Microbial community composition and diversity in Caspian Sea sediments

FEMS Microbiology Ecology

Volumn 91, Issue 1, 2015, Pages 1-11

  Mahmoudi, Nagissa ^a,c   Robeson, Michael S ^b   Castro, Hector F ^c   Fortney, Julian L ^a,c   Techtmann, Stephen M ^a,c   Joyner, Dominique C ^a,c   Paradis, Charles J ^c   Pfiffner, Susan M ^c   Hazen, Terry C ^a,b,c  

^a University of Tennessee   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Archaea; Bacteria; Caspian Sea; Illumina; Marine sediments; PLFA

Indexed keywords

AMMONIA; BIOMASS; COMMUNITY COMPOSITION; ENVIRONMENTAL FATE; EUKARYOTE; MARINE POLLUTION; MARINE SEDIMENT; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; MOLECULAR ANALYSIS; NITROGEN CYCLE; ORGANIC CARBON; OXYGEN; SPECIES DIVERSITY;

CASPIAN SEA;

ARCHAEA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

ARCHAEAL DNA; BACTERIAL DNA; RNA 16S;

ARCHAEON; BACTERIUM; BIODIVERSITY; BIOMASS; DNA SEQUENCE; ECOLOGY; GENETICS; MICROBIAL CONSORTIUM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; SEA; SEDIMENT; WATER POLLUTION;

ARCHAEA; BACTERIA; BASE SEQUENCE; BIODIVERSITY; BIOMASS; DNA, ARCHAEAL; DNA, BACTERIAL; ECOLOGY; GEOLOGIC SEDIMENTS; MICROBIAL CONSORTIA; OCEANS AND SEAS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER POLLUTION;

EID: 84943743996     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec/fiu013     Document Type: Article

References (89)

1. Biddle JF, Lipp JS, Lever MA, et al. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. P Natl Acad Sci USA 2006;103:3846-51.
2. Blazejak A, Schippers A. High abundance of JS1-and Chloroflexirelated Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol 2010;72:198-207.
3. Bokulich NA, Subramanian S, Faith JJ, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 2013;10:57-9.
4. Canfield DE, Jørgensen BB, Fossing H, et al. Pathways of organic carbon oxidation in three continental margin sediments. Mar Geol 1993;113:27-40.
5. Caporaso JG, Bittinger K, Bushman FD, et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010;26:266-7.
6. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-6.
7. Caporaso JG, Lauber CL,WaltersWA, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012;6:1621-4.
8. Carr S, Vogel S, Dunbar R, et al. Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica. Geobiology 2013;11:377-95.
9. Clarke KR. Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 1993;18:117-43.
10. D'Hondt S, Jørgensen BB, Miller DJ, et al. Distributions of microbial activities in deep subseafloor sediments. Science 2004;306:2216-21.
11. de Mora S, Sheikholeslami MR, Wyse E, et al. An assessment of metal contamination in coastal sediments of the Caspian Sea. Mar Pollut Bull 2004;48:61-77.
12. de Mora S, Villeneuve J-P, Reza Sheikholeslami M, et al. Organochlorinated compounds in Caspian Sea sediments. Mar Pollut Bull 2004;48:30-43.
13. DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb 2006;72:5069-72.
14. Diaconescu CC, Kieckhefer R, Knapp J. Geophysical evidence for gas hydrates in the deep water of the South Caspian Basin, Azerbaijan. Mar Pet Geol 2001;18:209-21.
15. Diaz RJ. Overview of hypoxia around the world. J Environ Qual 2001;30:275-81.
16. Diaz RJ, Rosenberg R. Marine benthic hypoxia: a review of its ecological effects and the behavioural responses of benthic macrofauna. Oceanogr Mar Biol 1995;33:245-303.
17. Dumont H. The Caspian Lake: history, biota, structure, and function. Limnol Oceanogr 1998;43:44-52.
18. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10:996-8.
19. Effimoff I. The oil and gas resource base of the Caspian region. J Petrol Sci Eng 2000;28:157-9.
20. Feng BW, Li XR, Wang JH, et al. Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiol Ecol 2009;70:236-48.
21. Francis CA, Roberts KJ, Beman JM, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. P Natl Acad Sci USA 2005;102:14683-8.
22. Fry JC, Parkes RJ, Cragg BA, et al. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 2008;66:181-96.
23. Fuerst JA, Sagulenko E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 2011;9:403-13.
24. Fukunaga Y, Kurahashi M, Sakiyama Y, et al. Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes. J Gen Appl Microbiol 2009;55:267-75.
25. Gibbons SM, Jones E, Bearquiver A, et al. Human and environmental impacts on river sediment microbial communities. PLoS One 2014;9:e97435.
26. Giovannelli D, Molari M, d'Errico G, et al. Large-scale distribution and activity of prokaryotes in deep-sea surface sediments of theMediterranean Sea and the adjacent Atlantic Ocean. PLoS One 2013;8:e72996.
27. Harrison BK, Zhang H, Berelson W, et al. Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microb 2009;75:1487-99.
28. Hassanshahian M, Emtiazi G, Cappello S. Isolation and characterization of crude-oil-degrading bacteria from the Persian Gulf and the Caspian Sea. Mar Pollut Bull 2012;64:7-12.
29. Hassanshahian M, Emtiazi G, Kermanshahi RK, et al. Comparison of oil degrading microbial communities in sediments from the Persian Gulf and Caspian Sea. Soil Sediment Contam 2010;19:277-91.
30. Hazen TC, Dubinsky EA, DeSantis TZ, et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 2010;330:204-8.
31. Hofmann A, Peltzer E, Walz P, et al. Hypoxia by degrees: establishing definitions for a changing ocean. Deep-Sea Res Pt I 2011;58:1212-26.
32. Hou M, Xiong J, Wang K, et al. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea. Mar Pollut Bull 2014;86:147-53.
33. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012;61:1061-7.
34. Inagaki F, Nunoura T, Nakagawa S, et al. Biogeographical distribution and diversity ofmicrobes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. P Natl Acad Sci USA 2006;103:2815-20.
35. Inagaki F, Suzuki M, Takai K, et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microb 2003;69:7224-35.
36. Jäntti H, Hietanen S. The effects of hypoxia on sediment nitrogen cycling in the Baltic Sea. Ambio 2012;41:161-9.
37. Jørgensen B. Processes at the sediment-water interface. In Bolin B, Cook R (eds). The Major Biogeochemical Cycles and Their Interactions. New York: Wiley, 1983;21:477-515.
38. Jørgensen BB. Mineralization of organic matter in the sea bed-the role of sulphate reduction. Nature 1982;296:643-5.
39. Jørgensen BB, Boetius A. Feast and famine-microbial life in the deep-sea bed. Nat Rev Microbiol 2007;5:770-81.
40. Jørgensen SL, Hannisdal B, Lanzén A, et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. P Natl Acad Sci USA 2012;109:E2846-55.
41. Kosarev AN. Physico-geographical conditions of the Caspian Sea. In: Kostianoy AG, Kosarev AN (eds). The Handbook of Environmental Chemistry, Berlin: Springer-Verlag, 2005, 5-31.
42. Kosarev AN, Yablonskaya E. The Caspian Sea, (Vol. 20). The Hague: SPB Academic Publishing, 1994.
43. Kristiansen KD, Kristensen E, Jensen EMH. The influence of water column hypoxia on the behaviour of manganese and iron in sandy coastal marine sediment. Estuar Coast Shelf S 2002;55:645-4.
44. Kubo K, Lloyd KG, Biddle JF, et al. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J 2012;6:1949-65.
45. Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006;442:806-9.
46. Leloup J, Fossing H, Kohls K, et al. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ Microbiol 2009;11:1278-91.
47. Leroy S, Marret F, Gibert E, et al. River inflowand salinity changes in the Caspian Sea during the last 5500 years. Quaternary Sci Rev 2007;26:3359-83.
48. Lloyd KG, Schreiber L, Petersen DG, et al. Predominant archaea in marine sediments degrade detrital proteins. Nature 2013;496:215-8.
49. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microb 2005;71:8228-35.
50. Lozupone CA, Knight R. Global patterns in bacterial diversity. P Natl Acad Sci USA 2007;104:11436-40.
51. McCarren J, Becker JW, Repeta DJ, et al. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. P Natl Acad Sci USA 2010;107:16420-7.
52. McDonald D, Clemente JC, Kuczynski J, et al. The Biological ObservationMatrix (BIOM) format or: howI learned to stopworrying and love the ome-ome. GigaScience 2012;1:7.
53. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics ofmicrobiome census data. PLoS One 2013;8:e61217.
54. Mahmoudi N, Fulthorpe RR, Burns L, et al. Assessing microbial carbon sources and potential PAH degradation using natural abundance 14C analysis. Environ Pollut 2013;175:125-30.
55. Mahmoudi N, Porter TM, Zimmerman AR, et al. Rapid degradation of deepwater horizon spilled oil by indigenous microbial communities in Louisiana saltmarsh sediments. Environ Sci Technol 2013;47:13303-12.
56. Mason OU, Hazen TC, Borglin S, et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 2012;6: 1715-27.
57. Meng J, Xu J, Qin D, He Y, et al. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J 2013;8:650-9.
58. Meyer-Reil L-A, Köster M. Eutrophication of marine waters: effects on benthic microbial communities. Mar Pollut Bull 2000;41:255-63.
59. Mills CT, Dias RF, Graham D, et al. Determination of phospholipid fatty acid structures and stable carbon isotope compositions of deep-sea sediments of the Northwest Pacific, ODP site 1179. Mar Chem 2006;98:197-209.
60. Musat N, Werner U, Knittel K, et al. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst Appl Microbiol 2006;29: 333-48.
61. Navas-Molina JA, Peralta-Sánchez JM, González A, et al. Advancing our understanding of the human microbiome using QIIME. Method Enzymol 2013;531:371-444.
62. Oksanen J, Blanchet F, Kindt R, et al. vegan: Community Ecology Package. R package version 2.1-27/r2451. 2013.
63. Orphan V, Hinrichs K-U, Ussler W, et al. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microb 2001;67: 1922-34.
64. Parkes RJ, Cragg BA, Wellsbury P. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 2000;8:11-28.
65. Parr T, Tait R, Maxon C, et al. A descriptive account of benthic macrofauna and sediment from an area of planned petroleum exploration in the southern Caspian Sea. Estuar Coast Shelf Sci 2007;71:170-80.
66. Parsons RJ, Nelson CE, Carlson CA, et al. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environ Microbiol 2014.
67. Peeters F, Kipfer R, Achermann D, et al. Analysis of deep-water exchange in the Caspian Sea based on environmental tracers. Deep-Sea Res Pt I 2000;47:621-54.
68. Peng X, Jayakumar A, Ward BB. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones. Front Microbiol 2013;4:177.
69. Polymenakou PN, Bertilsson S, Tselepides A, et al. Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol 2005;50:447-62.
70. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010;5:e9490.
71. R: a language and environment for statistical computing. Vienna: R foundation for statistical computing; 2012. 2013, ISBN 3-900051-07-0. http://www.R-project.org.
72. Reed DW, Fujita Y, Delwiche ME, et al. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microb 2002;68:3759-70.
73. Revsbech NP, Madsen B, Jørgensen B. Oxygen production and consumption in sediments determined at high spatial resolution by computer simulation of oxygenmicroelectrode data. Limnol Oceanogr 1986;31:293-304.
74. Rinke C, Schwientek P, Sczyrba A, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013;499:431-7.
75. Ruff SE, Arnds J, Knittel K, et al. Microbial communities of deepsea methane seeps at Hikurangi Continental Margin (New Zealand). PLoS One 2013;8:e72627.
76. Schippers A, Kock D, Höft C, et al. Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia. Front Microbiol 2012;3:16.
77. Stahl DA, de la Torre JR. Physiology and diversity of ammoniaoxidizing archaea. Annu Rev Microbiol 2012;66:83-101.
78. Tolosa I, de Mora S, Sheikholeslami MR, et al. Aliphatic and aromatic hydrocarbons in coastal Caspian Sea sediments. Mar Pollut Bull 2004;48:44-60.
79. Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 2007;73:5261-7.
80. Webster G, Parkes RJ, Fry JC, et al. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microb 2004;70:5708-13.
81. Webster G, Sass H, Cragg BA, et al. Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiol Ecol 2011;77:248-63.
82. Webster G, Yarram L, Freese E, et al. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiol Ecol 2007;62:78-89.
83. Werner JJ, Zhou D, Caporaso JG, et al. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J 2012;6:1273.
84. Wilson T. Salinity and the major elements of sea water. Chem Oceanogr 1975;1:B9.
85. Wu RS. Hypoxia: from molecular responses to ecosystem responses. Mar Pollut Bull 2002;45:35-45.
86. Wuchter C, Abbas B, Coolen MJ, et al. Archaeal nitrification in the ocean. P Natl Acad Sci USA 2006;103:12317-22.
87. Xu L, Reddy C, Farrington J, et al. Identification of a novel alkenone in Black Sea sediments. Org Geochem 2001;32: 633-45.
88. Zelles L. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fert Soils 1999;29:111-29.
89. Zonn IS. Environmental issues of the Caspian. In: Kostianoy AG, Kosarev AN (eds). The Handbook of Environmental Chemistry, Berlin: Springer, 2005, 223-42.