Molecular approaches to marine microbial ecology and the marine nitrogen cycle

Annual Review of Earth and Planetary Sciences

Volumn 33, Issue , 2005, Pages 301-333

  Ward, Bess B ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

16S rRNA; Diversity; Functional genes; Gene expression; Genomics

Indexed keywords

CATALYSIS; ECOLOGY; ENZYMES; GENES; NITROGEN; RNA; SURFACE WATERS;

BIOGEOCHEMICAL PROCESSES; MARINE FOOD WEB; MARINE NITROGEN CYCLE; MICROBIAL ECOLOGY;

OCEAN HABITATS;

GENE EXPRESSION; MICROBIAL ACTIVITY; NITROGEN CYCLE; RNA; SPECIES DIVERSITY;

EID: 20544477740     PISSN: 00846597     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.earth.33.092203.122514     Document Type: Review

References (105)

1. Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, et al. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69:6875-87
2. Baldwin BR, Nakatsu CH, Nies L. 2003. Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl. Environ. Microbiol. 69:3350-58
3. Bartlett JMS, Stirling C. 2003. PCR Protocols. Totowa, NJ: Humana Press. 545 pp.
4. Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-5
5. Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-89
6. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. 2003. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5:566-82
7. Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-26
8. Braker G, Ayala-del-Rio HL, Devol AH, Fesefeldt A. Tiedje JM. 2001. Community structure of denitrifiers, Bacteria and Archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67:1893-901
9. Braker G, Zhou JZ, Wu LY, Devol AH, Tiedje JM. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl. Environ. Microbiol. 66:2096-104
10. Caffrey JM, Harrington N, Solem I, Ward BB. 2003. Biogoechemical processes in a small California estuary. 2. Nitrificaiton activity, community structure and role in nitrogen budgets. Mar. Ecol. Prog. Ser. 248:27-40
11. Casciotti KL, Sigman DM, Ward BB. 2003. Linking diversity and biogeochemistry in ammonia-oxidizing bacteria. Geomicrobiol. J. 20:335-53
12. Castro HF, Williams NH, Ogram A. 2000. Phylogeny of sulfate-reducing bacteria. FEMS Microbiol. Ecol. 31:1-9
13. Chain P, Lamerdin J, Larimer FW, Regala W, Lao V, et al. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185:2759-73
14. Chapelle FH, O'Neill K, Bradley PM, Methe BA, Ciufo SA, et al. 2002. A hydrogen-based subsurface microbial community dominated by methanogens. Nature 413:312-15
15. Chisholm SW, Olson RJ, Zettler ET, Goericke R, Waterbury JB, Welschmeyer NA. 1988. A novel free-living Prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-43
16. Cho J-C, Tiedje JM. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67: 3677-82
17. Costello AM, Lidstrom ME. 1999. Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl. Environ. Microbiol. 65:5066-74
18. Curtis TP, Sloan WT, Scannell JW. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99:10494-99
19. 2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422:606-8
20. De Kruif P. 1996. Microbe Hunters. San Diego, CA: Harcourt Brace. 357 pp.
21. DeLong EF, Pace NR. 2001. Environmental diversity of Bacteria and Archaea. Syst. Biol. 50:470-78
22. DeLong EF, Taylor LT, Marsh TL, Preston CM. 1999. Visualization and enumeration of marine planktonic archaea and bacteria by using polynucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65:5554-63
23. DeLong EF, Wu KY, Prezelin BB, Jovine RVM. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-97
24. Detmers J, Bruchert V, Habicht KS, Kuever J. 2001. Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes. Appl. Environ. Microbiol. 67:888-94
25. Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML. 2003. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microbiol. 69:2765-72
26. Dionisi HM, Layton AC, Harms G, Gregory IR, Robinson KG, Sayler GS. 2002. Quantification of Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and Nitrospira spp. from full-scale wastewater treatment plants by competitive PCR. Appl. Environ. Microbiol. 68:245-53
27. Francis CA, O'Mullan GD, Ward BB. 2003. Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1: 129-40
28. Friedrich MW. 2002. Phylogenetic analysis reveals multiple lateral transfers of adenosine5′-phosphosulfate reductase genes among sulfate-reducing microorganisms. J. Bacteriol. 184:278-89
29. Fukuba T, Ogawa M, Fujii T, Naganuma T. 2003. Phylogenetic diverstiy of dissimilatory sulfite reductase genes from deep-sea cold seep sediment. Mar. Biotechnol. 5:458-68
30. Furhman JA, McCallum K, Davis A.A. 1992. Novel major Archaebacterial group from marine plankton. Nature 356:148-49
31. Garcia J-L, Patel BKC, Ollivier G. 2000. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea. Anaerobe 6: 205-26
32. Gieseke A, Purkhold U, Wagner M, Amann R, Schramm A. 2001. Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl. Environ. Microbiol. 67:1351-62
33. Giovannoni SJ, Britschgi RB, Moyer CL, Field KG. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
34. Giovannoni SJ, Rappe MS. 2000. Evolution diversity and molecular ecoology of marine prokaryotes. In Microbial Ecology of the Oceans, ed. DL Kirchman. New York: Wiley-Liss
35. Glockner AB, Jungst A, Zumft WG. 1993. Copper-containing nitrite reductase from Pseudomonas aureofaciens is functional in a mutationally cytochrome cd1-free background (NirS-) of Pseudomonas stutzeri. Arch. Microbiol. 160:18-26
36. Graham CA, Hill AJM. 2001. DNA Sequencing Protocols. Totowa, NJ: Humana Press. 244 pp.
37. Granger J, Ward BB. 2003. Accumulation of nitrogen oxides in copper-limited cultures of denitrifying bacteria. Limnol. Oceanogr. 48:313-18
38. Hillis DM, Moritz C, Mable BK. 1996. Molecular Systematics. Sunderland, MA: Sinauer Assoc. 655 pp.
39. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-406
40. Jayakumar DA, Francis CA, Naqvi SWA, Ward BB. 2004. Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea. Aquat. Microb. Ecol. 34: 69-78
41. Jenkins BD, Steward GF, Ward BB, Zehr JP. 2004. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl. Environ. Microbiol. 70:1767-76
42. Jetten MSM, Strous M, van de Pas-Schoonen KT, Schalk J, van Dongen UJMG, et al. 1998. The anaerobic oxidation of ammonia. FEMS Microbiol. Ecol. 22:421-37
43. Junca H, Pieper DH. 2004. Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA finger-printing: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries. Environ. Microbiol. 6:95-110
44. Karner MB, DeLong EF, Karl DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-10
45. Klein M, Friedrich MW, Roger AJ, Hugenholtz P, Fishbain S, et al. 2001. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol. 183(20):6028-35
46. Kowalchuk GA, Stephen JR. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55: 485-529
47. Kuypers MMM, Sliekers AO, Lavik G, Schmid MC, Jorgensen BB, et al. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608-11
48. Li WKW. 1998. Annual average abundance of heterotrophic bacteria and Synechococcus in surface ocean waters. Limnol. Oceanogr. 43:1746-53
49. Liles MR, Manske BF, Bintrim SB, Handlesman J, Goodman RM. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69:2684-91
50. Loy A, Lehner A, Lee N, Adamszyk J, Meier H, et al. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064-81
51. MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, et al. 2001. Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl. Environ. Microbiol. 67:3908-22
52. Manefield M, Whiteley AS, Ostle N, Ineson P, Bailey MJ. 2002. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Comm. Mass Spec. 16:2179-83
53. Maranon E, Holligan PM, Barciela R, Gonzalez N, Mourino B, et al. 2001. Patterns of phytoplankton size structure and productivity in contrasting open-ocean environments. Mar. Ecol. Progr. Ser. 216:43-56
54. Massana R, Murray AI, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63:50-56
55. McTavish H, Fuchs JA, Hooper AB. 1993. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 175:2436-44
56. Mesarch MB, Nakatsu CH, Nies L. 2000. Development of catechol 2,3-dioxygenasespecific primers for monitoring bioremediation by competitive quantitative PCR. Appl. Environ. Microbiol. 66:678-83
57. Meyer S, Moser R, Neef A, Stahl U, Kampfer P. 1999. Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probes. Microbiology UK 145:1731-41
58. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, et al. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-10
59. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr 40:148-58
60. Mullis KB, Faloona FA. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain-reaction. Methods Enzymol. 155:335-50
61. Murrell JC, Radajewski S. 2000. Cultivation-independent techniques for studying methanotroph ecology. Res. Microbiol. 151:807-14
62. O'Mullan GD, Ward BB. 2005. Comparison of temporal and spatial variability of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, CA. Appl. Environ. Microbiol. In press
63. Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-40
64. Palenik B, Brahamsha B, Larimer FW, Land M, Hause L, et al. 2003. The genome of a motile marine Synechococcus. Nature 424:1037-42
65. Partensky F, Hess WR, Vaulot D. 1999. Prochlorococcus, a marine prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63:106-27
66. Paul JH, Alfreider A, Wawrik B. 2000a. Micro- and macrodiversity in rbcL sequences in ambient phytoplankton populations from the southeastern Gulf of Mexico. Mar Ecol. Progr Ser. 198:9-18
67. Paul JH, Kang JB, Tabita FR. 2000b. Diel patterns of regulation of rbcL transcription in a cyanobacterium and a prymnesiophyte. Mar. Biotechnol. 2:429-36
68. Perez-Jiminez JR, Young LY, Kerkhof LJ. 2001. Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsr AB) genes. FEMS Microbiol. Ecol 35:145-50
69. Postgate JR. 1992. Microbes and Man. New York: Cambridge Univ. Press. 297 pp.
70. Prieme A, Braker G, Tiedje JM. 2002. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl. Environ. Microbiol. 68:1893-900
71. Purkhold U, Pommerening-Roser A, Juretschko S, Schmid MC, Koops HP, Wagner M. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66:5368-82
72. Purkhold U, Wagner M, Timmermann G, Pommerening-Roser A, Koops HP. 2003. 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53:1485-94
73. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-33
74. Rappe MS, Giovannoni SJ. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369-94.
75. Rich JJ, Heichen RS, Bottomly PJ, Cromack K, Myrold DD. 2003. Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl. Environ. Microbiol. 69:5974-82
76. Rocap G, Distel DL, Waterbury JB, Chisholm SW. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S ribosomal DNA internal transcribed spacer sequences. Appl. Environ. Microbiol. 68:1180-91
77. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042-47
78. Rotthauwe J-H, Witzel K-P, Liesack W. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-12
79. Sahm K, MacGregor BJ, Jorgensen BB, Stahl DA. 1999. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Appl. Environ. Microbiol. 1:65-74
80. Saunders NFW, Thomas T, Curmi PMG, Mattick JS, Kuczek E, et al. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:1580-88
81. Scala DJ, Kerkhof LJ 1999. Diversity of nitrous oxide reductase (nos) genes in continental shelf sediments. Appl. Environ. Microbiol. 65:1681-87
82. Scala DJ, Kerkhof LJ. 2000. Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 66:1980-86
83. Short SM, Jenkins BD, Zehr JP. 2004. Spatial and temporal distribution of two diazotrophic bacteria in Chesapeake Bay. Appl. Environ. Microbiol. 70:2186-92
84. Siciliano SD, Germida JJ, Banks K, Greer CW. 2003. Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial. Appl. Environ. Microbiol. 69:483-89
85. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dood C, et al. 1986. Fluorescence detection in automated DNA-sequence analysis. Nature 321:674-79
86. Steward GF, Jenkins BD, Ward BB, Zehr JP. 2004. Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl. Environ. Microbiol. 70: 1455-65
87. Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, et al. 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6:347-63
88. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69:1159-71
89. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, et al. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36:664-75
90. Toh SK, Webb RI, Ashbolt NJ. 2002. Enrichment of autotrophic anaerobic ammonia-oxidizing consortia from various wastewaters. Microb. Ecol. 43:154-67
91. Tortell PD, Maldonado MT, Price NM. 1996. The role of heterotrophic bacteria in ironlimited ocean ecosystems. Nature 383:330-32
92. Venter CJ, Remington K, Heidelberg JG, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
93. Ward BB. 2002a. How many species of prokaryotes are there? Proc. Natl. Acad. Sci. USA 99:10234-36
94. Ward BB. 2002b. Nitrification in aquatic systems. In Encyclopedia of Environmental Microbiology, ed. DA Capone, pp. 2144-67. New York: Wiley
95. Ward DM. 1998. A natural species concept for prokaryotes. Curr Opin. Microbiol. 1:271-77
96. Waterbury JB, Watson SW, Guillard RRL, Brand LE. 1979. Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature 277:293-94
97. Wawrik B, Paul JH, Campbell MJ, Griffin L, Houchin L, et al. 2003. Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico. Mar Ecol. Progr. Ser. 251:87-101
98. Wawrik B, Paul JH, Tabita FR. 2002. Realtime PCR quantification of rbcL (ribulose-1, 5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl. Environ. Microbiol. 68:3771-79
99. Whitby CB, Hall G, Pickup R, Saunders JR, Ineson P, et al. 2001. C-13 incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett. Appl. Microbiol. 32:398-401
100. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51:221-71
101. Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad Sci. USA 74:5088-90
102. Woese CR, Magrum LJ, Fox GE. 1978. Archaebacteria. J. Mol. Evol. 11:245-52
103. Zehr JP, Jenkins BD, Short SM, Steward GF. 2003. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5:539-54
104. 2 in the subtropical North Pacific Ocean. Nature 412:635-38
105. Zumft WG. 1997. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61:533-616