Abstract
Many of the biogeochemical reactions that occur in marine sediments are catalyzed by the complex communities of bacteria and archaea living there. Linking specific microorganisms to specific chemical transformations has been a challenge for microbiologists, because microorganisms generally lack morphological detail and are therefore much more difficult to identify than macroorganisms. Identification has traditionally required pure-culture isolation, followed by often time-consuming chemotaxonomic characterization. In contrast to their narrow range of morphologies, microorganisms are genetically very diverse. This genetic diversity has recently been exploited for the in situ identification of individual microbial cells, and even of their biochemical activities. This paper is intended to give scientists of neighboring disciplines some insight into how nucleic acidbased tools such as cloning, sequencing and hybridization are used by microbiologists to analyze the diversity, structure and function of microbial communities.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990a) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbio 156:1919–1925
Amann RI, Krumholz L, Stahl DA (1990b) Fluorescentoligonucleotide probing of whole cells for determinative, phylogenetic, environmental studies in microbiology. J Bacteriol 172:762–770
Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich S, Gates CM, Feldman, RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289:1902–1906
Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O (2000) Microscopic identification of a microbial consortium apparently mediating anaerobic methane oxidation above marine gas hydrates. Nature 407:623–626
Boschker HTS, Nold SC, Wellsbury P, Bos D, Graaf W, Rel R, Parkes RJ, and Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392:801–805
Bowman JP, Rea SM, McCammon SA, McMeekin TA (2000) Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environ Microbiol 2:227–237
Cifuentes A, Anton J, Benlloch S, Donnelly A, Herbert RA, Rodriguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66:1715 –1719
Daims H, Brühl A, Amann R, Schleifer K-H (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22:434–444
DeLong EF, Taylor LT, Marsh TL, Preston CM (1999) Visualization and enumeration of marine planktonic Archaea and Bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl Environ Microbiol 65:5554–5563
Devereux R, Kane MD, Winfrey J, Stahl DA (1992) Genus- and group-specific hybridization probes for determinative and environmental studies of sulfatereducing bacteria. Syst Appl Microbiol 15:601–609
Devereux R, Mundfrom GW (1994) A phylogenetic tree of 16S ribosomal-RNA sequences from sulfatereducing bacteria. Appl Environ Microbiol 60:3437–3439
Gray JP, Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62:4049–4059
Hicks RE, Amann RI, Stahl DA (1992) Dual staining of natural bacterioplancton with 4′,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA se-quences. Appl Environ Microbiol 58:2158–2163
Hinrichs K-U, Hayes JM, Sylva SP, Brewer PG, DeLong EF (1999) Methane-consuming archaebacteria in marine sediments. Nature 398:802–805
Hristova KR, Mau M, Zheng D, Aminov RI, Mackie RI, Gaskins HR, Raskin L (2000) Desulfotomaculum genus- and subgenus-specific 16S rRNA hybridization probes for environmental studies. Environ Microbiol 2:143–159
Kopczynski ED, Bateson MM, Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated organisms. Appl Environ Microbiol 60:746–748
Liu W-T, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522
Llobet-Brossa E, Rossello-Mora R, Amann R (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64:2691–2696
Manz W, Amann R, Ludwig W, Wagner M, Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15:593–600
Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer K-H (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum CytophagaFlavobacter-Bacteroides in the natural environment. Microbiol 142:1097–1106
Manz W, Eisenbrecher M, Neu TR, Szewzyk U (1998) Abundance and spatial organization of gram negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol Ecol 25:43–61
Meier H, Amann R, Ludwig W, Schleifer K-H (1999) Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G+C content. Syst Appl Microbiol 22:186–196
Michotey V, Méjean V, Bonin P (2000) Comparison of methods for quantification of cytochrome cd 1 denitrifying bacteria in environmental marine samples. Appl Environ Microbiol 66: 1564–1571
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: 3581–3525
Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 60: 871–879
Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin Microbiol 2:317–322
Muyzer G, Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci Techn 32:1–9
Neef A (1997) Anwendung der in situ-EinzelzellIdentifizierung von Bakterien zur PopulationsAnalyse in komplexen mikrobiellen Biozönosen, Fakultät für Chemie, Biologie und Geowissenschaften. Dissertation. Technische Universität München, München, pp. 142
Neef A, Amann R, Schlesner H, Schleifer K-H (1998) Monitoring a widespread bacterial group: In situ detection of planctomycetes with 16S rRNA- targeted probes. Microbiol 144:3257–3266
Ouverney CC, Fuhrman JA (1999) Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65:1746–1752
Ramsing NB, Kühl M, Jørgensen BB (1993) Distribution of sulfate-reducing bacteria, O2 and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Appl Environ Microbiol 59: 3820–3849
Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989
Ravenschlag K, Sahm K, Knoblauch C, Jørgensen BB, Amann, R (2000) Community structure, cellular rRNA content and activity of sulfate-reducing bacteria in marine Arctic sediments. Appl Environ Microbiol 66:3592–3602
Roller C, Wagner M, Amann R, Ludwig W, Schleifer K-H (1994) In situ probing of gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides. Microbiol 140:2849–2858
Rossello-Mora R, Thamdrup B, Schäfer H, Weller R, Amann R (1999) The reponse of the microbial community of marine sediments to organic carbon input under anaerobic conditions. Syst Appl Microbiol 22:237–248
Sahm K, Knoblauch C, Amann R (1999a) Phylogenetic affiliation and quantification ofpsychrophilic sulfatereducing isolates in marine arctic sediments. Appl Environ Microbiol 65: 3976–3981
Sahm K, MacGregor BJ, Jørgensen BB, Stahl DA (1999b) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slotblot hybridization in a coastal marine sediment. Environ Microbiol 1:65–74
Sievert SM, Brinkhoff T, Muyzer G, Ziebis W, Kuever J (1999) Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl Environ Microbiol 65:3834–3842
Snaidr J, Amann R, Huber I, Ludwig W, Schleifer K-H (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63: 2884–2896
Stein JL, Marsh TL, Wu YK, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178:591–599
Tanner MA, Everett CL, Coleman WJ, Yang MM, Youvan DC (2000) Complex microbial consortia inhabiting hydrogen sulfide-rich black mud from marine coastal environments. Biotechn 8:1–16
Teske A, Ramsing NB, Habicht K, Fukui M, Küver J, Jørgensen BB, Cohen Y (1998) Sulfate-reducing bacteria and their activities in cyanobacterial mats of Solar Lake (Sinai, Egypt). Appl Environ Microbiol 64:2943–2951
Thamdrup B, Rosselló-Mora R, Amann R (2000) Microbial manganese and sulfate reduction in Black Sea shelf sediments. Appl Environ Microbiol 66:2888–2897
Todorov JR, Chistoserdov AY, Aller JY (2000) Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea. FEMS Microbiol Ecol 33:147–155
Urakawa H, Kita-Tsukamoto K, Ohwada K (1999) Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiol-UK 145:3305–3315
Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganism. Cytometry 14:136–143
Zani S, Mellon MT, Collier JL, Zehr JP (2000) Expression of nifHigenes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66:3119–3124
Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4314–4317
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
MacGregor, B.J., Ravenschlag, K., Amann, R. (2002). Nucleic Acid-Based Techniques for Analyzing the Diversity, Structure, and Function of Microbial Communities in Marine Waters and Sediments. In: Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., van Weering, T.C.E. (eds) Ocean Margin Systems. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-05127-6_26
Download citation
DOI: https://doi.org/10.1007/978-3-662-05127-6_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-07872-9
Online ISBN: 978-3-662-05127-6
eBook Packages: Springer Book Archive