Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Zhang, Weipeng ^a   Wang, Yong ^a   Lee, On On ^a   Tian, Renmao ^a   Cao, Huiluo ^a   Gao, Zhaoming ^a   Li, Yongxin ^a   Yu, Li ^a   Xu, Ying ^a   Qian, Pei Yuan ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ION; METAL; SEA WATER;

ADAPTATION; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; BIOFILM; CHEMISTRY; DIATOM; DNA SEQUENCE; DRUG EFFECTS; FUNGUS; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ION TRANSPORT; METABOLISM; METAGENOMICS; MICROBIOLOGY; OXIDATIVE STRESS; PHYSIOLOGY;

ADAPTATION, PHYSIOLOGICAL; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOFILMS; DATABASES, GENETIC; DIATOMS; FUNGI; ION TRANSPORT; IONS; METAGENOMICS; METALS; OXIDATIVE STRESS; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84887850682     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03180     Document Type: Article

References (55)

1. Costerton, J. W., Lewandowski, Z., Caldwell, D. E., Korber, D. R. & Lappin-Scott, H. M. Microbial biofilms. Annu Rev Microbiol 49, 711 (1995).
2. Lau, S. C., Thiyagarajan, V., Cheung, S. C. & Qian, P. Y. Roles of bacterial community in biofilms as mediator for larval settlement of marine invertebrates. Aquat Microb Ecol 38, 41-51 (2005). (Pubitemid 40263300)
3. Nocker, A., Lepo, J. E.,Martin, L. L. & Snyder, R. A. Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations. Microb Ecol 54, 532-542 (2007). (Pubitemid 47546807)
4. Qian, P. Y., Thiyagarajan, V., Lau, S. C. K. & Cheung, S. C. K. Relationship between bacterial community profile in biofilm and attachment of the acorn barnacle Balanus amphitrite. Aquat Microb Ecol 33, 225-237 (2003). (Pubitemid 37491931)
5. Decho, A. W. Microbial biofilms in intertidal systems: an overview. Contin Shelf Res 20, 1257-1273 (2000). (Pubitemid 30647422)
6. Ayling, A. M. The Role of Biological Disturbance in Temperate Subtidal Encrusting Communities. Ecology 62, 830-847 (1981).
7. Candela, J., Beardsley, R. C. & Limeburner, R. Separation of tidal and subtidal currents in ship-mounted acoustic Doppler current profiler observations. J Geophys Res 97, 769 (1992).
8. Tokeshi, M. in Aquatic Ecology: Scale, Pattern and Processes (eds Giller, P. S., Hildrew, A. G. & Raffaelli, D. G.) 63-92 (Blackwell, Oxford, 1994).
9. Somero, G. N. The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'. J Exp Biol 213, 912-920 (2010).
10. Marshall, D. J. & McQuaid, C. D. Warming reduces metabolic rate in marine snails: adaptation to fluctuating high temperatures challenges the metabolic theory of ecology. P Roy Soc B-Biol Sci 278, 281-288 (2011).
11. Keough, M. & Raimondi, P. Responses of settling invertebrate larvae to bioorganic films: effects of large-scale variation in films. J Exp Mar Biol Ecol 207, 59-78 (1996).
12. Thomason, J. C., Hills, J. M., Clare, A. S., Neville, A. & Richardson, M. Hydrodynamic consequences of barnacle colonization. Hydrobiologia 375, 191-201 (1998). (Pubitemid 28519344)
13. Miron, G., Boudreau, B. & Bourget, E. Intertidal barnacle distribution: a case study using multiple working hypotheses. Mar Ecol Prog Ser 189, 205-219 (1999).
14. Chung, H. C. et al. Bacterial community succession and chemical profiles of subtidal biofilms in relation to larval settlement of the polychaete Hydroides elegans. ISME J 4, 817-828 (2010).
15. Parks, D. H. & Beiko, R. G. Identifying biologically relevant differences between metagenomic communities. Bioinform 26, 715-721 (2010).
16. Silver, S. Bacterial resistances to toxic metal ions-a review. Gene 179, 9-19 (1996). (Pubitemid 26395071)
17. Green, N. M. ATP-driven cation pumps: alignment of sequences. Biochem Soc Trans 17, 970-972 (1989).
18. Fita, I. & Rossmann, M. G. The active center of catalase. J Mol Biol 185, 21-37 (1985). (Pubitemid 16250043)
19. Jeanjean, R. et al. Alarge gene cluster encoding peptide synthetases and polyketide synthases is involved in production of siderophores and oxidative stress response in the cyanobacterium Anabaena sp. strain PCC 7120. Environ Microbiol 10, 2574-2585 (2008).
20. Kim, E. et al. Evidence for the role of 2-hydroxychromene-2-carboxylate isomerase in the degradation of anthracene by Sphingomonas yanoikuyae B1. FEMS Microbio Let 153, 479-484 (1997). (Pubitemid 27359749)
21. Debiane, D. et al. In vitro evaluation of the oxidative stress and genotoxic potentials of anthracene on mycorrhizal chicory roots. Environ Exp Bot 64, 120-127 (2008).
22. Sander, C. S., Chang, H.,Hamm, F., Elsner, P.& Thiele, J. J. Role of oxidative stress and the antioxidant network in cutaneous carcinogenesis. Int J Dermatol 43, 326-335 (2004). (Pubitemid 38714593)
23. Barth, E. et al. Interplay of cellular cAMP levels, sS activity and oxidative stress resistance in Escherichia coli. Microbiology 155, 1680-1689 (2009).
24. Siegele, D. A. Universal stress proteins in Escherichia coli. J Bacteriol 187, 6253-6254 (2005). (Pubitemid 41318381)
25. Chen, J., Lee, S. M. & Mao, Y. Protective effect of exopolysaccharide colanic acid of Escherichia coli O157: H7 to osmotic and oxidative stress. Int J Food Microbiol 93, 281-286 (2004). (Pubitemid 38681002)
26. Keith, L. M. W. & Bender, C. L. AlgT (s22) controls alginate production and tolerance to environmental stress in Pseudomonas syringae. J Bacteriol 181, 7176-7184 (1999).
27. Beech, I. B. & Cheung, C. S. Interactions of exopolymers produced by sulphatereducing bacteria with metal ions. Int Biodeterior Biodegr 35, 59-72 (1995).
28. Kenne, L. & Lindberg, B. Bacterial polysaccharides. The polysaccharides 2, 287-363 (1983).
29. Bordo, D., Djinovic, K. & Bolognesi, M. Conserved patterns in the Cu, Zn superoxide dismutase family. J Mol Biol 238, 366-386 (1994). (Pubitemid 24154718)
30. Hughes, K. T. & Mathee, K. The anti-sigma factors. Annu Rev Microbiol 52, 231-286 (1998). (Pubitemid 28481193)
31. Lesser, M. P. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol 68, 253-278 (2006).
32. Zobayed, S. M. A., Afreen, F. & Kozai, T. Temperature stress can alter the photosynthetic efficiency and secondary metabolite concentrations in St. John's wort. Plant Physiol Biochem 43, 977-984 (2005). (Pubitemid 41785454)
33. Heeb, S., Valverde, C., Gigot-Bonnefoy, C. & Haas, D. Role of the stress sigma factor RpoS in GacA/RsmA-controlled secondary metabolism and resistance to oxidative stress in Pseudomonas fluorescens. FEMS Microbiol Let 243, 251-258 (2005). (Pubitemid 40164414)
34. Hanlon, A. Stress and release: chemical modulation of secondary metabolite production in Aspergillus sp. Massachusetts Institute of Technology. (2006).
35. Touati, D. Iron and oxidative stress in bacteria. Arch biochem biophys 373, 1-6 (2000). (Pubitemid 30046483)
36. Nuran, E., Gurer-Orhan, H. & Aykin-Burns, N. Toxic metals and oxidative stress part I: mechanisms involved in metal-induced oxidative damage. Curr Top Med Chem 6, 529-539 (2001).
37. Colvin, J. R. Synthesis of cellulose in ethanol extracts of Acetobacter xylinum. Nature 183, 1135-1136 (1959).
38. Booth, S. C. et al. Differences in metabolism between the biofilm and planktonic response to metal stress. J Proteome Res 10, 3190-3199 (2011).
39. Thomas, F., Hehemann, J.H., Rebuffet, E., Czjzek, M. & Michel, G. Environmental and gut Bacteroidetes: the food connection. Front Microbiol 2, 93 (2001).
40. Yang, X., Kang, C. M., Brody, M. S. & Price, C. W. Opposing pairs of serine protein kinases and phosphatases transmit signals of environmental stress to activate a bacterial transcription factor. Gene Dev 10, 2265-2275 (1996). (Pubitemid 26322363)
41. March, P. E. Membran-associated GTPases in bacteria. Mol Microbiol 6, 1253-1257 (1992).
42. Chun, M. J., Park, K. J. & Ohk, S. H. Putative down-stream signaling molecule of GTPase in Porphyromonas gingivalis. Appl Biochem Microbiol 48, 350-354 (2012).
43. Zhang, X. S., García-Contreras, R. & Wood, T. K. YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity. J Bacteriol 189, 3051-3062 (2007). (Pubitemid 46697394)
44. Müller, C. M. et al. Type 1 fimbriae, a colonization factor of uropathogenic Escherichia coli, are controlled by the metabolic sensor. PLoS pathog 5, e1000303 (2009).
45. Walderhaug, M. O. et al. KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators. J Bacteriol 174, 2152-2159 (1992).
46. Besemer, K.,Hödl, I., Singer, G. & Battin, T. J. Architectural differentiation reflects bacterial community structure in stream biofilms. ISME J 3, 1318-1324 (2009).
47. Davison, I. R. & Pearson, G. A. Stress tolerance in intertidal seaweeds. J Phycol 32, 196-211 (1996).
48. Wang, Y. et al. Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools. Sci Rep. 3, 01748; doi:10.1038/ srep01748 (2013).
49. Wang, Y., Lee, O. O., Yang, J. K., Li, T. G. & Qian, P. Y. Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea. Peer J 1, 69 (2013).
50. Patel, R. K. & Jain, M. NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7, e30619 (2012).
51. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30 (2000). (Pubitemid 30047706)
52. Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37, 233-238 (2009).
53. Tatusov, R. L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22-28 (2001). (Pubitemid 32054398)
54. Kristiansson, E., Hugenholtz, P. & Dalevi, D. ShotgunFunctionalizeR: An Rpackage for functional comparisons of metagenomes. Bioinform 25, 2737-2738 (2009).
55. Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res 17, 377-386 (2007). (Pubitemid 46376747)