Bacterial communities associated with the decomposition of Fucus vesiculosus in transitional waters

Estuarine, Coastal and Shelf Science

Volumn 110, Issue , 2012, Pages 116-124

  Martins, Patrícia ^a   Lopes, Marta Lobão ^a   Rodrigues, Ana Maria ^a   Gomes, Newton C M ^a   Quintino, Victor ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

Author keywords

Bacterial community; Decomposition process; DGGE; Fucus vesiculosus; Ria de Aveiro; Salinity gradient

Indexed keywords

ALGA; ASSESSMENT METHOD; BACTERIUM; COMMUNITY STRUCTURE; DECOMPOSITION; INTERSPECIFIC INTERACTION; MICROBIAL COMMUNITY; SALINITY; SEAWEED; SPATIOTEMPORAL ANALYSIS;

EID: 84865334934     PISSN: 02727714     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecss.2012.04.003     Document Type: Article

References (61)

1. Abelho M., Graça M. Litter in a first-order stream of a temperate deciduous forest (Margaraça Forest, central Portugal). Hydrobiologia 1998, 386:147-152.
2. ágoston-Szabó E., Dinka M., Némedi L., Horváth G. Decomposition of Phragmites australis rhizome in a shallow lake. Aquatic Botany 2006, 85:309-316.
3. Alvarez S., Rico E., Guerrero M.C., Montes C. Decomposition of Juncus maritimus in two shallow lakes of Doñana National Park. International Review of Hydrobiology 2001, 86:541-554.
4. Anderson M.J. A new method for non-parametric multivariate analysis of variance. Austral Ecology 2001, 26:32-46.
5. Anderson M.J., Gorley R.N., Clarke K.R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods 2008, PRIMER-E, Plymouth, UK, p. 214.
6. Anesio A.M., Abreu P.C., Biddanda B.A. The role of free and attached microorganisms in the decomposition of estuarine macrophyte detritus. Estuarine, Coastal and Shelf Science 2003, 56:197-201.
7. Araya R., Tani K., Takagi T., Yamaguchi N., Nasu M. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiology Ecology 2003, 43:111-119.
8. Bärlocher F., Corkum M. Nutrient enrichment overwhelms diversity effects in leaf decomposition by stream fungi. Oikos 2003, 101:247-252.
9. Bengtsson G. Interactions between fungi, bacteria and beech leaves in a stream microcosm. Oecologia 1992, 89:542-549.
10. Bergfur J., Friberg N. Trade-offs between fungal and bacterial respiration along gradients in temperature, nutrients and substrata: experiments with stream derived microbial communities. Fungal Ecology 2012, 5:46-52.
11. Buchan A., Newell S.Y., Butler M., Biers E.J., Hollibaugh J.T., Moran M.A. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Applied and Environmental Microbiology 2003, 69:6676-6687.
12. Byun S.O., Fang Q., Zhou H., Hickford J.G.H. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Analytical Biochemistry 2009, 385:174-175.
13. Castela J., Ferreira V., Graça M.A.S. Evaluation of stream ecological integrity using litter decomposition and benthic invertebrates. Environmental Pollution 2008, 153:440-449.
14. Chiu J.M.Y., Thiyagarajan V., Tsoi M.M.Y., Qian P.Y. Qualitative and Quantitative Changes in Marine Biofilms as a Function of Temperature and Salinity in Summer and Winter 2006, Cambridge University Press, pp. 1-13.
15. Clarke K.R., Gorley R.N. PRIMER v6: User Manual/Tutorial 2006, PRIMER-E, Plymouth, UK, p. 190.
16. Cleary D.F.R., Mendonça-Hagler L.C.S., Smalla K., Gomes N.C.M. Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PLoS ONE 2012, 7:e29380.
17. Dang H., Lovell C.R. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Applied and Environmental Microbiology 2000, 66:467-475.
18. Das M., Royer T.V., Leff L.G. Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream. Applied and Environmental Microbiology 2007, 73:756-767.
19. Duarte S., Pascoal C., Alves A., Correia A., Cássio F. Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques. Microbiological Research 2009, 165:351-362.
20. Ferris M.J., Muyzer G., Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Applied and Environmental Microbiology 1996, 62:340-346.
21. Gafan G.P., Lucas V.S., Roberts G.J., Petrie A., Wilson M., Spratt D.A. Statistical analyses of complex denaturing gradient gel electrophoresis profiles. Journal of Clinical Microbiology 2005, 43:3971-3978.
22. Gessner M.O. Breakdown and nutrient dynamics of submerged Phragmites shoots in the littoral zone of a temperate hardwater lake. Aquatic Botany 2000, 66:9-20.
23. Gomes N.C.M., Borges L.R., Paranhos R., Pinto F.N., Mendoça-Hagler F.N., Smalla K. Exploring the diversity of bacterial communities in sediments of urban mangrove forests. FEMS Microbiology Ecology 2008, 66:96-109.
24. Graça M.A.S. Patterns and processes in detritus-based stream systems. Limnologica 1993, 23:107-114.
25. Graça M.A.S. The role of invertebrates on leaf litter decomposition in streams - a review. International Review of Hydrobiology 2001, 86:383-393.
26. Gulis V., Suberkropp K. Effect of inorganic nutrients on relative contributions of fungi and bacteria to carbon flow from submerged decomposing leaf litter. Microbial Ecology 2003, 45:11-19.
27. Hagen E.M., Webster J.R., Benfield E.F. Are leaf breakdown rates a useful measure of stream integrity along an agricultural landuse gradient?. Journal of the North American Benthological Society 2006, 25:330-343.
28. Henriques I.S., Alves A., Tacão M., Almeida A., Cunha A., Correia A. Seasonal and spatial variability of free-living bacterial community composition along an estuarine gradient (Ria de Aveiro, Portugal). Estuarine, Coastal and Shelf Science 2006, 68:139-148.
29. Heuer H., Wieland G., Schönfeld J., Schönwälder S., Gomes N.C.M., Smalla K. Bacterial Community Profi{ligature}ling Using DGGE or TGGE Analysis. Environmental Molecular Microbiology: Protocols and Applications 2001, 177-190. Horizon Scientific Press, Wymondham, UK. P. Rouchelle (Ed.).
30. Heuer H., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. Modern Soil Microbiology 1997, 353-373. Marcel Dekker, New York. J.D. van Elsas, E.M.H. Wellington, J.T. Trevors (Eds.).
31. Hunter R.D. Changes in carbon and nitrogen content during decomposition of three macrophytes in freshwater and marine environments. Hydrobiologia 1976, 51:119-128.
32. Jackson C.R., Churchill P.F., Roden E.E. Successional changes in bacterial assemblage structure during epilithic biofilm development. Ecology 2001, 82:555-566.
33. Jones P., Cottrell M., Kirchman D., Dexter S. Bacterial community structure of biofilms on artificial surfaces in an estuary. Microbial Ecology 2007, 53:153-162.
34. Komínková D., Kuehn K.A., Büsing N., Steiner D., Gessner M.O. Microbial biomass, growth, and respiration associated with submerged litter of Phragmites australis decomposing in a littoral reed stand of a large lake. Aquatic Microbial Ecology 2000, 22:271-282.
35. Lau S.C.K., Thiyagarajan V., Cheung S.C.K., Qian P.-Y. Roles of bacterial community composition in biofilms as a mediator for larval settlement of three marine invertebrates. Aquatic Microbial Ecology 2005, 38:41-51.
36. Lee J.-W., Nam J.-H., Kim Y.-H., Lee K.-H., Lee D.-H. Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces. The Journal of Microbiology 2008, 46:174-182.
37. Logares R., Bråte J., Bertilsson S., Clasen J.L., Shalchian-Tabrizi K., Rengefors K. Infrequent marine freshwater transitions in the microbial world. Trends in Microbiology 2009, 17:414-422.
38. Lopes M.L., Martins P., Ricardo F., Rodrigues A.M., Quintino V. In situ experimental decomposition studies in estuaries: a comparison of Phragmites australis and Fucus vesiculosus. Estuarine. Coastal and Shelf Science 2011, 92:573-580.
39. McLusky D.S., Elliott M. The Estuarine Ecosystem. Ecology, Threats and Management 2004, Oxford University Press, Oxford, UK, p. 214. third ed.
40. Menendez M., Martinez M., Hernandez O., Comin F.A. Comparison of leaf decomposition in two Mediterranean rivers: a large eutrophic river and an oligotrophic stream (S Catalonia, NE Spain). International Review of Hydrobiology 2001, 86:475-486.
41. Muyzer G., Waal E.C.D., Uitierlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 1993, 59:695-700.
42. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Kluwer Academic Publishers 1998, 73:127-141.
43. Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology 1999, 2:317-322.
44. Nikolcheva L.G., Cockshutt A.M., Bärlocher F. Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Applied and Environmental Microbiology 2003, 69:2548-2554.
45. Nubel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. Journal of Bacteriology 1996, 178:5636-5643.
46. Pascoal C., Cássio F. Contribution of fungi and bacteria to leaf litter decomposition in a polluted river. Applied and Environmental Microbiology 2004, 70:5266-5273.
47. Petersen R.C., Cummins K.W. Leaf processing in a woodland stream. Freshwater Biology 1974, 4:343-368.
48. Pinna M., Fonnesu A., Sangiorgio F., Basset A. Influence of summer drought on spatial patterns of resource availability and detritus processing in mediterranean stream Sub-Basins (Sardinia, Italy). International Review of Hydrobiology 2004, 89:484-499.
49. Quintino V., Sangiorgio F., Ricardo F., Mamede R., Pires A., Freitas R., Rodrigues A.M., Basset A. In situ experimental study of reed leaf decomposition along a full salinity gradient. Estuarine, Coastal and Shelf Science 2009, 85:497-506.
50. Quintino V., Sangiorgio F., Mamede R., Ricardo F., Sampaio L., Martins R., Freitas R., Rodrigues A.M., Basset A. The leaf-bag and the sediment sample: two sides of the same ecological quality story?. Estuarine, Coastal and Shelf Science 2011, 95:326-337.
51. Reice S.R., Herbst G. The role of salinity in decomposition leaves of Phragmites australis in desert streams. Journal of Arid Environments 1982, 5:361-368.
52. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Research 2001, 11:3-11.
53. Ryckegem G.V., Verbeken A. Fungal diversity and community on Phragmites australis (poaceae) along a salinity gradient in the Scheldt estuary (Belgium). Nova Hedwigia 2005, 80:173-197.
54. Sampaio A., Cortes R., Leão C. Yeast and macroinvertebrate communities associated with leaf litter decomposition in a second order stream. International Review of Hydrobiology 2004, 89:453-466.
55. Sangiorgio F., Basset A., Pinna M., Sabetta L., Abbiati M., Ponti M., et al. Ecosystem processes: litter breakdown patterns in Mediterranean and Black Sea transitional waters. Transitional Waters Bulletin 2007, 3:51-55.
56. Simon M., Grossart H., Schweitzer B., Ploug H. Microbial ecology of organic aggregates in aquatic ecosystems. Aquatic Microbial Ecology 2002, 28:175-211.
57. Sinsabaugh R.L., Linkins A.E. Enzymic and chemical analysis of particulate organic matter from a boreal river. Freshwater Biology 1990, 23:301-309.
58. Suberkropp K., Klug M.J. Fungi and bacteria associated with leaves during processing in a woodland stream. Ecology 1976, 57:707-719.
59. Suberkropp K. Fungal growth, production, and sporolation during leaf decomposition in two streams. Applied and Environmental Microbiology 2001, 67:5063-5068.
60. Sweet M.J., Croquer A., Bythell J.C. Development of bacterial biofilms on artificial corals in comparison to surface-associated microbes of hard corals. PLoS ONE 2011, 6:e21195.
61. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 1991, 173:697-703.