Temporal patterns of microbial community structure in the Mid-Atlantic Bight

FEMS Microbiology Ecology

Volumn 65, Issue 3, 2008, Pages 484-493

  Nelson, Joshua D ^b   Boehme, Susan E ^c   Reimers, Clare E ^d   Sherrell, Robert M ^a   Kerkhof, Lee J ^a  

^a RUTGERS UNIVERSITY   (United States)

^b Pt Pleasant High School   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d OREGON STATE UNIVERSITY   (United States)

Author keywords

16S rRNA gene; Microbial community structure; Spatio temporal variability; TRFLP

Indexed keywords

RNA 16S;

BACTERIOPLANKTON; BIOMASS; CLUSTER ANALYSIS; COMMUNITY STRUCTURE; MICROBIAL COMMUNITY; POPULATION DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; SPATIOTEMPORAL ANALYSIS; TEMPORAL ANALYSIS;

ARTICLE; BACTERIOPLANKTON; BIOMASS; CLUSTER ANALYSIS; COMMUNITY STRUCTURE; ECOSYSTEM; MICROBIAL COMMUNITY; MICROBIAL POPULATION DYNAMICS; NONHUMAN; OCEANOGRAPHY; PARTIAL LEAST SQUARES REGRESSION; PHYTOPLANKTON; PRINCIPAL COORDINATE ANALYSIS; PRIORITY JOURNAL; REGRESSION ANALYSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA FINGERPRINTING; SEASHORE; STATISTICAL MODEL; TIME SERIES ANALYSIS; UNITED STATES;

ATLANTIC OCEAN; BACTERIA; BIOMASS; CLUSTER ANALYSIS; DNA, BACTERIAL; GENES, BACTERIAL; GENES, RRNA; LEAST-SQUARES ANALYSIS; NEW JERSEY; OCEANOGRAPHY; PHYLOGENY; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; WATER MICROBIOLOGY;

ATLANTIC OCEAN; MIDDLE ATLANTIC BIGHT;

BACTERIA (MICROORGANISMS);

EID: 49249109199     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2008.00553.x     Document Type: Article

References (32)

1. Aluwihare LI, Repeta DJ Chen RF (2002) Chemical composition and cycling of dissolved organic matter in the Mid-Atlantic Bight. Deep-Sea Res Part II 49 : 4421 4437.
2. Avaniss-Aghajani E, Jones K, Chapman D Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17 : 144 146.
3. Bano N Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68 : 505 518.
4. Berardesco G, Dyhrman S, Gallagher E Shiaris MP (1998) Spatial and temporal variation of phenanthrene-degrading bacteria in intertidal sediments. Appl Environ Microbiol 64 : 2560 2565.
5. 2 fluxes from a coastal transect: a time-series approach. Mar Chem 63 : 49 67.
6. 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 1901.
7. Clement BG, Kehl LE, DeBord KL Kitts CL (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J Microbiol Methods 31 : 135 142.
8. Crump BC Hobbie JA (2005) Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol Oceanogr 50 : 1718 1729.
9. Crump BC, Armbrust EV Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65 : 3192 3204.
10. Del Vecchio R Blough NV (2004) Spatial and seasonal distribution of chromophoric dissolved organic matter and dissolved organic carbon in the Middle Atlantic Bight. Mar Chem 89 : 169 187.
11. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV Naeem S (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci 103 : 13104 13109.
12. Gonzalez JM, Simo R, Massana R, Covert JS, Casamayor EO, Pedros-Alio C Moran MA (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66 : 4237 4246.
13. Hollibaugh JT, Bano N Ducklow HW (2002) Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria. Appl Environ Microbiol 68 : 1478 1484.
14. Judd KE, Crump BC Kling GW (2006) Variation in dissolved organic matter controls bacterial production and community composition. Ecology 87 : 2068 2079.
15. Kan JB, Crump C, Wang K Cheng F (2006) Bacterioplankton community in Chesapeake Bay: predictable or random assemblages. Limnol Oceanogr 51 : 2157 2169.
16. Kerkhof L (1997) Quantification of total RNA by ethidium bromide fluorescence may not accurately reflect the RNA mass. J Biochem Biophys Methods 34 : 147 154.
17. Kerkhof LJ, Voytek MA, Sherrell RM, Millie D Schofield O (1999) Variability in bacterial community structure during upwelling in the coastal ocean. Hydrobiologia 401 : 139 148.
18. Lane D (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E Goodfellow M, eds), pp. 115 175. John Wiley & Sons, New York.
19. McGarigal K, Stafford S Cushman S (2000) Multivariate Statistics for Wildlife and Ecology Research. Springer, New York.
20. Moeseneder MM, Arrieta JM, Muyzer G, Winter C Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65 : 3518 3525.
21. Moeseneder MM, Winter C, Arrieta JM Herndl GJ (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J Microbiol Methods 44 : 159 172.
22. 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 : 148 158.
23. Murray AE, Preston CM, Massana R, Taylor LT, Blakis A, Wu K DeLong EF (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64 : 2585 2595.
24. Murray AE, Blakis A, Massana R, Strawzeski S, Passow U, Alldredge A DeLong EF (1999) A time series assessment of planktonic archaeal variability in the Santa Barbara Channel. Aquat Microb Ecol 20 : 129 145.
25. Nelson JD (2002) Time series analysis using TRFLP analysis and DNA sequencing of 16S rDNA genes to assess background bacterioplankton variability and to identify dominant microorganisms off the coast of New Jersey. Master of Science, Rutgers University, New Brunwick, NJ.
26. Rappe MS, Kemp PF Giovannoni SJ (1997) Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 42 : 811 826.
27. Rappe MS, Vergin K Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33 : 219 232.
28. 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 1986.
29. Suzuki MT Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62 : 625 630.
30. Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, Benoit J, Sarma-Rupavtarm R, Distel DL Polz MF (2005) Genotypic diversity within a natural coastal bacterioplankton population. Science 307 : 1311 1313.
31. von Alt CJ Grassle JF (1992) LEO-15: an unmanned long-term environmental observatory. Proc Oceans 2 : 849 854.
32. Wawrik B, Kerkhof L, Kukor J Zylstra G (2005) Effect of different carbon sources on community composition of bacterial enrichments from soil. Appl Environ Microbiol 71 : 6776 6783.