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Screening For Genetic Diversity Of Isolates Of Anaerobic Fe(II)-oxidizing Bacteria Using DGGE And Wh

B. Buchholz-Cleven, Birgit Rattunde, K. L. Straub
Published 1997 · Biology

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Summary Nitrate-reducing bacteria, which grow anaerobically with Fe(II) as electron donor, were isolated from freshwater mud samples. Since extensive phylogenetic and physiological characterization of multiple strains is very time-consuming and labour-intensive, the isolates were first screened for genetic diversity by denaturing gradient gel electrophoresis (DGGE) and whole-cell hybridization. DGGE analysis of 16S rDNA fragments amplified from 12 strains indicated that three different types of bacteria had been independently isolated (type A–C). Whole-cell hybridization with domain- and group-specific oligonucleotide probes suggested that the type-A and -C isolates were members of the β-subdivision of the Proteobacteria. The type-B isolates hybridized only with the bacterial probe but not with any of the probes specific for the α-, β- or γ-Proteobacteria. Based on these results representative strains of each type were chosen for further phylogenetic characterization using 16S rDNA sequencing. This analysis confirmed that the type-A and -C isolates were members of the β-Proteobacteria. The type-B isolate was shown to be a member of the Xanthomonas group of the γ-Proteobacteria. Our results demonstrate that probe GAM42a (specific for γ-Proteobacteria; Manz et al., 1992) does not hybridize to the 23S rRNA target sequence of this group of deep branching γ-Proteobacteria: this was confirmed by hybridization experiments with Xanthomonas fragariae , which also failed to hybridize to this probe. 23S rDNA sequence analysis revealed that probe GAM42a has one mismatch with the target sequence of the type-B isolate and two mismatches with the target sequence of X. fragariae . Furthermore it was shown that double stranded DNA fragments of 626 bp length, which differed by as many as two to three nucleotides were not separated by DGGE. This suggested that rDNA fragments of closely related bacteria (99.8% sequence similarity or more) are not resolved by DGGE. We propose that the combined use of DGGE and whole-cell hybridization provides a rapid way to distinguish distantly related microbial isolates.
This paper references
10.1016/0022-2836(81)90508-8
Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli.
J. Brosius (1981)
10.1128/AEM.61.6.2286-2291.1995
Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR.
B. Neilan (1995)
10.1128/AEM.61.4.1555-1562.1995
Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii.
C. Moyer (1995)
10.1016/S0723-2020(11)80121-9
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions
Werner Manz (1992)
10.1128/AEM.61.6.2203-2210.1995
Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments.
C. Wawer (1995)
10.1093/NAR/13.9.3131
Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.
R. Myers (1985)
10.1016/S0723-2020(11)80133-5
Diversity Among Fibrobacter Isolates: Towards a Phylogenetic Classification
R. Amann (1992)
10.1016/0076-6879(87)55033-9
Detection and localization of single base changes by denaturing gradient gel electrophoresis.
R. Myers (1987)
10.1038/313495A0
Detection of single base substitutions in total genomic DNA
R. Myers (1985)
10.1128/AEM.62.4.1458-1460.1996
Anaerobic, nitrate-dependent microbial oxidation of ferrous iron.
K. L. Straub (1996)
10.1093/nar/24.1.6
The European Bioinformatics Institute (EBI) databases
P. Rodriguez-Tomé (1996)
10.1128/AEM.59.11.3840-3849.1993
Distribution of sulfate-reducing bacteria, O2, and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes.
N. Ramsing (1993)
10.1128/MMBR.59.1.143-169.1995
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
R. Amann (1995)
10.1128/AEM.62.4.1391-1404.1996
Distribution of bacterial populations in a stratified fjord (mariager fjord, denmark) quantified by in situ hybridization and related to chemical gradients in the water column.
N. Ramsing (1996)
10.1128/AEM.62.11.4210-4215.1996
Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures.
A. Teske (1996)
Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction
J. Versalovic (1994)
10.1007/978-3-642-78991-5_21
Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA
G. Muyzer (1994)
10.1007/978-94-011-0351-0_20
Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis(ARDRA)
A. Massol-Deya (1995)
10.1128/AEM.56.6.1919-1925.1990
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.
R. Amann (1990)
10.1128/AEM.62.4.1405-1415.1996
Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments.
A. Teske (1996)
10.1093/nar/21.13.3021
The ribosomal database project
N. Larsen (1993)
16S/23S rRNA sequencing
D. J. Lane (1991)
10.1128/AEM.59.3.695-700.1993
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
G. Muyzer (1993)
10.1016/S0723-2020(11)80092-5
16S-rDNA analysis of Spirochaeta thermophila: Its phylogenetic position and implications for the systematics of the order Spirochaetales
F. Rainey (1992)
10.1073/PNAS.86.1.232
Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.
V. Sheffield (1989)
10.1093/NAR/13.9.3111
Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis.
R. Myers (1985)
10.1128/AEM.61.6.2270-2275.1995
Unraveling the extent of diversity within the order Planctomycetales.
N. Ward (1995)
10.1093/NAR/19.14.4008
'Touchdown' PCR to circumvent spurious priming during gene amplification.
R. Don (1991)



This paper is referenced by
10.1002/LNO.10612
Interactive regulations by viruses and dissolved organic matter on the bacterial community
Hongbin Liu (2017)
10.1080/01490450303884
Use of Ferric and Ferrous Iron Containing Minerals for Respiration by Desulfitobacterium frappieri
E. Shelobolina (2003)
10.1016/S1389-1723(01)80059-1
Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter.
M. Pedro (2001)
10.1128/AEM.68.1.316-325.2002
Characterization of an Autotrophic Sulfide-Oxidizing Marine Arcobacter sp. That Produces Filamentous Sulfur
C. Wirsen (2002)
10.1128/AEM.69.3.1397-1407.2003
Optimization Strategies for DNA Microarray-Based Detection of Bacteria with 16S rRNA-Targeting Oligonucleotide Probes
J. Peplies (2003)
10.1016/S0168-6496(03)00135-1
Microbial community variation in pristine and polluted nearshore Antarctic sediments.
S. Powell (2003)
10.1007/978-1-4020-2177-0_3
Section 3 update - Identification and classification of microbes using DNA and RNA sequences
R. Devereux (2004)
10.1007/978-1-4020-2177-0_313
Denaturing gradient gel electrophoresis (DGGE) in microbial ecology.
G. Muyzer (2004)
10.1128/AEM.67.6.2723-2733.2001
Changes in Bacterial Community Composition and Dynamics and Viral Mortality Rates Associated with Enhanced Flagellate Grazing in a Mesoeutrophic Reservoir
K. Šimek (2001)
Survival of sulfate-reducing bacteria in oxic oligotrophic environments related to drinking water
Vom Fachbereich (2000)
10.1099/ijs.0.058677-0
Pedobacter nutrimenti sp. nov., isolated from chilled food.
Julia Derichs (2014)
10.3390/EN10020258
The Influence of Micro-Oxygen Addition on Desulfurization Performance and Microbial Communities during Waste-Activated Sludge Digestion in a Rusty Scrap Iron-Loaded Anaerobic Digester
R. Ruan (2017)
10.1016/j.watres.2013.04.027
Biotic and abiotic processes contribute to successful anaerobic degradation of cyanide by UASB reactor biomass treating brewery waste water.
D. Novak (2013)
10.1007/s00248-001-1014-8
Sulfate Reduction at a Lignite Seam: Microbial Abundance and Activity
J. Detmers (2001)
10.3389/fmicb.2012.00026
Anoxic Iron Cycling Bacteria from an Iron Sulfide- and Nitrate-Rich Freshwater Environment
S. Haaijer (2012)
10.1128/AEM.65.9.3976-3981.1999
Phylogenetic Affiliation and Quantification of Psychrophilic Sulfate-Reducing Isolates in Marine Arctic Sediments
K. Sahm (1999)
10.1007/s00792-004-0409-0
Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen
T. Groudieva (2004)
10.1016/j.biortech.2016.08.041
Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment.
Xiaoxin Zhang (2016)
10.1128/genomeA.01651-15
Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6
Xiaoxin Zhang (2016)
10.1007/978-3-540-31292-5_3
DNA Fingerprinting Techniques Applied to the Identification, Taxonomy and Community Analysis of Prokaryotes
R. Pukall (2006)
10.1017/CBO9780511790461.011
Bacterial Physiology and Metabolism: Chemolithotrophy
B. H. Kim (2008)
10.1111/J.1574-6941.1999.TB00642.X
Searching for predominant soil bacteria: 16S rDNA cloning versus strain cultivation.
Felske (1999)
The Psychrophile Shewanella arctica sp. Nov: A New Source of Industrially Important Enzyme Systems
T. Brück (2014)
10.1023/A:1000669317571
Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
G. Muyzer (2004)
10.1128/AEM.63.10.3789-3796.1997
Increased species diversity and extended habitat range of sulfur-oxidizing Thiomicrospira spp.
T. Brinkhoff (1997)
10.1111/j.1365-2672.2007.03496.x
Diversity and antimicrobial susceptibility of oxytetracycline‐resistant isolates of Stenotrophomonas sp. and Serratia sp. associated with Costa Rican crops
C. Rodríguez (2007)
Diversity of the human gastrointestinal microbiota : novel perspectives from high throughput analyses
M. Rajilić-Stojanović (2007)
10.1007/s00248-011-9882-z
Effects of Continuous Thermophilic Composting (CTC) on Bacterial Community in the Active Composting Process
Y. Xiao (2011)
10.1039/C5EW00112A
Enhancement of sludge decomposition and hydrogen production from waste activated sludge in a microbial electrolysis cell with cheap electrodes
Yinghong Feng (2015)
10.1016/J.FEMSLE.2004.11.004
Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria.
N. Siyambalapitiya (2005)
10.3354/MEPS322029
Pathways of carbon oxidation in an Arctic fjord sediment (Svalbard) and isolation of psychrophilic and psychrotolerant Fe(III)-reducing bacteria
V. Vandieken (2006)
Evaluación de la fermentación y la microbiotica ruminal promovidas por dietas convencionales y no convencionales en caprino y en sistemas in vitro
E. Martín (2012)
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