Microbial diversity and functional characterization of sediments from reservoirs of different trophic state

Gächter, 1993, The role of microorganisms in mobilization and fixation of phosphorus in sediments, Hydrobiologia, 253, 103, 10.1007/BF00050731 Goedkoop, 1997, Microbial response of a freshwater benthic community to a simulated diatom sedimentation event: Interactive effects of benthic fauna, Microb. Ecol., 34, 131, 10.1007/s002489900043 Sander, 1993, Factors controlling bacterial production in marine and freshwater sediments, Microb. Ecol., 26, 79, 10.1007/BF00177045 Törnblom, 1998, Bacterial and phosphorus dynamics in profundal Lake Erken sediments following the deposition of diatoms: a laboratory study, Hydrobiologia, 364, 55, 10.1023/A:1003199505396 Boschker, 1998, Patterns of extracellular enzyme activities in littoral sediments of Lake Gooimeer, The Netherlands, FEMS Microbiol. Ecol., 25, 79, 10.1111/j.1574-6941.1998.tb00461.x Head, 1998, Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms, Microb. Ecol., 35, 1, 10.1007/s002489900056 Torsvik, 2002, Microbial diversity and function in soils: from genes to ecosystems, Curr. Opin. Microbiol., 5, 240, 10.1016/S1369-5274(02)00324-7 DeLong, 1993, Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages, Limnol. Oceanogr., 38, 924, 10.4319/lo.1993.38.5.0924 Gray, 1996, Phylogenetic analysis of the bacterial communities in marine sediments, Appl. Environ. Microbiol., 62, 4049, 10.1128/AEM.62.11.4049-4059.1996 Ravenschlag, 2001, Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard), Appl. Environ. Microbiol., 67, 387, 10.1128/AEM.67.1.387-395.2001 Riemann, 2000, Dynamics of bacterial community composition and activity during a mesocosm diatom bloom, Appl. Environ. Microbiol., 66, 578, 10.1128/AEM.66.2.578-587.2000 Urakawa, 1999, Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis, Microbiology, 145, 3305, 10.1099/00221287-145-11-3305 Chan, 2002, Methanogenic archaeal community in the sediment of an artificially partitioned acidic bog lake, FEMS Microbiol. Ecol., 42, 119, 10.1111/j.1574-6941.2002.tb01001.x Costello, 1999, Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments, Appl. Environ. Microbiol., 65, 5066, 10.1128/AEM.65.11.5066-5074.1999 Li, 1999, Seasonal changes in ribosomal RNA of sulfate-reducing bacteria and sulfate reducing activity in a freshwater lake sediment, FEMS Microbiol. Ecol., 28, 31, 10.1111/j.1574-6941.1999.tb00558.x Miskin, 1999, Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using rapid RNA extraction procedure and RT-PCR, Microbiology, 145, 1977, 10.1099/13500872-145-8-1977 Stein, 2002, Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir, FEMS Microbiol. Ecol., 42, 431, 10.1111/j.1574-6941.2002.tb01032.x Amann, 2000, Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology, FEMS Microbiol. Rev., 24, 555, 10.1111/j.1574-6976.2000.tb00557.x Wagner, 2002, Bacterial community composition and function in sewage treatment systems, Curr. Opin. Biotechnol., 13, 218, 10.1016/S0958-1669(02)00315-4 Llobet-Brossa, 1998, Microbial community composition of wadden sea sediments as revealed by fluorescence in situ hybridization, Appl. Environ. Microbiol., 64, 2691, 10.1128/AEM.64.7.2691-2696.1998 Purdy, 1997, Use of 16S rRNA-targeted oligonucleotide probes to investigate the occurrence and selection of sulfate-reducing bacteria in response to nutrient addition to sediment slurry microcosms from a Japanese estuary, FEMS Microbiol. Ecol., 24, 221, 10.1111/j.1574-6941.1997.tb00439.x Uhlmann, 2000, Microbial and chemical composition of the upper sediment layers in a man-made lake, Verh. Int. Ver. Limnol., 27, 866 Hesslein, 1976, An in situ sampler for close interval pore water studies, Limnol. Oceanogr., 22, 913 Manz, 1994, In situ characterization of the microbial consortia active in two wastewater treatment plants, Water Res., 28, 1715, 10.1016/0043-1354(94)90243-7 Snaidr, 1997, Phylogenetic analysis and in situ identification of bacteria in activated sludge, Appl. Environ. Microbiol., 63, 2884, 10.1128/AEM.63.7.2884-2896.1997 Amann, 1990, Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations, Appl. Environ. Microbiol., 56, 1919, 10.1128/AEM.56.6.1919-1925.1990 Manz, 1992, Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions, Syst. Appl. Microbiol., 15, 593, 10.1016/S0723-2020(11)80121-9 Roller, 1994, In situ probing of Gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides, Microbiology, 140, 2849, 10.1099/00221287-140-10-2849 Manz, 1996, Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment, Microbiology, 142, 1097, 10.1099/13500872-142-5-1097 Neef, 1998, Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes, Microbiology, 144, 3257, 10.1099/00221287-144-12-3257 Amann, 1990, Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology, J. Bacteriol., 172, 762, 10.1128/jb.172.2.762-770.1990 Schuppler, 1995, Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis, Microbiology, 141, 513, 10.1099/13500872-141-2-513 Marchesi, 1998, Design and evaluation of useful Bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA, Appl. Environ. Microbiol., 64, 795, 10.1128/AEM.64.2.795-799.1998 Coates, 1999, Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria, Appl. Environ. Microbiol., 65, 5234, 10.1128/AEM.65.12.5234-5241.1999 Glöckner, 2000, Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria, Appl. Environ. Microbiol., 66, 5053, 10.1128/AEM.66.11.5053-5065.2000 Martin, 2002, Phylogenetic approaches for describing and comparing the diversity of microbial communities, Appl. Environ. Microbiol., 68, 3673, 10.1128/AEM.68.8.3673-3682.2002 Daims, 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, 10.1016/S0723-2020(99)80053-8 Dunbar, 1999, Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning, Appl. Environ. Microbiol., 65, 1662, 10.1128/AEM.65.4.1662-1669.1999 Hill, 2003, Using ecological diversity measures with bacterial communities, FEMS Microbiol. Ecol., 43, 1, 10.1111/j.1574-6941.2003.tb01040.x Hughes, 2001, Counting the uncountable: Statistical approaches to estimating microbial diversity, Appl. Environ. Microbiol., 67, 4399, 10.1128/AEM.67.10.4399-4406.2001 McCaig, 1999, Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures, Appl. Environ. Microbiol., 65, 1721, 10.1128/AEM.65.4.1721-1730.1999 Juretschko, 2002, The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach, Syst. Appl. Microbiol., 25, 84, 10.1078/0723-2020-00093 Maaßen, 2003, Chemical and microbial composition of sediments in reservoirs with different trophic state, Int. Rev. Hydrobiol., 88, 508, 10.1002/iroh.200310596 Dabert, 2001, Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration, Appl. Microbiol. Biotechnol., 55, 500, 10.1007/s002530000529 Dojka, 1998, Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation, Appl. Environ. Microbiol., 64, 3869, 10.1128/AEM.64.10.3869-3877.1998 Phelps, 1998, Molecular characterization of a sulfate-reducing consortium which mineralizes benzene, FEMS Microbiol. Ecol., 27, 269, 10.1111/j.1574-6941.1998.tb00543.x Li, 1999, Bacterial diversity in deep-sea sediments from different depths, Biodivers. Conserv., 8, 659, 10.1023/A:1008848203739 Sinsabaugh, 1995, Microbial production, enzyme activity, and carbon turnover in surface sediments of the Hudson river estuary, Microb. Ecol., 30, 127, 10.1007/BF00172569 Roselló-Mora, 2001, The species concept for prokaryotes, FEMS Microbiol. Rev., 25, 39, 10.1016/S0168-6445(00)00040-1 Chandler, 1997, Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries, Mol. Ecol., 6, 475, 10.1046/j.1365-294X.1997.00205.x Farrelly, 1995, Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species, Appl. Environ. Microbiol., 61, 2798, 10.1128/AEM.61.7.2798-2801.1995 Reysenbach, 1992, Differential amplification of rRNA genes by polymerase chain reaction, Appl. Environ. Microbiol., 58, 3417, 10.1128/AEM.58.10.3417-3418.1992 Hiorns, 1997, Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences, Appl. Environ. Microbiol., 63, 2957, 10.1128/AEM.63.7.2957-2960.1997 Martin-Laurent, 2001, DNA extraction from soils: old bias for new microbial diversity analysis methods, Appl. Environ. Microbiol., 67, 2354, 10.1128/AEM.67.5.2354-2359.2001 Karner, 1997, Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining, Appl. Environ. Microbiol., 63, 1208, 10.1128/AEM.63.4.1208-1213.1997 Kirchman, 2002, The ecology of Cytophaga–Flavobacteria in aquatic environments, FEMS Microbiol. Ecol., 39, 91 Crump, 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, 10.1128/AEM.65.7.3192-3204.1999 Frischer, 1996, Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure, Can. J. Microbiol., 42, 1061, 10.1139/m96-136 O'Farrell, 1999, Detection of Verrucomicrobia in a pasture soil by PCR-mediated amplification of 16S rRNA genes, Appl. Environ. Microbiol., 65, 4280, 10.1128/AEM.65.9.4280-4284.1999 Hugenholtz, 1998, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J. Bacteriol., 180, 4765, 10.1128/JB.180.18.4765-4774.1998 Weiss, 1996, Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow), Appl. Environ. Microbiol., 62, 1998, 10.1128/AEM.62.6.1998-2005.1996 Coates, 2002, Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration, Appl. Environ. Microbiol., 68, 2445, 10.1128/AEM.68.5.2445-2452.2002 Jansson, 1988, Phosphatases: origin, characteristics and function in lakes, Hydrobiologia, 170, 157, 10.1007/BF00024903 Sala, 2001, Measurement of ectoenzyme activities as an indication of inorganic nutrient imbalance in microbial communities, Aquat. Microb. Ecol., 23, 301, 10.3354/ame023301 Bittl, 1996, Microbial activity in an artificially divided acidic lake, Arch. Hydrobiol. Spec. Iss. (Adv. Limnol.), 48, 113 Münster, 1992, Extracellular enzymes in a small polyhumic lake: origin, distribution and activities, Hydrobiologia, 243/244, 47, 10.1007/BF00007019 Ommen Kloeke, 1999, Localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs, Microb. Ecol., 38, 201, 10.1007/s002489900170 Lee, 1999, Combination of fluorescent in situ hybridization and microautoradiography – a new tool for structure–function analyses in microbial ecology, Appl. Environ. Microbiol., 65, 1289, 10.1128/AEM.65.3.1289-1297.1999