Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps

FEMS Microbiology Ecology

Volumn 87, Issue 1, 2014, Pages 153-163

  Lecleir, Gary R ^a   Debruyn, Jennifer M ^a   Maas, Elizabeth W ^b   Boyd, Philip W ^c,d   Wilhelm, Steven W ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

^c UNIVERSITY OF OTAGO   (New Zealand)

^d UNIVERSITY OF TASMANIA   (Australia)

Author keywords

DNA sequencing; Marine bacteria; Marine snow; Sediment traps

Indexed keywords

ALGAL BLOOM; BACTERIOPLANKTON; BACTERIUM; CLADISTICS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PHYLOGENY; PHYTOPLANKTON; RELATIVE ABUNDANCE; SEDIMENT TRAP; SNOW; TEMPORAL VARIATION;

PACIFIC OCEAN;

ACTINOBACTERIA; ALGAE; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CANDIDATUS PELAGIBACTER; FLAVOBACTERIA; ROSEOBACTER; SULFITOBACTER;

BACTERIAL DNA; RNA 16S; SEA WATER;

ARTICLE; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MARINE BACTERIA; MARINE SNOW; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PHYLOGENY; SEDIMENT; SEDIMENT TRAPS;

DNA SEQUENCING; MARINE BACTERIA; MARINE SNOW; SEDIMENT TRAPS;

BACTERIA; BASE SEQUENCE; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER;

EID: 84891492452     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12213     Document Type: Article

References (56)

1. Alldredge AL & Silver MW (1988) Characteristics, dynamics and significance of marine snow. Prog Oceanogr 20: 41-82.
2. Alldredge AL & Youngbluth MJ (1985) The significance of macroscopic aggregates (marine snow) as sites for heterotrophic bacterial production in the mesopelagic zone of the subtropical Atlantic. Deep-Sea Res Part I Oceanogr Res Pap 32: 1445-1456.
3. Bearon RN (2007) A model for bacterial colonization of sinking aggregates. Bull Math Biol 69: 417-431.
4. Boyd PW, Strzepek R, Chiswell S et al. (2012) Microbial control of diatom bloom dynamics in the open ocean. Geophys Res Lett 39: L18601.
5. Brinkhoff T, Bach G, Heidorn T, Liang LF, Schlingloff A & Simon M (2004) Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates. Appl Environ Microbiol 70: 2560-2565.
6. Buchan A, Gonzalez JM & Moran MA (2005) Overview of the marine Roseobacter lineage. Appl Environ Microbiol 71: 5665-5677.
7. Caron DA, Davis PG, Madin LP & Sieburth JM (1986) Enrichment of microbial-populations in macroaggregates (marine snow) from surface waters of the North Atlantic. J Mar Res 44: 543-565.
8. Clarke K & Gorley R (2006) PRIMER v6: User Manual/Tutorial. Bretonside Copy, Plymouth.
9. Cude WN, Mooney J, Tavanaei AA et al. (2012) Production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp strain Y4I. Appl Environ Microbiol 78: 4771-4780.
10. Dang HY & Lovell CR (2000) Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66: 467-475.
11. Dang HY & Lovell CR (2002) Seasonal dynamics of particle-associated and free-living marine Proteobacteria in a salt marsh tidal creek as determined using fluorescence in situ hybridization. Environ Microbiol 4: 287-295.
12. Dang H, Li T, Chen M & Huang G (2008) Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl Environ Microbiol 74: 52-60.
13. Davis MB (1967) Pollen deposition in lakes as measured by sediment traps. Geol Soc Am Bull 78: 849-858.
14. Delong EF, Franks DG & Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 38: 924-934.
15. Denman K, Hofmann E & Marchant H (1996) Marine biotic responses to environmental change and feedbacks to climate. Climate Change 1995: The Science of Climate Change (Houghton JT, Meira Filho LG, Callander BA, Harris N, Kattenberg A & Maskell K, eds), pp. 483-516. Cambridge University press, Cambridge.
16. Giovannoni SJ, Tripp HJ, Givan S et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
17. Grossart HP, Levold F, Allgaier M, Simon M & Brinkhoff T (2005) Marine diatom species harbour distinct bacterial communities. Environ Microbiol 7: 860-873.
18. Hall JA, Safi K, James MR, Zeldis J & Weatherhead M (2006) Microbial assemblage during the spring-summer transition on the northeast continental shelf of New Zealand. NZJ Mar Freshw Res 40: 195-210.
19. Harms G, Layton AC, Dionisi HM et al. (2003) Real-Time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37: 343-351.
20. Hoppe HG, Ducklow H & Karrasch B (1993) Evidence for dependency of bacterial growth on enzymatic hydrolysis of particulate organic matter in the mesopelagic ocean. Mar Ecol Prog Ser 93: 277-283.
21. Jiao N, Herndl GJ, Hansell DA et al. (2010) Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat Rev Microbiol 8: 593-599.
22. Jing HM, Shek L, Yung WY, Jin XW & Liu HB (2012) Dynamics of bacterial community composition during degradation of copepod fecal pellets. J Plankton Res 34: 700-710.
23. Kellogg CTE & Deming JW (2009) Comparison of free-living, suspended particle, and aggregate-associated bacterial and archaeal communities in the Laptev Sea. Aquat Microb Ecol 57: 1-18.
24. King AL, Sanudo-Wilhelmy SA, Boyd PW et al. (2012) A comparison of biogenic iron quotas during a diatom spring bloom using multiple approaches. Biogeosciences 9: 667-687.
25. Kirchman D (2001) Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. Methods Microbiol, Vol. 30 (Paul J, ed.), pp. 227-237. Academic Press, San Diego, CA.
26. Knauer GA, Karl DM, Martin JH & Hunter CN (1984) In-situ effects of selected preservatives on total carbon, nitrogen and metals collected in sediment traps. J Mar Res 42: 445-462.
27. Kwon EY, Primeau F & Sarmiento JL (2009) The impact of remineralization depth on the air-sea carbon balance. Nat Geosci 2: 630-635.
28. Lozupone CA, Hamady M, Kelley ST & Knight R (2007) Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585.
29. Martens T, Gram L, Grossart H-P et al. (2007) Bacteria of the Roseobacter clade show potential for secondary metabolite production. Microb Ecol 54: 31-42.
30. Martin JH, Knauer GA, Karl DM & Broenkow WW (1987) Vertex - carbon cycling in the Northeast Pacific. Deep-Sea Res Part I Oceanogr Res Pap 34: 267-285.
31. Matteson AR, Loar SN, Pickmere S et al. (2012) Production of viruses during a spring phytoplankton bloom in the South Pacific Ocean near New Zealand. FEMS Microbiol Ecol 79: 709-719.
32. Matteson AR, Rowe JM, Ponsero AJ, Pimentel TM, Boyd PW & Wilhelm SW (2013) High abundances of cyanomyoviruses in marine ecosystems demonstrate ecological relevance. FEMS Microbiol Ecol 84: 223-234.
33. Mc Carren J, Becker JW, Repeta DJ et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. P Natl Acad Sci USA 107: 16420-16427.
34. Methe BA, Nelson KE, Pop M et al. (2012) A framework for human microbiome research. Nature 486: 215-221.
35. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA & Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
36. Muller-Niklas G, Schuster S, Kaltenbock E & Herndl GJ (1994) Organic content and bacterial metabolism in amorphous aggregations of the northern Adriatic Sea. Limnol Oceanogr 39: 58-68.
37. Murphy RJ, Pinkerton MH, Richardson KM, Bradford-Grieve JM & Boyd PW (2001) Phytoplankton distributions around New Zealand derived from SeaWiFS remotely-sensed ocean colour data. NZJ Mar Freshw Res 35: 343-362.
38. Nedashkovskaya OI, Kim SB, Han SK et al. (2003) Mesonia algae gen. nov., sp nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kutz) Kornm. Int J Syst Evol Microbiol 53: 1967-1971.
39. Nodder SD, Boyd PW, Chiswell SM, Pinkerton MH, Bradford-Grieve JM & Greig MJN (2005) Temporal coupling between surface and deep ocean biogeochemical processes in contrasting subtropical and subantarctic water masses, southwest Pacific Ocean. J Geophys Res-Oceans 110: c12017.
40. Pomeroy LR, Hanson RB, McGillivary PA, Sherr BF, Kirchman D & Deibel D (1984) Microbiology and chemistry of fecal products of pelagic tunicates- rates and fates. Bull Mar Sci 35: 426-439.
41. Quince C, Lanzen A, Curtis TP et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
42. Rappe MS, Connon SA, Vergin KL & Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
43. Riemann L, Steward GF & Azam F (2000) Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol 66: 578-587.
44. Riley GA (1970) Particulate matter in seawater. Adv Mar Biol 8: 1-118.
45. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
46. Shanks AL & Trent JD (1979) Marine snow- microscale nutrient patches. Limnol Oceanogr 24: 850-854.
47. Smith DC, Simon M, Alldredge AL & Azam F (1992) Intense hydrolytic enzyme-activity on marine aggregates and implications for rapid particle dissolution. Nature 359: 139-142.
48. Taylor GT, Thunell R, Varela R, Benitez-Nelson C & Scranton MI (2009) Hydrolytic ectoenzyme activity associated with suspended and sinking organic particles within the anoxic Cariaco Basin. Deep-Sea Res Part I Oceanogr Res Pap 56: 1266-1283.
49. Teeling H, Fuchs BM, Becher D et al. (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608-611.
50. Wagner-Döbler I, Rheims H, Felske A et al. (2004) Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites. Int J Syst Evol Microbiol 54: 1177-1184.
51. Wang Y & Qian P-Y (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS ONE 4: e7401.
52. Weller DI, Law CS, Marriner A, Nodder SD, Chang FH, Stephens JA, Wilhelm SW, Boyd PW & Sutton PJH (2013) Temporal variation of dissolved methane in a subtropical mesoscale eddy during a phytoplankton bloom in the southwest Pacific Ocean. Progr Oceanogr 116: 193-206.
53. Welschmeyer NA (1994) Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39: 1985-1992.
54. Wilhelm SW, King AL, Twining BS et al. (2013) Elemental quotas and physiology of a southwestern Pacific Ocean plankton community as a function of iron availability. Aquat Microb Ecol 68: 185-194.
55. Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ, Raftery MJ & Cavicchioli R (2012) The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol 15: 1302-1317.
56. Zimmermann H (1997) The microbial community on aggregates in the Elbe Estuary, Germany. Aquat Microb Ecol 13: 37-46.