Reclassification of ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus

Karavaiko, G. I.; Bogdanova, T. I.; Tourova, T. P.; Tf, Kondrat'eva; Цаплина, И. А.; Егорова, М.А.; Krasil’nikova, E. N.; Zakharchuk, L. M.

doi:10.1099/ijs.0.63300-0

Cited by 109 publications

(59 citation statements)

References 27 publications

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“…They are nearly identical to each other (0.2% difference) and 19% different from Z21979. In 2005, S. thermosulfidooxidans strain K1 was reclassified as the type strain of a new species, A. tolerans (14). In our analysis, however, the sequence for K1 given in the naming paper (accession number AF137502) is 8% different from that for Z21979.…”

Section: Discussioncontrasting

confidence: 40%

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Wang

Tiedje

Cole

2007

Appl Environ Microbiol

16,947

11,815

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The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (>95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and Starting in the mid-1980s, Carl Woese revolutionized the field of microbiology with his rRNA-based phylogenetic comparisons delineating the three main branches of life (28). Today, rRNA-based analysis remains a central method in microbiology, used not only to explore microbial diversity but also as a day-to-day method for bacterial identification. Identification methods are conceptually easier to interpret than molecular phylogenetic analyses and are often preferred when the groups are well understood. Most rRNA identification (classification) methods, as opposed to phylogenetic (clustering) methods, have been nearest-neighbor-based classification schemes (10, 18; however, see reference 4). In some part, this was due to the lack of a consistent, higher-level bacterial classification structure (taxonomy). Several recent events have helped change this situation. In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology (24) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny (12, 13).The naïve Bayesian classification method is simple yet can be extremely efficient. "Naïve" refers to the (naïve) assumption that data attributes are independent. Domingos and Pazzani (11) showed that the Bayesian method can still be optimal even when this attribute independency is violated. The method has also been reported to perform well on problems similar to the classification of sequence data, such as the classification of text documents, that have a high-dimensional feature space and sparse data (16).The Ribosomal Database Project II (RDP) provides data, tools, and services related to rRNA sequences to the rese...

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Section: Discussioncontrasting

confidence: 40%

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Wang

Tiedje

Cole

2007

Appl Environ Microbiol

16,947

11,815

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“…Characterization of these acidophilic ironand sulfur-oxidizing Firmicutes shows that they are aerobes or facultative anaerobes with considerable metabolic versatility (46,75). Thirteen of our tested isolates could oxidize Fe(II) and reduce schwertmannite, but the extent of Fe(II) formation was not enhanced under strictly anoxic conditions.…”

Section: Discussionmentioning

confidence: 96%

Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments

Gischkat

Reiche

et al. 2010

Appl Environ Microbiol

138

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Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocellarelated strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacterrelated clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 ؋ 10 5 gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratorybased studies that showed this trait to be widespread among acidophiles.

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“…Strain ZJ-6 T had MK-7 as the major respiratory quinone, which accounted for 97 % of the total, and MK-6 as a minor component (3 %). The DNA G+C content of strain ZJ-6 T was 51.2 mol%, which is within the range for recognized Alicyclobacillus species (48.7-62.7 mol%) (Karavaiko et al, 2005).…”

mentioning

confidence: 80%

“…Growth in 5 % NaCl 2 2 2 2 Goto et al (2007). dData from Karavaiko et al (2005). §Data from Simbahan et al (2004).…”

mentioning

confidence: 99%

Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine

Guo

You

Liu

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A novel mesophilic, acidophilic, endospore-forming bacterium, designated strain ZJ-6 T , was isolated from Zi-Jin copper mine in Inner Mongolia, China. Cells of strain ZJ-6 T were rod-shaped, stained Gram-positive or were Gram-variable, and grew aerobically at 25-35 6C (optimum, 30 6C) and pH 2.0-6.0 (optimum, pH 3.5). 16S rRNA gene sequence analysis showed that strain ZJ-6 T was related phylogenetically to members of the genus Alicyclobacillus, with 16S rRNA gene sequence similarities of 89.5-94.2 %. Cells contained MK-7 as the major quinone and the DNA G+C content was 51.2 mol%. Strain ZJ-6 T possessed a number of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including its growth temperature, assimilation of various carbon sources, production of acids from a range of compounds, and the ability to grow chemoautotrophically using ferrous iron, elemental sulfur and tetrathionate as electron donors. The predominant cellular fatty acids of strain ZJ-6 T were anteiso-C 15 : 0 (67.1 %), iso-C 16 : 0 (7.7 %) and anteiso-C 17 : 0 (7.4 %); v-alicyclic fatty acids were not found. On the basis of these results, it is concluded that strain ZJ-6 T represents a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus aeris sp. nov. is proposed; the type strain is ZJ-6 T (5CGMCC 1.7072 T 5NBRC 104953 T ).

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Reclassification of ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus

Cited by 109 publications

References 27 publications

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments

Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine

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