Prokaryotes in salt marsh sediments of Ria de Aveiro: Effects of halophyte vegetation on abundance and diversity

Estuarine, Coastal and Shelf Science

Volumn 110, Issue , 2012, Pages 61-68

  Oliveira, Vanessa ^a   Santos, Ana L ^a   Aguiar, Claúdia ^a   Santos, Luisa ^a   Salvador, Ângelo C ^a   Gomes, Newton C M ^a   Silva, Helena ^a   Rocha, Sílvia M ^a   Almeida, Adelaide ^a   Cunha, Ângela ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

Author keywords

Archaea; Prokaryote communities; Root exudates; Salt marsh; SRB

Indexed keywords

ABUNDANCE; COASTAL SEDIMENT; COLONIZATION; DOMINANCE; ESTUARINE ENVIRONMENT; EXUDATION; GRASS; HALOPHYTE; LITHOLOGY; PRINCIPAL COMPONENT ANALYSIS; PROKARYOTE; RELATIVE ABUNDANCE; ROOT SYSTEM; SALTMARSH; SPECIES DIVERSITY; VERTICAL DISTRIBUTION;

AVEIRO [PORTUGAL]; PORTUGAL; RIA DE AVEIRO;

ARCHAEA; BACTERIA (MICROORGANISMS); HALIMIONE PORTULACOIDES; PROKARYOTA; SPARTINA MARITIMA;

EID: 84865313329     PISSN: 02727714     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecss.2012.03.013     Document Type: Article

References (71)

1. Almeida M.A., Alcantara F. Bacterial colonization of seston particles in brackish waters (Ria de Aveiro, Portugal). Marine Ecology Progress Series 1992, 89:165-173.
2. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Journal of Bacteriology 1990, 56:762-770.
3. Asensio D., Peñuelas J., Filella I., Llusià J. On-line screening of soil VOCs exchange responses to moisture, temperature and root presence. Plant and Soil 2007, 291:249-261.
4. Berg G., Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology 2009, 68:1-13.
5. Bertin C., Yang X., Weston L.A. The role of root exudates and allelochemicals in the rhizosphere. Plant and Soil 2003, 256:67-83.
6. Bezemer T.M., van Dam N.M. Linking aboveground and belowground interactions via induced plant defenses. Trends in Ecology & Evolution 2005, 20:617-624.
7. Bouvier T., Del Giorgio P.A. Factors influencing the detection of bacterial cells using fluorescence in situ hybridization (FISH): a quantitative review of published reports. FEMS Microbiology Ecology 2003, 44:3-15.
8. Bowen J.L., Crump B.C., Deegan L.A., Hobbie J.E. Salt marsh sediment bacteria: their distribution and response to external nutrient inputs. ISME Journal 2009, 3:924-934.
9. Burke D.J., Hamerlynck E.P., Hahn D. Interactions among plant species and microorganisms in salt marsh sediments. Applied and Environmental Microbiology 2002, 68:1157-1164.
10. Cébron A., Louvel B., Faure P., France-Lanord C., Chen Y., Murrell J.C., Leyval C. Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates. Environmental Microbiology 2011, 13:722-736.
11. Christopher E.B., Megan D., Peter W.B., Charles R.L. Host-specific ecotype diversity of rhizoplane diazotrophs of the perennial glasswort Salicornia virginica and selected salt marsh grasses. Aquatic Microbial Ecology 2001, 23:293-300.
12. Cole J.R., Chai B., Farris R.J., Wang Q., Kulam-Syed-Mohideen A.S., McGarrell D.M., Tiedje J.M. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research 2007, 35:D169-D172.
13. Créach V., Lucas F., Deleu C., Bertru G., Mariotti A. Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment. Journal of Microbiological Methods 1999, 38:43-52.
14. Cunha M.A., Pedro R., Almeida M.A., Silva M.H. Activity and growth efficiency of heterotrophic bacteria in a salt marsh (Ria de Aveiro, Portugal). Microbiological Research 2005, 160:279-290.
15. Cunha A., Almeida A., Re A., Martins A., Alcantara F. Perylene toxicity in the estuarine environment of Ria de Aveiro (Portugal). Ecotoxicology 2006, 15:171-185.
16. Daims H., Brühl A., Amann R., Schleifer K.H., Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Systematics and Applied Microbiology 1999, 22:434-444.
17. Dennis P.G., Miller A.J., Hirsch P.R. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?. FEMS Microbiology Ecology 2010, 72:313-327.
18. Dias J.M., Lopes J.F., Dekeyser I. Hydrological characterisation of Ria de Aveiro, Portugal, in early summer. Oceanologica Acta 1999, 22:473-485.
19. Eddy N.O., Awe F.E., Siaka A.A., Magaji L., Ebenso E.E. Chemical information from GC-MS studies of ethanol extract of Andrographis paniculata and their corrosion inhibition potentials on mild steel in HCl solution. International Journal of Electrochemical Science 2011, 6:4316-4328.
20. Ens E., Bremner J., French K., Korth J. Identification of volatile compounds released by roots of an invasive plant, bitou bush (Chrysanthemoides monilifera spp. rotundata), and their inhibition of native seedling growth. Biological Invasions 2009, 11:275-287.
21. Fan T.W.M., Lane A.N., Pedler J., Crowley D., Higashi R.M. Comprehensive analysis of organic ligands in whole root exudates using nuclear magnetic resonance and gas chromatography-mass spectrometry. Analytical Biochemistry 1997, 251:57-68.
22. First M.R., Hollibaugh J.T. Environmental factors shaping microbial community structure in salt marsh sediments. Marine Ecology Progress Series 2010, 399:15-26.
23. Goulhen F., Gloter A., Guyot F., Bruschi M. Cr(VI) detoxification by Desulfovibrio vulgaris strain Hildenborough: microbe-metal interactions studies. Applied Microbiology and Biotechnology 2006, 71:892-897.
24. Grasshoff K. Determination of nitrite. Methods of Seawater Analysis 1983, 180-187. Wiley-VCH. M.E.K. Grasshoff, K. Kremling (Eds.).
25. Grayston S.J., Vaughan D., Jones D. Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Applied Soil Ecology 1997, 5:29-56.
26. Grayston S.J., Wang S., Campbell C.D., Edwards A.C. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biology and Biochemistry 1998, 30:369-378.
27. Haichar F.Z., Marol C., Berge O., Rangel-Castro J.I., Prosser J.I., Balesdent J., Achouak W. Plant host habitat and root exudates shape soil bacterial community structure. ISME Journal 2008, 2:1221-1230.
28. Hewson L., O'neil J.M., Fuhrman J.A., Dennison W.C. Virus-like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries. Applied and Environmental Microbiology 2001, 46:1734-1746.
29. Hines M.E., Evans R.S., Willis S.G., Rooney-Varga J.N., Genthner B.R.S., Friedman S., Devereux R. Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Applied and Environmental Microbiology 1999, 65:2209-2216.
30. Jorgensen B.B. Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature 1982, 296:643-645.
31. Jorgensen B.B., Bak F. Pathways and microbiology of thiosulfate transformations and sulfate reduction in a marine sediment (Kattegat, Denmark). Applied and Environmental Microbiology 1991, 57:847-856.
32. Joye S.B., Paerl H.W. Contemporaneous nitrogen fixation and denitrification in intertidal microbial mats: rapid response to runoff events. Marine Ecology Progress Series 1933, 94:267-274.
33. Kim B., Oh H.-M., Kang H., Chun J. Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. Journal Microbiology 2005, 43:141-151.
34. Kolmert å, Wikström P., Hallberg K.B. A fast and simple turbidimetric method for the determination of sulfate in sulfate-reducing bacterial cultures. Journal of Microbiological Methods 2000, 41:179-184.
35. Langenheim J.H. Higher plant terpenoids: a phytocentric overview of their ecological roles. Journal of Chemical Ecology 1994, 20:1223-1280.
36. LaRocque J.R., Bergholz P.W., Bagwell C.E., Lovell C.R. Influence of host plant-derived and abiotic environmental parameters on the composition of the diazotroph assemblage associated with roots of Juncus roemerianus. Antonie van Leeuwenhoek 2004, 86:249-261.
37. Larsonneur C. La cartographie des dépots meubles sur le plateau continental français: méthodo mise au point et utilisée en Manche. Journal de Recherche Oceanographique 1977, 2:34-39.
38. Llobet-Brossa E., Rosselló-Mora R., Amann R. Microbial community composition of Wadden Sea sediments as revealed by fluorescent in situ hybridization. Applied and Environmental Microbiology 1998, 64:2691-2696.
39. Llobet-Brossa E., Rabus R., Böttcher M.E., Könneke M., Finke N., Schramm A., Amann R. Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multi-method approach. Aquatic Microbial Ecology 2002, 29:211-226.
40. Loy A., Maixner F., Wagner M., Horn M. ProbeBase-an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Research 2007, 35:D800-D804.
41. Mendonça A., Duarte A.C., Santos E.B.H. Spectroscopic properties of sedimentary humic acids from a salt marsh (Ria de Aveiro, Portugal): comparison of sediments colonized by Halimione portulacoides (L.) Aellen and non-vegetated sediments. Biogeochemistry 2004, 69:159-174.
42. Moin N.S., Nelson K.A., Bush A., Bernhard A.E. Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments. Applied and Environmental Microbiology 2009, 75:7461-7468.
43. Moriarty D.J.W., Pollard P.C. DNA synthesis as a measure isotope analysis of microbial biomarkers of bacterial production in seagrass sediments. Marine Ecology Progress Series 1981, 5:151-156.
44. Moter A., Göbel U.B. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiological Methods 2000, 41:85-112.
45. Munson M.A., Nedwell D.B., Embley T.M. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Applied and Environmental Microbiology 1997, 63:4729-4733.
46. Nedwell D.B., Embley T.M., Purdy K.J. Sulphate reduction, methanogenesis and phylogenetics of the sulphate reducing bacterial communities along an estuarine gradient. Aquatic Microbial Ecology 2004, 37:209-217.
47. Nelson K.A., Moin N.S., Bernhard A.E. Archaeal diversity and the prevalence of Crenarchaeota in salt marsh sediments. Applied and Environmental Microbiology 2009, 75:4211-4215.
48. Owen S.M., Clark S., Pompe M., Semple K.T. Biogenic volatile organic compounds as potential carbon sources for microbial communities in soil from the rhizosphere of Populus tremula. FEMS Microbiology Letters 2007, 268:34-39.
49. Pernthaler J., Glöckner F.O., Schönhuber W., Amann R. Fluorescence in situ hybridization. Methods in Microbiology 2001, 207-210. Academic Press. J. P (Ed.).
50. Piceno Y.M., Lovell C.R. Stability in natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microbial Ecology 2000, 39:32-40.
51. Purdy K.J., Embley T.M., Nedwell D.B. The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments. Antonie van Leeuwenhoek 2002, 81:181-187.
52. Purdy K.J., Nedwell D.B., Martin E.T., Takii S. Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments. FEMS Microbiology Ecology 2001, 36:165-168.
53. Quintino V., Rodrigues A.M., Gentil F. Assessment of macrozoobenthic communities in the lagoon of óbidos, western coast of Portugal. Scientia Marina 1989, 53:645-654.
54. Rabus R., Widdel F., Fukui M. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Applied and Environmental Microbiology 1996, 62:3605-3613.
55. Roden E., Tuttle J. Inorganic sulfur turnover in oligohaline estuarine sediments. Biogeochemistry 1993, 22:81-105.
56. Rogers S.W., Ong S.K., Moorman T.B. Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH. Chemosphere 2007, 69:1563-1573.
57. Sahm K., Knoblauch C., Amann R. Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine Arctic sediments. Applied and Environmental Microbiology 1999, 65:3976-3981.
58. Santos L., Cunha A., Silva H., Cacador I., Dias J.M., Almeida A. Influence of salt marsh on bacterial activity in two estuaries with different hydrodynamic characteristics (Ria de Aveiro and Tagus Estuary). FEMS Microbiology Ecology 2007, 60:429-441.
59. Schubauer J.P., Hopkinson C.S. Above- and belowground emergent macrophyte production and turnover in a coastal marsh ecosystem, Georgia. Limnology and Oceanography 1984, 29:1052-1065.
60. Silva H., Dias J.M., Caçador I. Is the salt marsh vegetation a determining factor in the sedimentation processes?. Hydrobiologia 2008, 621:33-47.
61. Silva I., Rocha S.M., Coimbra M.A., Marriott P.J. Headspace solid-phase microextraction combined with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry for the determination of volatile compounds from marine salt. Journal of Chromatography A 2010, 1217:5511-5521.
62. Singh B.K., Millard P., Whiteley A.S., Murrell J.C. Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiology 2004, 12:386-393.
63. Smalla K., Wieland G., Buchner A., Zock A., Parzy J., Kaiser S., Berg G. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Applied and Environmental Microbiology 2001, 67:4742-4751.
64. Steeghs M., Bais H.P., de Gouw J., Goldan P., Kuster W., Northway M., Vivanco J.M. Proton-transfer-reaction mass spectrometry as a new tool for real time analysis of root-secreted volatile organic compounds in Arabidopsis. Plant Physiology 2004, 135:47-58.
65. Torsvik V., Øvreås L. Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology 2002, 5:240-245.
66. Vladár P., Rusznyák A., Márialigeti K., Borsodi A. Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach. Microbial Ecology 2008, 56:64-75.
67. Biology of Halophytes 1972, Academic Press, New York. Y. Waisel (Ed.).
68. Walker T.S., Bais H.P., Grotewold E., Vivanco J.M. Root exudation and rhizosphere biology. Plant Physiol 2003, 132:44-51.
69. Webster G., Rinna J., Roussel E.G., Fry J.C., Weightman A.J., Parkes R.J. Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of the Severn Estuary, UK, revealed by stable-isotope probing. FEMS Microbiology Ecology 2010, 72:179-197.
70. Wilms R., Sass H., Kopke B., Koster J., Cypionka H., Engelen B. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Applied and Environmental Microbiology 2006, 72:2756-2764.
71. Yang C.H., Crowley D.E. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Applied and Environmental Microbiology 2000, 66:345-351.