An Oligonucleotide Primer System for Amplification of the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Genes of Bacteria of Various Taxonomic Groups

Spiridonova, Elizaveta M.; Berg, Ivan A.; Колганова, Т. В.; Ivanovsky, R. N.; Кузнецов, Б. Б.; Tourova, T. P.

doi:10.1023/b:mici.0000032243.93917.30

Cited by 45 publications

(42 citation statements)

References 18 publications

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“…The primer set RuIIF2/RuIIR2 (Spiridonova et al, 2004) used in our previous work for the detection of the cbbM gene was inefficient for the investigated strains of halophilic SOB. Better results were obtained using a combination of the newly designed forward primer RubII331f and a modified version of the reverse primer (RubII1113r) described by Elsaied et al (2007) (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…Detection of the cbb genes in pure cultures of halophilic SOB At first, the detection of cbb genes in pure cultures of halophilic SOB was attempted using the primer set RubIgF/RubIgR specific for the 'green-like' cbbL form I (Spiridonova et al, 2004). Despite the good results previously obtained with these primers for the haloalkaliphilic SOB (Tourova et al, 2006(Tourova et al, , 2007, they gave positive amplification among the halophilic SOB only for representatives of the genera Halothiobacillus, Thiohalomonas, Thiohalophilus and Thiohalobacter.…”

Section: Resultsmentioning

confidence: 99%

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Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

et al. 2010

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The presence and diversity of the cbb genes encoding the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin-Benson cycle of autotrophic CO 2 assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

et al. 2010

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“…cbbL and nifH gene fragments were amplified using specially developed and previously tested primers (Boulygina et al, 2002;Spiridonova et al, 2004;Marusina et al, 2001). PCR products were purified from lowmelting-point agarose using the Wizard PCR Preps kit (Promega).…”

Section: -1492rmentioning

confidence: 99%

Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes

Горленко

Bryantseva

Rabold

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…Degenerate primers for the amplification of RuBisCO type II (cbbM) gene of the CBB cycle were used to test for the presence of the gene in the genome of strain. The designed primers were utilized as previously described (see Supplementary Information online, Table S1) 29 . The PCR amplification parameters were similar to the protocol explained above.…”

Section: Pcr Amplification Of Mam Genes and Genes Involved In Co 2 Fimentioning

confidence: 99%

Diversity of <i>Magnetospirillum</i> Sp. from the Southern Coast of India

et al. 2016

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Magnetotactic bacteria (MTB) are ubiquitous in the aquatic environment and have been identified from almost every continent; however, there are only a few reports of MTB from India. This article studies the diversity of cultivable MTB from the southern coast of India. Five strains of MTB have been identified in this study using gradient culturing; three of the five strains were isolated in pure culture. The strains identified are vibrioid to helical in morphology and grow microaerophilically in oxygen-sulphide gradient media. Phylogenetic analysis of isolates based on 16S rRNA gene sequences shows that they belong to the family Rhodospirillaceae, class Alphaproteobacteria, and genus Magnetospirillum. The three isolated strains were physiologically characterized and found to utilize a wide range of substrates as electron donors and electron acceptors for metabolism. The autotrophic growth of the strains was confirmed by the detection of type-II RuBisCO (cbbM) gene by PCR amplification. The presence of key magnetosome formation (mam) genes in the strains confirms the similar mechanism of magnetosome biomineralization among Magnetospirillum species. These reports of MTB from the Indian coast would contribute to the study of their evolution and biomineralization.

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An Oligonucleotide Primer System for Amplification of the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Genes of Bacteria of Various Taxonomic Groups

Cited by 45 publications

References 18 publications

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes

Diversity of <i>Magnetospirillum</i> Sp. from the Southern Coast of India

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