Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we devel...

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Veröffentlicht in:	Environmental microbiology Jg. 11; H. 2; S. 289 - 299
Hauptverfasser:	Loy, Alexander, Duller, Stephan, Baranyi, Christian, Mußmann, Marc, Ott, Jörg, Sharon, Itai, Béjà, Oded, Le Paslier, Denis, Dahl, Christiane, Wagner, Michael
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.02.2009 Blackwell Publishing Ltd Wiley
Schlagworte:	Archaea Archaea - classification Archaea - enzymology Archaea - genetics Bacteria Bacteria - classification Bacteria - enzymology Bacteria - genetics BASIC BIOLOGICAL SCIENCES chemistry classification DNA, Bacterial DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal DNA, Ribosomal - chemistry DNA, Ribosomal - genetics enzymes enzymology genes genetics Hydrogensulfite Reductase Hydrogensulfite Reductase - genetics lakes metabolism methods Microbiology Molecular Sequence Data Oxidation-Reduction Phylogeny polymerase chain reaction Polymerase Chain Reaction - methods prokaryotic cells ribosomal RNA RNA, Ribosomal, 16S RNA, Ribosomal, 16S - genetics sediments sequence analysis Sequence Analysis, DNA sulfur Sulfur Compounds Sulfur Compounds - metabolism topology trees
ISSN:	1462-2912, 1462-2920, 1462-2920
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Abstract	Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.
AbstractList	Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. Summary Sulfur‐oxidizing prokaryotes (SOP) catalyse a central step in the global S‐cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB‐encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound‐exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. SummarySulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.
Author	Baranyi, Christian Ott, Jörg Béjà, Oded Sharon, Itai Duller, Stephan Wagner, Michael Mußmann, Marc Le Paslier, Denis Loy, Alexander Dahl, Christiane
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Snippet	Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered... Summary Sulfur‐oxidizing prokaryotes (SOP) catalyse a central step in the global S‐cycle and are of major functional importance for a variety of natural and... Sulfur‐oxidizing prokaryotes (SOP) catalyse a central step in the global S‐cycle and are of major functional importance for a variety of natural and engineered... SummarySulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and...
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SubjectTerms	Archaea Archaea - classification Archaea - enzymology Archaea - genetics Bacteria Bacteria - classification Bacteria - enzymology Bacteria - genetics BASIC BIOLOGICAL SCIENCES chemistry classification DNA, Bacterial DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal DNA, Ribosomal - chemistry DNA, Ribosomal - genetics enzymes enzymology genes genetics Hydrogensulfite Reductase Hydrogensulfite Reductase - genetics lakes metabolism methods Microbiology Molecular Sequence Data Oxidation-Reduction Phylogeny polymerase chain reaction Polymerase Chain Reaction - methods prokaryotic cells ribosomal RNA RNA, Ribosomal, 16S RNA, Ribosomal, 16S - genetics sediments sequence analysis Sequence Analysis, DNA sulfur Sulfur Compounds Sulfur Compounds - metabolism topology trees
Title	Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes
URI	https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fj.1462-2920.2008.01760.x https://www.ncbi.nlm.nih.gov/pubmed/18826437 https://www.proquest.com/docview/20335033 https://www.proquest.com/docview/46134263 https://www.proquest.com/docview/66894119 https://www.osti.gov/servlets/purl/1625896 https://pubmed.ncbi.nlm.nih.gov/PMC2702494
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