACILLUS;

BACTERIA; BETAPROTEOBACTERIA; BIODIVERSITY; DNA PRIMERS; ECOSYSTEM; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PHYLOGENY; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY; SULFUR;

EID: 84901691373     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12323     Document Type: Article

References (40)

1. Baker BJ & Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44: 139-152.
2. Banerjee MR & Chapman SJ (1996) The significance of microbial biomass sulphur in soil. Biol Fertil Soils 22: 116-125.
3. Beller HR, Chain PSG, Letain TE et al. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188: 1473-1488.
4. Boden R, Cleland D, Green PN, Katayama Y, Uchino Y, Murrell JC & Kelly DP (2012) Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus. Arch Microbiol 194: 187-195.
5. Bourne DG, van der Zee MJJ, Botté ES & Sato Y (2013) Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions. Environ Microbiol Rep 5: 518-524.
6. Bunemann EK & Condron LM (2007) Phosphorus and sulphur cycling in terrestrial ecosystems. Nutrient Cycling in Terrestrial Ecosystems (Marschner P & Rengel Z, eds), pp. 65-94. Springer-Verlag, New York, NY.
7. Burton ED, Bush RT, Johnston SG, Sullivan LA & Keene AF (2011) Sulfur biogeochemical cycling and novel Fe-S mineralization pathways in a tidally re-flooded wetland. Geochim Cosmochim Acta 75: 3434-3451.
8. Chapman SJ (1997) Carbon substrate mineralization and sulphur limitation. Soil Biol Biochem 29: 115-122.
9. Chivian D, Brodie EL, Alm EJ et al. (2008) Environmental genomics reveals a single-species ecosystem deep within earth. Science 322: 275-278.
10. Dick RP & Deng S (1991) Multivariate factor analysis of sulfur oxidation and rhodanese activity in soils. Biogeochemistry 12: 87-101.
11. Drobner E, Huber H, Rachel R & Stetter KO (1992) Thiobacillus plumbophilus spec. nov., a novel galena and hydrogen oxidizer. Arch Microbiol 157: 213-217.
12. Friedrich CG, Rother D, Bardischewsky F, Ouentmeier A & Fischer J (2001) Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl Environ Microbiol 67: 2873-2882.
13. Friedrich CG, Bardischewsky F, Rother D, Quentmeier A & Fischer J (2005) Prokaryotic sulfur oxidation. Curr Opin Microbiol 8: 253-259.
14. Ghosh W & Dam B (2009) Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 33: 999-1043.
15. Ghosh W, George A, Agarwal A, Raj P, Alam M, Pyne P & Gupta SKD (2011) Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis. J Bacteriol 193: 5553-5554.
16. Gregersen LH, Bryant DA & Frigaard NU (2011) Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front Microbiol 2: art. no. Article 116.
17. Grimm F, Franz B & Dahl C (2008) Thiosulfate and Sulfur Oxidation in Purple Sulfur Bacteria. Springer, Berlin.
18. Headd B & Engel AS (2013) Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions. Appl Environ Microbiol 79: 1171-1182.
19. Hensen D, Sperling D, Trüper HG, Brune DC & Dahl C (2006) Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Mol Microbiol 62: 794-810.
20. Jones DT, Taylor WR & Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
21. Kelly DP & Wood AP (2000) Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol 50: 511-516.
22. Kirkby CA, Kirkegaard JA, Richardson AE, Wade LJ, Blanchard C & Batten G (2011) Stable soil organic matter: a comparison of C:N:P: S ratios in Australian and other world soils. Geoderma 163: 197-208.
23. Kuenen JG & Beudeker RF (1982) Microbiology of thiobacilli and other sulphur-oxidizing autotrophs, mixotrophs and heterotrophs. Philos Trans R Soc Lond B Biol Sci 298: 473-497.
24. Lenk S, Arnds J, Zerjatke K, Musat N, Amann R & Mußmann M (2011) Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. Environ Microbiol 13: 758-774.
25. Lenk S, Moraru C, Hahnke S et al. (2012) Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. ISME J 6: 2178-2187.
26. Loy A, Duller S, Baranyi C et al. (2009) Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes. Environ Microbiol 11: 289-299.
27. Luo JF, Lin WT & Guo Y (2011) Functional genes based analysis of sulfur-oxidizing bacteria community in sulfide removing bioreactor. Appl Microbiol Biotechnol 90: 769-778.
28. McGill WB & Cole CV (1981) Comparative aspects of cycling of organic C, N, S and P through soil organic matter. Geoderma 26: 267-286.
29. Meyer B & Kuever J (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl Environ Microbiol 73: 7664-7679.
30. Meyer B, Imhoff JF & Kuever J (2007) Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - Evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol 9: 2957-2977.
31. Pedersen RB, Rapp HT, Thorseth IH et al. (2010) Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge. Nat Commun 1: art. no. 126.
32. Pepper IL & Gerba CP (2004) Oxidation of Sulfur in Soil. Environmental Microbiology - A Laboratory Manual, 2nd edn, pp 61-69. Elsevier, San Diego, CA.
33. Petri R, Podgorsek L & Imhoff JF (2001) Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. FEMS Microbiol Lett 197: 171-178.
34. Pham VH, Yong JJ, Park SJ, Yoon DN, Chung WH & Rhee SK (2008) Molecular analysis of the diversity of the sulfide: quinone reductase (sqr) gene in sediment environments. Microbiology 154: 3112-3121.
35. Rice P, Longden I & Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276-277.
36. Rozen S & Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S & Misener S, eds), pp. 365-386. Humana Press, Totowa, NJ.
37. Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
38. Tourova TP, Slobodova NV, Bumazhkin BK, Kolganova TV, Muyzer G & Sorokin DY (2013) Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes using soxB as a functional molecular marker. FEMS Microbiol Ecol 84: 280-289.
39. Varon-Lopez M, Dias ACF, Fasanella CC, Durrer A, Melo IS, Kuramae EE & Andreote FD (2014) Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 16: 845-855.
40. Wächtershäuser G (2006) From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Philos Trans R Soc Lond B Biol Sci 361: 1787-1806.