401
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Power M, van der Meer JR, Tchelet R, Egli T, Eggen R. Molecular-based methods can contribute to assessments of toxicological risks and bioremediation strategies. J Microbiol Methods 1998. [DOI: 10.1016/s0167-7012(98)00018-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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402
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Stapleton RD, Ripp S, Jimenez L, Cheol-Koh S, Fleming JT, Gregory IR, Sayler GS. Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J Microbiol Methods 1998. [DOI: 10.1016/s0167-7012(98)00021-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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403
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Byers HK, Stackebrandt E, Hayward C, Blackall LL. Molecular investigation of a microbial mat associated with the Great Artesian Basin. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00491.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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404
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Grosskopf R, Janssen PH, Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 1998; 64:960-9. [PMID: 9501436 PMCID: PMC106352 DOI: 10.1128/aem.64.3.960-969.1998] [Citation(s) in RCA: 423] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/1997] [Accepted: 12/17/1997] [Indexed: 02/06/2023] Open
Abstract
A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum, six were closely related but not identical to those of strains of Methanosaeta concilii, two grouped with members of the genus Methanosarcina, and two were related to the methanogenic endosymbiont of Plagiopyla nasuta. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10(7) per g of dry soil for the H2-CO2-utilizing methanogens and of up to 10(6) for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H2-CO2, grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta-like group and the Methanobacterium-like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 microM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.
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Affiliation(s)
- R Grosskopf
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
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405
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Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998; 180:366-76. [PMID: 9440526 PMCID: PMC106892 DOI: 10.1128/jb.180.2.366-376.1998] [Citation(s) in RCA: 563] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609-1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among > 300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (> or = 98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing delta-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.
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Affiliation(s)
- P Hugenholtz
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, USA
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406
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Stroes-Gascoyne S, Pedersen K, Haveman SA, Dekeyser K, Arlinger J, Daumas S, Ekendahl S, Hallbeck L, Hamon CJ, Jahromi N, Delaney TL. Occurrence and identification of microorganisms in compacted clay-based buffer material designed for use in a nuclear fuel waste disposal vault. Can J Microbiol 1997; 43:1133-46. [PMID: 9476350 DOI: 10.1139/m97-162] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A full-scale nuclear fuel waste disposal container experiment was carried out 240 m below ground in an underground granitic rock research laboratory in Canada. An electric heater was surrounded by buffer material composed of sand and bentonite clay and provided heat equivalent to what is anticipated in a Canadian nuclear fuel waste repository. During the experiment, the heat caused a mass transport of water and moisture content gradients developed in the buffer ranging from 13% closest to the heater to 23% at the rock wall of the deposition hole. Upon decommissioning after 2.5 years, microorganisms could be cultured from all samples having a moisture content above 15% but not from samples with a moisture content below 15%. Heterotrophic aerobic and anaerobic bacteria were found in numbers ranging from 10(1) to 10(6) cells/g dry weight buffer. Approximately 10(2), or less, sulphate-reducing bacteria and methanogens per gram of dry weight buffer were also found. Identification of buffer population members was performed using Analytical Profile Index (API) strips for isolated bacteria and 16S rRNA gene sequencing for in situ samples. A total of 79 isolates from five buffer layers were identified with API strips as representing the beta, gamma and delta groups of Proteobacteria and Gram-positive bacteria. Sixty-seven 16S rRNA clones that were obtained from three buffer layers were classified into 21 clone groups representing alpha and gamma groups of Proteobacteria, Gram-positive bacteria, and a yeast. Approximately 20% of the population comprised Gram-positive bacteria. Members of the genera Amycolatopsis, Bacillus, and Nocardia predominated. Among Gram-negative bacteria, the genera Acinetobacter and Pseudomonas predominated. Analysis of lipid biomarker signatures and in situ leucine uptake demonstrated that the buffer population was viable. The results suggest that a nuclear fuel waste buffer will be populated by active microorganisms only if the moisture content is above a value where free water is available for active life.
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Affiliation(s)
- S Stroes-Gascoyne
- Atomic Energy of Canada Limited, Whiteshell Laboratories, Pinawa, MB, Canada
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407
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von Wintzingerode F, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997; 21:213-29. [PMID: 9451814 DOI: 10.1111/j.1574-6976.1997.tb00351.x] [Citation(s) in RCA: 1054] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
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MESH Headings
- Artifacts
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Environmental Microbiology
- Equipment Contamination
- False Negative Reactions
- False Positive Reactions
- Mutagenesis
- Polymerase Chain Reaction/instrumentation
- Polymerase Chain Reaction/methods
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal/genetics
- RNA, Ribosomal/isolation & purification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
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Affiliation(s)
- F von Wintzingerode
- Institut für Mikrobiologie und Hygiene, Universitätsklinikum Charité, Berlin, Germany
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408
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Liu WT, Marsh TL, Cheng H, Forney LJ. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 1997; 63:4516-22. [PMID: 9361437 PMCID: PMC168770 DOI: 10.1128/aem.63.11.4516-4522.1997] [Citation(s) in RCA: 1122] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.
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Affiliation(s)
- W T Liu
- Department of Microbiology, Michigan State University, East Lansing 48824, USA
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409
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Investigation of the potential for microbial contamination of deep granitic aquifers during drilling using 16S rRNA gene sequencing and culturing methods. J Microbiol Methods 1997. [DOI: 10.1016/s0167-7012(97)00066-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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410
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Kuske CR, Barns SM, Busch JD. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 1997; 63:3614-21. [PMID: 9293013 PMCID: PMC168668 DOI: 10.1128/aem.63.9.3614-3621.1997] [Citation(s) in RCA: 191] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have performed a phylogenetic survey of microbial species present in two soils from northern Arizona. Microbial DNA was purified directly from soil samples and subjected to PCR amplification with primers specific for bacterial 16S rRNA gene sequences (rDNAs). Clone libraries from the two soils were constructed, and 60 clone inserts were partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity. Most of the analyzed sequences (64%) fell into five novel clusters having no known cultured members. Extensive analysis of 10 nearly full-length rDNAs from clones representative of the novel groups indicated that four of the five groups probably cluster into a large "supergroup" which is as distinct from currently recognized bacterial divisions as the latter are from each other. From this we postulate the existence of a major bacterial lineage, previously known only from a single cultured representative, whose diversity and ecology we are only beginning to explore. Analysis of our data and that from other rDNA sequence-based studies of soils from different geographic regions shows considerable overlap of sequence types. Taken together, these groups encompass most of the novel rDNA sequences recovered in each comparable analysis reported to date, despite large differences in soil types and geographic sources. Our results indicate that members of these new groups comprise a phylogenetically diverse, geographically widespread, and perhaps numerically important component of the soil microbiota.
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Affiliation(s)
- C R Kuske
- Environmental Molecular Biology Group, Los Alamos National Laboratory, New Mexico 87545, USA.
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411
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Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 1997; 63:2884-96. [PMID: 9212435 PMCID: PMC168584 DOI: 10.1128/aem.63.7.2884-2896.1997] [Citation(s) in RCA: 527] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The bacterial community structure of activated sludge of a large municipal wastewater treatment plant was investigated by use of the rRNA approach. Almost-full-length genes coding for the small-subunit rRNA (rDNA) were amplified by PCR and subsequently cloned into the pGEM-T vector. Clones were screened by dot blot hybridization with group-specific oligonucleotide probes. The phylogenetic affiliations of clones were compared with the results obtained with the original sample by in situ hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes and found to be in general agreement. Twenty-five 16S rDNA clones were fully sequenced, 11 were almost fully (> 80%) sequenced, and 27 were partially sequenced. By comparative sequence analyses, the majority of the examined clones (35 of 67) could be affiliated with the beta subclass of the class Proteobacteria. The gamma and alpha subclasses of Proteobacteria were represented by 13 and 4 clones, respectively. Eight clones grouped with the epsilon group of Proteobacteria, and five clones grouped with gram-positive bacteria with a low DNA G+C content. The 16S rDNA of two clones showed similarity with 16S rDNA genes of members of the phyla Chlamydiae and Planctomyces. 16S rRNA-targeted oligonucleotide probes were designed and used for the enumeration of the respective bacteria. Interestingly, potentially pathogenic representatives of the genus Arcobacter were present in significant numbers (4%) in the activated sludge sample examined. Pairs of probes targeted to the 5' and 3' regions were used for detection of chimeric sequences by in situ hybridization. Two clones could be identified as chimera by applying such a pair of probes.
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Affiliation(s)
- J Snaidr
- Lehrstuhl für Mikrobiologie, Technische Universität München, Germany
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412
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413
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Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 1997; 63:2802-13. [PMID: 9212428 PMCID: PMC168577 DOI: 10.1128/aem.63.7.2802-2813.1997] [Citation(s) in RCA: 588] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The bacterial community structure of a fluidized-bed reactor fed by vinasses (wine distillation waste) was analyzed. After PCR amplification, four small-subunit (SSU) rDNA clone libraries of Bacteria, Archaea, Procarya, and Eucarya populations were established. The community structure was determined by operational taxonomic unit (OTU) phylogenetic analyses of 579 partial rDNA sequences (about 500 bp long). A total of 146 OTUs were found, comprising 133, 6, and 7 from the Bacteria, Archaea, and Eucarya domains, respectively. A total of 117 bacterial OTU were affiliated with major phyla: low-G+C gram-positive bacteria, Cytophaga-Flexibacter-Bacteroides, Proteobacteria, high-G+C gram-positive bacteria, and Spirochaetes, where the clone distribution was 34, 26, 17, 6, and 4%, respectively. The other 16 bacterial OTUs represent 13% of the clones. They were either affiliated with narrow phyla such as Planctomyces-Chlamydia, green nonsulfur bacteria, or Synergistes, or deeply branched on the phylogenetic tree. A large number of bacterial OTUs are not closely related to any other hitherto determined sequences. The most frequent bacterial OTUs represents less than 5% of the total bacterial SSU rDNA sequences. However, the 20 more frequent bacterial OTUs describe at least 50% of these sequences. Three of the six Archaea OTUs correspond to 95% of the Archaea population and are very similar to already known methanogenic species: Methanosarcina barkeri, Methanosarcina frisius, and Methanobacterium formicicum. In contrast, the three other Archaea OTUs are unusual and are related to thermophilic microorganisms such as Crenarchaea or Thermoplasma spp. Five percent of the sequences analyzed were chimeras and were removed from the analysis.
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Affiliation(s)
- J J Godon
- Laboratoire de Biotechnologie de l'Environnement, Institut National de la Recherche Agronomique, Narbonne, France.
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414
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Chandler DP, Brockman FJ, Fredrickson JK. Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol Rev 1997. [DOI: 10.1111/j.1574-6976.1997.tb00310.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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415
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Ferris MJ, Nold SC, Revsbech NP, Ward DM. Population structure and physiological changes within a hot spring microbial mat community following disturbance. Appl Environ Microbiol 1997; 63:1367-74. [PMID: 9097433 PMCID: PMC168430 DOI: 10.1128/aem.63.4.1367-1374.1997] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The influence of disturbance on a hot spring cyanobacterial mat community was investigated by physically removing the top 3.0 mm, which included the entire cyanobacterial layer. Changes in 16S rRNA-defined populations were monitored by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments. Some previously absent cyanobacterial populations colonized the disturbed areas, while some populations which were present before the disturbance remained absent for up to 40 days. Changes in physiological activity were measured by oxygen microelectrode analyses and by 14CO2 incorporation into cyanobacterial molecular components. These investigations indicated substantial differences between the disturbed and undisturbed mats, including an unexplained light-induced oxygen consumption in the freshly exposed mat, increased carbon partitioning by phototrophs into growth-related macromolecules, bimodal vertical photosynthesis profiles, and delayed recovery of respiration relative to photosynthesis.
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Affiliation(s)
- M J Ferris
- Department of Microbiology, Montana State University, Bozeman 59717, USA
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416
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Ferris MJ, Ward DM. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 1997; 63:1375-81. [PMID: 9097434 PMCID: PMC168431 DOI: 10.1128/aem.63.4.1375-1381.1997] [Citation(s) in RCA: 231] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments was used to examine the distributions of bacterial populations within a hot spring microbial mat (Octopus Spring, Yellowstone National Park). Populations at sites along the thermal gradient of the spring's effluent channel were surveyed at seasonal intervals. No shift in the thermal gradient was detected, and populations at spatially or temperature-defined sites exhibited only slight changes over the annual sampling period. A new cyanobacterial 16S rRNA sequence type was detected at temperatures from 63 to 75 degrees C. A new green nonsulfur bacterium-like sequence type was also detected at temperatures from 53 to 62 degrees C. Genetically unique though closely related cyanobacterial and green nonsulfur bacterium-like populations were successively distributed along the thermal gradient of the Octopus Spring effluent channel. At least two cyanobacterial populations were detected at each site; however, a limited ability to detect some cyanobacterial populations suggests that only dominant populations were observed.
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Affiliation(s)
- M J Ferris
- Microbiology Department, Montana State University, Bozeman 59717, USA
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417
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Polz MF, Cavanaugh CM. A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl Environ Microbiol 1997; 63:1028-33. [PMID: 9055419 PMCID: PMC168394 DOI: 10.1128/aem.63.3.1028-1033.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A simple method for the quantification of uncultured microorganisms in the environment was developed. In vitro-transcribed 16S rRNA is used as a template for midpoint dissociation temperature (Td) determinations of specific oligonucleotide probes and as a standard in quantitative probing. It replaces the need for total nucleic acids extracted from pure cultures of the organisms to be quantified. A sense RNA of a size almost identical to that of native 16S rRNA can be transcribed from ribosomal DNA clones recovered in studies of the phylogenetic diversity of microbial communities. This in vitro-transcribed rRNA yields dissociation curves typical of oligonucleotides. They parallel curves determined with total nucleic acids but yield slightly higher Td values. Neither unspecific sticking of the probe nor probe washing off the DNA template at low temperatures fully accounted for the discrepancy in probe release from the two templates. This suggests that the native rRNA itself has melting characteristics different from those of its in vitro-transcribed counterpart. However, this difference does not affect the performance of in vitro-transcribed rRNA compared with total nucleic acids as a standard in quantitative hybridizations. No difference was found between the estimates of the relative quantity of a single bacterial species in a mixed community obtained with the two standards, regardless of whether DNA was removed from the samples. This protocol will allow the large-scale quantification of the ecological importance of uncultured microorganisms in natural environments for the first time.
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Affiliation(s)
- M F Polz
- Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
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418
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Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM. Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci U S A 1997; 94:277-82. [PMID: 8990199 PMCID: PMC19314 DOI: 10.1073/pnas.94.1.277] [Citation(s) in RCA: 274] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cultivation methods have contributed to our present knowledge about the presence and diversity of microbes in naturally occurring communities. However, it is well established that only a small fraction of prokaryotes have been cultivated by standard methods and, therefore, the prokaryotes that are cultivated may not reflect the composition and diversity within those communities. Of the two prokaryotic phylogenetic domains, Bacteria and Archaea, members of the former have been shown to be ubiquitous in nature, with ample evidence of vast assemblages of uncultured organisms. There is also now increasingly compelling evidence that the Archaea, which were once thought to occupy a limited number of environments, are also globally widespread. Here we report the use of molecular phylogenetic techniques, which are independent of microbial cultivation, to conduct an assessment of Archaea in a soil microbial community. Small subunit ribosomal RNA genes of Archaea were amplified from soil and cloned. Phylogenetic and nucleotide signature analyses of these cloned small subunit ribosomal RNA gene sequences revealed a cluster of Archaea from a soil microbial community that diverge deeply from the crenarchaeotal line of descent and has the closest affiliation to the lineage of planktonic Archaea. The identification and phylogenetic classification of this archaeal lineage from soil contributes to our understanding of the ecological significance of Archaea as a component of microbial communities in non-extreme environments.
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Affiliation(s)
- S B Bintrim
- Department of Plant Pathology, University of Wisconsin-Madison, 53706, USA
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419
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Evaluation of a 23S rRNA Insertion as Target for the Analysis of Uncultured Frankia Populations in Root Nodules of Alders by Whole Cell Hybridization. Syst Appl Microbiol 1997. [DOI: 10.1016/s0723-2020(97)80056-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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420
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Lanoil BD, Ciuffetti LM, Giovannoni SJ. The marine bacterium Pseudoalteromonas haloplanktis has a complex genome structure composed of two separate genetic units. Genome Res 1996; 6:1160-9. [PMID: 8973910 DOI: 10.1101/gr.6.12.1160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated the fragments using pulsed-field gel electrophoresis (PFGE), and summed the sizes of the fragments. The P. haloplanktis genome was 3512 +/- 112 kb by Notl digestion and 3468 +/- 54.1 kb by Sfil digestion. P. haloplanktis is also shown to have a complex genome structure, composed of two large replicons of approximately 2700 and 800 kb. Three pieces of evidence support this conclusion: (1) Two separate bands are always seen in PFGE of undigested P. haloplanktis DNA; (2) restriction digests of the larger band are missing a band of approximately 650 kb compared with restriction digests of total genomic DNA; and (3) a 16S rDNA probe hybridized to the larger replicon but not to the smaller. To our knowledge, P. haloplanktis is the first marine bacterium shown to have a complex genome structure.
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Affiliation(s)
- B D Lanoil
- Department of Microbiology, Oregon State University, Corvallis 97331, USA
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421
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Nold SC, Kopczynski ED, Ward DM. Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat. Appl Environ Microbiol 1996; 62:3917-21. [PMID: 8899976 PMCID: PMC168207 DOI: 10.1128/aem.62.11.3917-3921.1996] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The diversity of aerobic chemoorganotrophic bacteria inhabiting the Octopus Spring cyanobacterial mat community (Yellowstone National Park) was examined by using serial-dilution enrichment culture and a variety of enrichment conditions to cultivate the numerically significant microbial populations. The most abundant bacterial populations cultivated from dilutions to extinction were obtained from enrichment flasks which contained 9.0 x 10(2) primary producer (Synechococcus spp.) cells in the inoculum. Two isolates exhibited 16S rRNA nucleotide sequences typical of beta-proteobacteria. One of these isolates contained a 16S rRNA sequence identical to a sequence type previously observed in the mat by molecular retrieval techniques. Both are distantly related to a new sequence directly retrieved from the mat and contributed by a beta-proteobacterial community member. Phenotypically diverse gram-positive isolates genetically similar to Bacillus flavothermus were obtained from a variety of dilutions and enrichment types. These isolates exhibited identical 16S rRNA nucleotide sequences through a variable region of the molecule. Of the three unique sequences observed, only one had been previously retrieved from the mat, illustrating both the inability of the cultivation methods to describe the composition of a microbial community and the limitations of the ability of molecular retrieval techniques to describe populations which may be less abundant in microbial communities.
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Affiliation(s)
- S C Nold
- Department of Microbiology, Montana State University, Bozeman 59717, USA
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422
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Stephen JR, McCaig AE, Smith Z, Prosser JI, Embley TM. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl Environ Microbiol 1996; 62:4147-54. [PMID: 8900005 PMCID: PMC168236 DOI: 10.1128/aem.62.11.4147-4154.1996] [Citation(s) in RCA: 314] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have conducted a preliminary phylogenetic survey of ammonia-oxidizing beta-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing beta-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonas-like sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types.
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Affiliation(s)
- J R Stephen
- Department of Zoology, Natural History Museum, London, United Kingdom
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423
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Abstract
▪ Abstract With the discovery of the eukaryote nucleus, all living organisms were neatly divided into prokaryotes, which lacked a nucleus, and eukaryotes, which possessed it. As data derived directly from the genome became available, it was clear that prokaryotes were comprised of two groups, Eubacteria and Archaebacteria. These were subsequently renamed at the new taxonomic level of Domain as Bacteria and Archaea, with the eukaryotes named as the Eucarya Domain. The interrelationships of the three Domains are still subject to discussion and evaluation, as is their monophyly. Further data, drawn from various protein sequences, suggest conflicting schemes, and resolution may not be straightforward. Additionally, Bacteria and Archaea as well as Eucarya are largely based on organisms already in culture. Investigation of the potentially enormous quantity of uncultured organisms in nature is likely to have as broad-ranging implications as the exploration of new protein sequences.
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Affiliation(s)
- David M. Williams
- The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - T. Martin Embley
- The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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424
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Devereux R, Hines ME, Stahl DA. S Cycling: Characterization of Natural Communities of Sulfate-Reducing Bacteria by 16S rRNA Sequence Comparisons. MICROBIAL ECOLOGY 1996; 32:283-292. [PMID: 8849423 DOI: 10.1007/bf00183063] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Past studies of microbial communities responsible for geochemical transformations have been limited by an inability to representatively cultivate, and then identify, the constituent members. Ribosomal RNA sequences, particularly 16S-like rRNAs, provide a measure of phylogenetic relationship that can now be used to examine the structure and diversity of microbial communities. Sulfate-reducing bacteria (SRB) play an important role in the sulfur cycle and the terminal mineralization of organic matter in estuarine and marine environments. Because the Gram-negative mesophilic SRB comprise a phylogenetically coherent assemblage, their communities are well suited to explorations through rRNA sequence-based methodologies. In this study we related molecular biological methods using rRNA probes to geochemical measurements at two different sites. At an unvegetated site in northwest Florida, rates of sulfate reduction were low and SRB rRNA comprised about 5% of the total rRNA extracted from the sediment. The other site, a salt marsh in New Hampshire, had higher rates of sulfate-reduction with SRB rRNA accounting for up to 30% of the total rRNA extracted from the sediment. SRB community structure differed dramatically between the two sites with Desulfobulbus rRNA much less abundant in the unvegetated site than in the salt marsh. The differences in these SRB communities reflect differences in the ecology of their habitats.
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Affiliation(s)
- R Devereux
- Microbial Ecology, United States Environmental Protection Agency, 1 Sabine Island Drive, Gulf Breeze, Fl 32561, USA
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425
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Abstract
For the phylogenetic analysis of microbial communities present in environmental samples microbial DNA can be extracted from the sample, 16S rDNA can be amplified with suitable primers and the PCR, and clonal libraries can be constructed. We report a protocol that can be used for efficient cell lysis and recovery of DNA from marine sediments. Key steps in this procedure include the use of a bead mill homogenizer for matrix disruption and uniform cell lysis and then purification of the released DNA by agarose gel electrophoresis. For sediments collected from two sites in Puget Sound, over 96% of the cells present were lysed. Our method yields high-molecular-weight DNA that is suitable for molecular studies, including amplification of 16S rRNA genes. The DNA yield was 47 micrograms per g (dry weight) for sediments collected from creosote-contaminated Eagle Harbor, Wash. Primers were selected for the PCR amplification of (eu)bacterial 16S rDNA that contained linkers with unique 8-base restriction sites for directional cloning. Examination of 22 16S rDNA clones showed that the surficial sediments in Eagle Harbor contained a phylogenetically diverse population of organisms from the Bacteria domain (G. J. Olsen, C. R. Woese, and R. Overbeek, J. Bacteriol. 176:1-6, 1994) with members of six major lineages represented: alpha, delta, and gamma Proteobacteria; the gram-positive high G+C content subdivision; clostridia and related organisms; and planctomyces and related organisms. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA database. The analysis of clonal representives in the first report using molecular techniques to determine the phylogenetic composition of the (eu)bacterial community present in coastal marine sediments.
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Affiliation(s)
- J P Gray
- School of Fisheries, College of Ocean and Fishery Sciences, University of Washington, Seattle 98105-6715, USA
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426
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Lee SY, Bollinger J, Bezdicek D, Ogram A. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl Environ Microbiol 1996; 62:3787-93. [PMID: 8837435 PMCID: PMC168187 DOI: 10.1128/aem.62.10.3787-3793.1996] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Strain EA25 was identified in a clone library of bacterial 16S rRNA gene sequences that had been amplified from DNA extracted from soil collected in eastern Washington State. EA25 was subsequently shown to be related to members of the genera Planctomyces and Chlamydia and most closely related (93% similarity) to strain MC18, a strain identified in an Australian soil sample (W. Liesack and E. Stackebrandt, J. Bacteriol. 174:5072-5078, 1992). A competitive quantitative PCR method developed by Zachar et al. (V. Zachar, R.A. Thomas, and A.S. Goustin, Nucleic Acids Res. 21:2017-2018, 1993) was used to estimate the abundance of this uncultured strain in soil. An estimation of the abundance of EA25 was based on the number of copies of the sequence in the DNA extracted and the efficiency of the DNA extraction. In addition, amplification rates of Escherichia coli DNAs added to soil were shown to be similar to those of DNAs from laboratory cultures of E. coli. The number of EA25 16S rRNA genes was estimated to be 2.17 x 10(8) copies per g of soil, suggesting that strains similar to EA25 and the similar Australian strain could be widely distributed and present in significant numbers in soils from temperate regions. This represents the first enumeration of 16S rDNA copies from an uncultured strain in soil.
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MESH Headings
- Chlamydia/genetics
- Chlamydia/isolation & purification
- Cloning, Molecular
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Genes, Bacterial/genetics
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/isolation & purification
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Washington
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Affiliation(s)
- S Y Lee
- Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420, USA
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427
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McVeigh HP, Munro J, Embley TM. Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J Ind Microbiol Biotechnol 1996. [DOI: 10.1007/bf01574693] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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428
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Boivin-Jahns V, Ruimy R, Bianchi A, Daumas S, Christen R. Bacterial diversity in a deep-subsurface clay environment. Appl Environ Microbiol 1996; 62:3405-12. [PMID: 8795233 PMCID: PMC168139 DOI: 10.1128/aem.62.9.3405-3412.1996] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The presence of bacteria in a deep clay sediment was analyzed in a 20-m-long core horizontally drilled from a mine gallery at a depth of 224 m in the Boom clay formation (Mol, Belgium). This clay deposit is the result of a marine sedimentary process that occurred 35 million years ago. Bacterial activities were estimated by measuring respiration on [14C]glucose. Using the same samples, universal primers for the genes coding for eubacterial 16S rRNA were used to amplify extracted DNA. PCR products were then cloned, sequenced, and analyzed by molecular phylogeny. Our data showed a decrease in bacterial densities as a function of distance from the gallery, with few bacteria detectable by culture at more than 80 cm from the gallery wall. PCR experiments showed the presence of bacteria in all samples, and phylogenetic analyses were then used to tentatively identify these organisms. Because of low bacterial densities in deep clay samples, direct counts and enumeration of viable bacteria on diverse culture media remained negative. All experiments, both cultures and PCR, demonstrated the difficulty of analyzing samples that contain only a few poorly active bacteria as it is difficult to avoid a small contamination by active bacteria during sampling. Since the porosity of the Boom clay formation is less than the expected size of bacteria, it is possible that some of the bacteria present in this 35-million-year-old deep clay deposit derive from cells initially trapped during the sedimentation process.
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Affiliation(s)
- V Boivin-Jahns
- Observatoire Océanologique, Centre National de la Recherche Scientifique and Université Paris, France
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429
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Lee DH, Zo YG, Kim SJ. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 1996; 62:3112-20. [PMID: 8795197 PMCID: PMC168103 DOI: 10.1128/aem.62.9.3112-3120.1996] [Citation(s) in RCA: 223] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We describe a new method for studying the structure and diversity of bacterial communities in the natural ecosystem. Our approach is based on single-strand-conformation polymorphism (SSCP) analysis of PCR products of 16S rRNA genes from complex bacterial populations. A pair of eubacterial universal primers for amplification of the variable V3 region were designed from the 16S rRNA sequences of 1,262 bacterial strains. The PCR conditions were optimized by using genomic DNAs from five gram-positive and seven gram-negative strains. The SSCP analysis of the PCR products demonstrated that a bacterial strain generated its characteristic band pattern and that other strains generated other band patterns, so that the relative diversity in bacterial communities could be measured. In addition, this method was sensitive enough to detect a bacterial population that made up less than 1.5% of a bacterial community. The distinctive differences between bacterial populations were observed in an oligotrophic lake and a eutrophic pond in a field study. The method presented here, using combined PCR amplification and SSCP pattern analyses of 16S rRNA genes, provides a useful tool to study bacterial community structures in various ecosystems.
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Affiliation(s)
- D H Lee
- Department of Microbiology, College of Natural Sciences, Seoul National University, Korea
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430
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Murray AE, Hollibaugh JT, Orrego C. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 1996; 62:2676-80. [PMID: 8779608 PMCID: PMC168051 DOI: 10.1128/aem.62.7.2676-2680.1996] [Citation(s) in RCA: 194] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The phylogenetic compositions of bacterioplankton assemblages from San Francisco Bay and Tomales Bay, Calif., differed substantially when analyzed by PCR-denaturing gradient gel electrophoresis; these differences are consistent with the results of previous studies demonstrating differences in their metabolic capabilities. PCR-denaturing gradient gel electrophoresis analysis of complex microbial assemblages was sensitive and reliable, and the results were reproducible as shown by experiments with constructed and naturally occurring assemblages.
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Affiliation(s)
- A E Murray
- Center for Environmental Studies, San Francisco State University, Tiburon, California 94920, USA
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431
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Pedersen K, Arlinger J, Hallbeck L, Pettersson C. Diversity and distribution of subterranean bacteria in groundwater at Oklo in Gabon, Africa, as determined by 16S rRNA gene sequencing. Mol Ecol 1996; 5:427-36. [PMID: 8688960 DOI: 10.1111/j.1365-294x.1996.tb00332.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This paper describes how ground water was sampled, DNA extracted, amplified and cloned and how information available in the ribosomal 16S rRNA gene was used for mapping diversity and distribution of subterranean bacteria in groundwater at the Bangombé site in the Oklo region. The results showed that this site was inhabited by a diversified population of bacteria. Each borehole was dominated by species that did not dominate in any of the other boreholes; a result that probably reflects documented differences in the geochemical environment. Two of the sequences obtained were identified at genus level to represent Acinetobacter and Zoogloea, but most of the 44 sequences found were only distantly related to species in the DNA database. The deepest borehole, BAX01 (105 m), had the highest number of bacteria and also total organic carbon (TOC). This borehole harboured only Proteobacteria beta group sequences while sequences related to Proteobacteria beta, gamma and delta groups and Gram-positive bacteria were found in the other four boreholes. Two of the boreholes, BAX02 (34 m) and BAX04 (10 m) had many 16S rRNA gene sequences in common and also had similar counts of bacteria, content of TOC, pH and equal conductivity, suggesting a hydraulic connection between them.
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Affiliation(s)
- K Pedersen
- Department of General and Marine Microbiology, The Lundberg Institute, Göteborg University, Sweden
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432
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Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 1996; 62:1935-43. [PMID: 8787391 PMCID: PMC167971 DOI: 10.1128/aem.62.6.1935-1943.1996] [Citation(s) in RCA: 386] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A culture-independent survey of the soil microbial diversity in a clover-grass pasture in southern Wisconsin was conducted by sequence analysis of a universal clone library of genes coding for small-subunit rRNA (rDNA). A rapid and efficient method for extraction of DNA from soils which resulted in highly purified DNA with minimal shearing was developed. Universal small-subunit-rRNA primers were used to amplify DNA extracted from the pasture soil. The PCR products were cloned into pGEM-T, and either hypervariable or conserved regions were sequenced. The relationships of 124 sequences to those of cultured organisms of known phylogeny were determined. Of the 124 clones sequenced, 98.4% were from the domain Bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Two of the 124 sequences were of nuclear origin, one being fungal and the other a plant sequence. No sequences of the domain Archaea were found. Within the domain, Bacteria, three kingdoms were highly represented: the Proteobacteria (16.1%), the Cytophaga-Flexibacter-Bacteroides group (21.8%), and the low G+C-content gram-positive group (21.8%). Some kingdoms, such as the Thermotogales, the green nonsulfur group, Fusobacteria, and the Spirochaetes, were absent. A large number of the sequences (39.4%) were distributed among several clades that are not among the major taxa described by Olsen et al. (G.J. Olsen, C.R. Woese, and R. Overbeek, J. Bacteriol., 176:1-6, 1994). From the alignments of the sequence data, distance matrices were calculated to display the enormous microbial diversity found in this soil in two ways, as phylogenetic trees and as multidimensional-scaling plots.
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Affiliation(s)
- J Borneman
- Department of Agronomy, University of Wisconsin-Madison 53706, USA
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433
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Farrelly V, Rainey FA, Stackebrandt E. Effect of genome size andrrn gene copy numbers of PCR amplification products of 16S rRNA genes from mixed bacterial species. ACTA ACUST UNITED AC 1996. [DOI: 10.1007/bf01919508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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434
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Pedersen K, Arlinger J, Ekendahl S, Hallbeck L. 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Ãspö hard rock laboratory, Sweden. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00217.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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435
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Gordon DA, Giovannoni SJ. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl Environ Microbiol 1996; 62:1171-7. [PMID: 8919778 PMCID: PMC167883 DOI: 10.1128/aem.62.4.1171-1177.1996] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A gene lineage (SAR406) related to Chlorobium and Fibrobacter species was found in 16S rRNA gene clone libraries prepared from samples from two oceans. The clone libraries were constructed from total picoplankton genomic DNA to assess bacterial diversity in the lower surface layer. The samples were collected by filtration from a depth of 80 m at a site in the western Sargasso Sea and from a depth of 120 m at a site in the Pacific Ocean, approximately 70 km from the Oregon coast. The PCR and primers which amplified nearly full-length 16S rRNA genes were used to prepare the clone libraries. Among the diverse gene clones in these libraries were two related clones (SAR406 and OCS307) which could not be assigned to any of the major bacterial phyla. Phylogenetic analyses demonstrated that these genes were distant relatives of the genus Fibrobacter and the green sulfur bacterial phylum, which includes the genus Chlorobium. The inclusion of SAR406 in phylogenetic trees inferred by several methods resulted in support from bootstrap replicates for the conclusion that Fibrobacter and Chlorobium species and SAR406 are a monophyletic group. An oligonucleotide probe that selectively hybridized to clone SAR406 was used to examine the distribution of this gene lineage in vertical profiles from the Atlantic and Pacific Oceans and in monthly time series at 0 and 200 m in the Atlantic Ocean. During stratified periods, the genes were most abundant slightly below the deep chlorophyll layer. Seasonal changes in the surface abundance of SAR406 rDNA were highly correlated with chlorophyll a levels (r = 0.75).
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Affiliation(s)
- D A Gordon
- Department of Microbiology, Oregon State University, Corvallis 97331, USA
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436
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Lim EL. Molecular identification of nanoplanktonic protists based on small subunit ribosomal RNA gene sequences for ecological studies. J Eukaryot Microbiol 1996; 43:101-6. [PMID: 8720940 DOI: 10.1111/j.1550-7408.1996.tb04488.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nanoplanktonic protists are comprised of a diverse assemblage of species which are responsible for a variety of trophic processes in marine and freshwater ecosystems. Current methods for identifying small protists by electron microscopy do not readily permit both identification and enumeration of nanoplanktonic protists in field samples. Thus, one major goal in the application of molecular approaches in protistan ecology has been the detection and quantification of individual species in natural water samples. Sequences of small subunit ribosomal RNA (SSU rRNA) genes have proven to be useful towards achieving this goal. Comparison of sequences from clone libraries of protistan SSU rRNA genes amplified from natural assemblages of protists by the polymerase chain reaction (PCR) can be used to examine protistan diversity. Furthermore, oligonucleotide probes complementary to short sequence regions unique to species of small protists can be designed by comparative analysis of rRNA gene sequences. These probes may be used to either detect the RNA of particular species of protists in total nucleic acid extracts immobilized on membranes, or the presence of target species in water samples via in situ hybridization of whole cells. Oligonucleotide probes may also serve as primers for the selective amplification of target sequences from total population DNA by PCR. Thus, molecular sequence information is becoming increasingly useful for identifying and enumerating protists, and for studying their spatial and temporal distribution in nature. Knowledge of protistan species composition, abundance and variability in an environment can ultimately be used to relate community structure to various aspects of community function and biogeochemical activity.
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Affiliation(s)
- E L Lim
- Biology Department, Woods Hole Oceanographic Institution, Massachusetts 02543, USA
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437
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Rosado A, Seldin L, Wolters A, Elsas J. Quantitative 16S rDNA-targeted polymerase chain reaction and oligonucleotide hybridization for the detection of Paenibacillus azotofixans in soil and the wheat rhizosphere. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00208.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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438
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Ferris MJ, Muyzer G, Ward DM. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 1996; 62:340-6. [PMID: 8593039 PMCID: PMC167804 DOI: 10.1128/aem.62.2.340-346.1996] [Citation(s) in RCA: 516] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene segments was used to profile microbial populations inhabiting different temperature regions in the microbial mat community of Octopus Spring, Yellowstone National Park. DGGE allowed a rapid evaluation of the distributions of amplifiable sequence types. Profiles were essentially identical within regions of the mat defined by one temperature range but varied between sites with different temperature ranges. Individual DGGE bands were sequenced, and the sequences were compared with those previously obtained from the mat by cloning and from cultivated Octopus Spring isolates. Two known cyanobacterial populations and one known green nonsulfur bacterium-like population were detected by DGGE, as were many new cyanobacterial and green nonsulfur and green sulfur bacterium-like populations and a novel bacterial population of uncertain phylogenetic affiliation. The distributions of several cyanobacterial populations compared favorably with results obtained previously by oligonucleotide probe analyses and suggest that adaptation to temperature has occurred among cyanobacteria which are phylogenetically very similar.
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Affiliation(s)
- M J Ferris
- Department of Microbiology, Montana State University, Bozeman 59717, USA.
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