Effects of organic perturbation on marine sediment betaproteobacterial ammonia oxidizers and on benthic nitrogen biogeochemistry

Marine Ecology Progress Series

Volumn 392, Issue , 2009, Pages 17-32

  Bissett, A ^a,b,f   Cook, P L M ^c   Macleod, C ^d   Bowman, J P ^b   Burke, C ^a,e  

^a School of Aquaculture   (Australia)

^b UNIVERSITY OF TASMANIA   (Australia)

^c MONASH UNIVERSITY   (Australia)

^d UNIVERSITY OF TASMANIA   (Australia)

^e UNIVERSITY OF TASMANIA   (Australia)

^f CSIRO   (Australia)

Author keywords

Ammonia oxidising bacteria; Denitrification; Eutrophication; Nitrification; Sediment

Indexed keywords

AMMONIA; BENTHOS; BIOGEOCHEMISTRY; COMMUNITY STRUCTURE; DENITRIFICATION; DNA; ELECTROKINESIS; EUTROPHICATION; GEL; MARINE SEDIMENT; MICROBIAL COMMUNITY; NITROGEN CYCLE; ORGANIC POLLUTANT; POLLUTANT REMOVAL; POLYMERASE CHAIN REACTION; POREWATER; SEDIMENT CHEMISTRY; SEDIMENT POLLUTION;

BACTERIA (MICROORGANISMS); NITROSOMONADALES;

EID: 70350344070     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps08244     Document Type: Article

References (58)

1. Aakra A, Utaker J, Nes I (1999) RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. Int J Syst Bacteriol 49:123-130
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI- BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Anderson MJ (2003a) CAP: a FORTRAN computer program for canonical analysis of principle coordinates. Department of Statistics, University of Auckland, New Zealand
4. Anderson MJ (2003b) DISTLM, Vol 2: a FORTRAN computer program to calculate a distance-based multivariate analysis for a linear model. Department of Statistics, University of Auckland, New Zealand
5. Anderson MJ (2003c) NPMANOVA: a FORTRAN computer program for non-parametric multivariate analysis of variance (for any two factor design) using permutation tests. Department of Statistics, University of Auckland
6. Anderson MJ (2003d) XMATRIX: a FORTRAN computer program for calculating design matrices for terms in ANOVA designs in a linear model. Department of Statistics, University of Auckland
7. Atlas RM, Bartha R (1998) Development of microbial communities. In: Atlas RM, Bartha R (eds) Microbial ecology: fundamentals and applications. Benjamin Cummings, San Francisco, CA
8. Bissett A, Bowman J, Burke C (2006) Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiol Ecol 55:48-56
9. Bissett A, Burke C, Bowman JP, Cook PLM (2007) Bacterial community shifts in organically perturbed sediments. Environ Microbiol 9:46-60
10. Blackburn TH, Blackburn ND (1992) Model of nitrification and denitrification in marine sediments. FEMS Microbiol Lett 100:517-522
11. Butler ECV (2006) The tail of two rivers in Tasmania; the Derwent and Huon Estuaries. In: Wangersky P (ed) Handbook of environmental chemistry, Vol 5H. Springer, Berlin, p 1-49
12. Christensen PB, Rysgaard S, Sloth NP, Dalsgaard T, Schwaerter S (2000) Sediment mineralization, nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium in an estuarine fjord with sea cage trout farms. Aquat Microb Ecol 21:73-84
13. Clarke KR, Warwick RM (2001) Change in marine communities: an approach to statistical analysis and interpretation, 2nd edn. PRIMER-E, Plymouth
14. Craib JS (1965) A sampler for taking short undisturbed marine cores. ICES J Mar Sci 30:34-39
15. Dalsgaard T, Nielsen LP, Brotas V, Viaroli P and others (2000) Protocol handbook for NICE-nitrogen cycling in estuaries: a project under the EU research programme: Marine Science and Technology (MAST III), National Environmental Research Institute, Denmark, Silkeborg
16. Dalsgaard T, Thamdrup B, Canfield DE (2005) Anaerobic ammonium oxidation (anammox) in the marine environment. Res Microbiol 156:457-464
17. Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G (2008) Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology 154:2084-2095
18. de Bie MJM, Speksnijder A, Kowalchuk GA, Schuurman T and others (2001) Shifts in the dominant populations of ammonia-oxidizing beta-subclass Proteobacteria along the eutrophic Schelde estuary. Aquat Microb Ecol 23: 225-236
19. Dong LF, Thornton DCO, Nedwell DB, Underwood GJC (2000) Denitrification in sediments of the River Colne estuary, England. Mar Ecol Prog Ser 203:109-122
20. Grasshoff K (1983) Methods of seawater analysis, 2nd edn. Verlag Chemie, Weinheim
21. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
22. Heilskov A, Holmer M (2001) Effects of benthic fauna on organic matter mineralization in fish farm sediments: importance of size and abundance. J Mar Sci 58:427-434
23. Hermansson A, Lindgren PE (2001) Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl Environ Microbiol 67:972-976
24. Hinck S, Neu TR, Lavik G, Mussmann M, de Beer D, Jonkers HM (2007) Physiological adaptation of a nitrate-storing Beggiatoa sp. to diel cycling in a phototrophic hypersaline mat. Appl Environ Microbiol 73:7013-7022
25. Jensen KM, Jensen MH, Kristensen E (1996) Nitrification and denitrification in Wadden Sea sediments (Konigshafen, Island of Sylt, Germany) as measured by nitrogen isotope pairing and isotope dilution. Aquat Microb Ecol 11: 181-191
26. Joye SB, Hollibaugh JT (1995) Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270:623-625
27. Kowalchuk GA, Stephen J, De Boer W, Prosser J, Embley T, Woldendorp J (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel elec- trophoresis and sequencing of PCR-amplified 16S riboso- mal DNA fragments. Appl Environ Microbiol 63: 1489-1497
28. Kowalchuk GA, Bodelier PLE, Heilig GHJ, Stephen JR, Laanbroek HJ (1998) Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol Ecol 27:339-350
29. Kristensen E (1988) Benthic fauna and biogeochemical processes in marine sediments: microbial activities and fluxes. In: Blackburn TH, Sorensen J (eds) Nitrogen cycling in coastal marine environments, Vol 33. John Wiley & Sons, Chichester, p 275-299
30. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, p 115-175
31. Legendre P, Anderson MJ (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69:1-24
32. Leininger S, Urich T, Schloter M, Schwark L and others (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809
33. Ludwig W, Strunk O, Klugbauer S, Klugbauer N and others (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568
34. Macdonald RM (1986) Nitrification in soil: an introductory history. In: Prosser JI (ed) Nitrification. IRL Press, Oxford, p 1-16
35. Macleod CKA, Bissett A, Burke C, Forbes S and others (2004) Development of novel methods for the assessment of sediment condition and determination of management protocols for sustainable finfish cage aquaculture operations. Aquafin CRC, Adelaide, South Australia, http://www.tafi.org.au/publications/ FRDC-2000-164-Aug04.pdf
36. Macleod CK, Crawford CM, Moltschaniwskyj NA, Forbes SE (2006) Evaluation of short-term fallowing as a strategy for the management of recurring organic enrichment under salmon cages. Mar Pollut Bull 52:1458-1466
37. Macleod CK, Moltschaniwskyj NA, Crawford CM (2007) Biological recovery from organic enrichment: some systems cope better than others. Mar Ecol Prog Ser 342:41-53
38. Magalhães CM, Joye SB, Moreira RM, Wiebe WJ, Bordalo AA (2005) Effect of salinity and inorganic nitrogen concentrations on nitrification and denitrification rates in intertidal sediments and rocky biofilms of the Douro River estuary, Portugal. Water Res 39:1783-1794
39. McCaig AE, Phillips CJ, Stephen JR, Kowalchuk GA and others (1999) Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl Environ Microbiol 65:213-220
40. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction- amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700
41. Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966-2978
42. Nielsen LP (1992) Denitrification in sediment determined from nitrogen isotope pairing. FEMS Microbiol Ecol 86: 357-362
43. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35: 7188-7196
44. Purdy KJ, Embley TM, Takii S, Nedwell DB (1996) Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl Environ Microbiol 62:3905-3907
45. 15N techniques. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, London, p 287-295
46. Risgaard-Petersen N, Nielsen LP, Rysgaard S, Dalsgaard T, Meyer RL (2003) Application of the isotope pairing technique in sediments where anammox and denitrification coexist. Limnol Oceanogr Meth 1:63-73
47. Santoro AE, Francis CA, de Sieyes NR, Boehm AB (2008) Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ Microbiol 10: 1068-1079
48. Sloth NP, Blackburn H, Hansen LS, Risgaard-Petersen N, Lomstein BA (1995) Nitrogen cycling in sediments with different organic loading. Mar Ecol Prog Ser 116:163-170
49. Soetaert K, Middelburg JJ, Herman PMJ, Buis K (2000) On the coupling of benthic and pelagic biogeochemical models. Earth Sci Rev 51:173-201
50. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103:12115-12120
51. Stephen JR, McCaig AE, Smith Z, Prosser JI, Embley TM (1996) Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia- oxidizing bacteria. Appl Environ Microbiol 62:4147-4154
52. Sundberg C, Stendahl JSK, Tonderski K, Lindgren PE (2007) Overland flow systems for treatment of landfill leachates-potential nitrofication and structure of the ammonia-oxidising bacterial community during a growing season. Soil Biol Biochem 39:127-138
53. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
54. Valderrama JC (1981) The simultaneous analysis of TP and TN in natural waters. Mar Chem 10:109-122
55. Watson RJ, Butler ECV, Clemenston LA, Berry KM (2005) Flow injection analysis with fluorescence detection for the determination of trace levels of ammonium in seawater. J Environ Monit 7:37-42
56. Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Guillaumaud N, Le Roux X (2007) Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environ Microbiol 9:2211-2219
57. Wildish DJ, Hargrave BT, Macleod CKA, Crawford CM (2003) Detection of organic enrichment near finfish net-pens by sediment profile imaging at SCUBA-accessible depths. J Exp Mar Biol Ecol 285-286:403-413
58. Wu SS, Tsutsumi H, Kita-tsukamoto K, Kogure K, Ohwada K, Wada M (2003) Visualization of the respiring bacteria in sediments inhabited by Capitella sp. 1. Fish Sci 69: 170-175