Chapter 25
Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia
David A. Walsh,
Steven J. Hallam,
David A. Walsh
University of British Columbia, Vancouver, British Columbia, Canada
Search for more papers by this authorSteven J. Hallam
University of British Columbia, Vancouver, British Columbia, Canada
Search for more papers by this authorDavid A. Walsh,
Steven J. Hallam,
David A. Walsh
University of British Columbia, Vancouver, British Columbia, Canada
Search for more papers by this authorSteven J. Hallam
University of British Columbia, Vancouver, British Columbia, Canada
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
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Materials and Methods
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Results
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Discussion
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Internet Resources
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References
INTERNET RESOURCES
- Bellerophon (http://greengenes.lbl.gov/cgi-bin/nphbel3_interface.cgi)
- Mallard (http://www.bioinformatics-toolkit.org/)
- DOTUR and SONS (http://www.mothur.org/wiki/Main_Page)
- PC-ORD (http://home.centurytel.net/ mjm/pcordwin. htm)
- Greengenes (http://greengenes.lbl.gov/cgi-bin/nphindex.cgi)
- NCBI blast (http://blast.ncbi.nlm.nih.gov/)
- SILVA (http://www.arb-silva.de/)
- Muscle (http://www.drive5.com/muscle/)
- MacClade (http://macclade.org/macclade.html)
- PhyML (http://code.google.com/p/phyml/)
- bubble.pl (http://www.cmde.science.ubc.ca/hallam/ bubble.php)
- REFERENCES
-
Anderson JJ, Devol AH. 1973. Deep water renewal in Saanich Inlet, an intermittently anoxic basin. Estuarine Coastal Mar. Sci. 1: 1–10.
10.1016/0302-3524(73)90052-2 Google Scholar
- Arrigo KR. 2005. Marine microorganisms and global nutrient cycles. Nature 437: 349– 355.
- Bano N, Hollibaugh JT. 2002. Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl. Environ. Microbiol. 68: 505– 518.
-
Binqiu Z, Wong CS, et al. 1992. Distribution of dissolved and particulate trace metals in anoxic seawater, Saanich Inlet, BC Canada. Chinese J. Oceanol. Limnol. 10: 75–83.
10.1007/BF02844302 Google Scholar
- Brewer PG, Peltzer ET. 2009. OCEANS. Limits to marine life. Science 324: 347– 348.
- Codispoti LA, Brandes JA, et al. 2001. The oceanic fixed nitrogen and nitrous oxide budgets: Moving targets as we enter the anthropocene? Sci. Mar. 65: 85–105.
- Crump BC, Peranteau C, et al. 2007. Respiratory succession and community succession of bacterioplankton in seasonally anoxic estuarine waters. Appl. Environ. Microbiol. 73: 6802– 6810.
- DeSantis TZ, Hugenholtz P, et al. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72: 5069– 5072.
- Devol AH. 1978. Bacterial oxygen uptake kinetics as related to biological processes in oxygen deficient zones of the oceans. Deep-Sea Res. 25: 137– 146.
- Devol AH. 1983. Methane oxidation rates in the anaerobic sediments of Saanich Inlet. Limnol. Oceanogr. 28: 738– 742.
- Devol AH, Ahmed SI. 1981. Are high rates of sulphate reduction associated with anaerobic oxidation of methane? Nature 291: 407– 408.
- Diaz RJ, Rosenberg R. 2008. Spreading dead zones and consequences for marine ecosystems. Science 321: 926– 929.
- Drinnan RW, Emmett B, et al. 1995. Saanich Inlet Study: Water Use Inventory and Water Quality Assessment. Water Quality Branch, B.C. Ministry of Environment, Lands and Parks, Victoria.
- Edgar RC. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792– 1797.
- Emerson S, Cranston RE, et al. 1979. Redox species in a reducing fjord: Equilibrium and kinetic considerations. Deep-Sea Res. 26A: 859– 878.
- Emerson S, Kalhorn S, et al. 1982. Environmental oxidation rate of manganese(II): Bacterial catalysis. Geochim. Cosmochim. Acta 46: 1073– 1079.
- Gargett AE, Stucchi D, et al. 2003. Physical processes associated with high primary production in Saanich Inlet, British Columbia. Estuarine Coastal Shelf Sci. 56: 1141– 1156.
- Gruber N, Sarmiento JL. 1997. Global patterns of marine nitrogen fixation and denitrification. Global Biogeochem. Cycles 11: 235– 266.
- Guindon S, Lethiec F, et al. 2005. PHYML Online—A web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33(Web Server issue): W557–W559.
- Harley CD, Hughes AR, et al. 2006. The impacts of climate change in coastal marine systems. Ecol. Lett. 9: 228– 241.
- Herlinveaux RH. 1962. Oceanography of Saanich Inlet in Vancouver Island, British Columbia. J. Fisheries Res. Board Canada 19: 1–37.
- Juniper SK, Brinkhurst RO. 1986. Water-column dark CO2 fixation and bacterial-mat growth in intermittently Anoxic Saanich Inlet, British-Columbia. Mar. Ecol. Prog. Ser. 33: 41–50.
- Kwon EY, Primeau F, et al. 2009. The impact of remineralization depth on the air–sea carbon balance. Nat. Geosci. 2: 630– 635.
- Lam P, Lavik G, et al. 2009. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. USA 106: 4752– 4757.
- Lavik G, Stuhrmann T, et al. 2009. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457: 581– 584.
- Leopold A. 1949. A Sand County Almanac. New York: Ballantine Books.
- Levin LA. 2003. Oxygen minimum zone benthos: adaptations and community response to hypoxia. Oceanogra. Mar. Biol. 41: 1–45.
- Lilley MD, Baross JA, et al. 1982. Dissolved hydrogen and methane in Saanich Inlet, British Columbia. Deep Sea Res. 29: 1471– 1484.
- Ludwig W, Strunk O, et al. 2004. ARB: A software environment for sequence data. Nucleic Acids Res. 32: 1363– 1371.
- Maddison DR, Maddison WP. 2003. MacClade 4. Sunderland, MA: Sinauer Associates.
-
McCune B, Grace JB, et al. 2002. Analysis of Ecological Communities. Gleneden Beach, OR: MJM Software Design.
10.1046/j.1439-0310.2002.00768.x Google Scholar
- Murray AE, Grzymski JJ. 2007. Diversity and genomics of Antarctic marine micro-organisms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362: 2259– 2271.
- Paulmier A, Ruiz-Pino D. 2008. Oxygen minimum zones (OMZs) in the modern ocean. Prog. Oceanogr. 80: 113– 128.
- Pruesse E, Quast C, et al. 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35: 7188– 7196.
- Rabalais N, Diaz RJ, et al. 2010. Dynamics and distribution of natural and human-caused hypoxia. Biogeosciences 7: 585–619.
-
Sarmiento JL, Gruber N. 2006. Ocean Biogeochemical Dynamics. Princeton, NJ: Princeton University Press.
10.1515/9781400849079 Google Scholar
- Schloss, PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71(3): 1501– 1506.
- Schloss PD, Handelsman J. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl. Environ. Microbiol. 72: 6773– 6779.
- Schmidtova, J, Hallam SJ, et al. 2009. Phylogenetic diversity of transition and anoxic zone bacterial communities within a near-shore anoxic basin: Nitinat Lake. Environ. Microbiol. 11: 3233– 3251.
- Stevens H, Ulloa O. 2008. Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific. Environ. Microbiol. 10: 1244– 1259.
- Stramma L, Johnson GC, et al. 2008. Expanding oxygen-minimum zones in the tropical oceans. Science 320: 655– 658.
- Sunamura M, Higashi Y, et al. 2004. Two bacteria phylotypes are predominant in the Suiyo seamount hydrothermal plume. Appl. Environ. Microbiol. 70: 1190– 1198.
- Tebo BM, Emerson S. 1985. Effect of oxygen-tension, Mn(Ii) concentration, and temperature on the microbially catalyzed Mn(Ii) oxidation rate in a marine fiord. Appl. Environ. Microbiol. 50: 1268– 1273.
- Timothy DA, Soon MYS. 2001. Primary production and deep-water oxygen content of two British Columbian fjords. Mar. Chem. 73: 37–51.
- Walsh DA, Zaikova E, et al. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326: 578– 582.
- Ward BB, Kilpatrick AE. 1990. Relationship between substrate concentration and oxidation of ammonium and methane in a stratified water column. Cont. Shelf Res. 10: 1193– 1208.
- Ward BB, Kilpatrick AE, et al. 1989. Methane oxidation in Saanich Inlet. Cont. Shelf Res. 9: 65–75.
- Ward BB, Devol AH, et al. 2009. Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature 461: 78– 81.
- Whitney FA, Freeland HJ, et al. 2007. Decreasing oxygen levels in the interior waters of the subarctic Pacific. Prog. Oceanogr. 75: 179–199.
- Woebken D, Fuchs BM, et al. 2007. Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl. Environ. Microbiol. 73: 4648– 657.
- Zaikova E, Walsh DA, et al. 2010. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ. Microbiol. 12: 172– 191.
- Zehnder AJ, Stumm W. 1988. Geochemistry and biogeochemistry of anaerobic habitats. In Zehnder AJ, ed. Biology of Anaerobic Microorganisms. New York: John Wiley & Sons.