Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona.

Palmisano, Margaret M.; Nakamura, L. K.; Duncan, Kathleen E.; Istock, Conrad A.; Cohan, Frederick M.

doi:10.1099/00207713-51-5-1671

Cited by 121 publications

(72 citation statements)

References 29 publications

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“…We have employed the community phylogeny approach to examine three clades whose ecological diversity and habitats have been intensively studied (Cohan et al submitted), including isolates of the Bacillus subtilis-Bacillus licheniformis clade (Palmisano et al 2001) from 'Evolution Canyon' III of the Negev Desert Figure 4. The community phylogeny simulation.…”

Section: Identifying the Sequence Clusters Corresponding To Ecotypesmentioning

confidence: 99%

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Cohan

2006

Phil. Trans. R. Soc. B

184

167

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To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed 'community phylogeny' approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.

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Section: Identifying the Sequence Clusters Corresponding To Ecotypesmentioning

confidence: 99%

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Cohan

2006

Phil. Trans. R. Soc. B

184

167

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“…All these Bacillus species can be considered as environmental contaminants, because they are commonly associated with soil (Palmisano et al 2001), facilities (Venkateswaran et al 2003) and cryotubes for collecting air (Shivaji et al 2006(Shivaji et al , 2009. The other species identified from food ice samples, including all pseudomonads, brevibacteria, lysinobacilli, Microbacterium proteolyticum and Pseudoxanthomonas japonensis, are of environmental origin and do not generally represent a risk for humans.…”

Section: Discussionmentioning

confidence: 99%

Presence of pathogenic bacteria in ice cubes and evaluation of their survival in different systems

Settanni

Gaglio

Stucchi³

et al. 2017

Ann Microbiol

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In this study, 60 samples of ice cubes produced at different levels (domestic, restaurant and industrial facilities), within a restricted geographical area, were investigated for their general microbiological characteristics through the analysis of populations other than enteric bacteria. Total mesophilic bacteria were in the range 1.01 × 10 2 -9.55 × 10 3 , 3.12 × 10 2 -6.31 × 10 3 and 1.30 × 10 2 -3.99 × 10 3 CFU/ 100 mL of thawed ice from domestic freezer (DF), stock boxes (SB) for self-production performed with ice machines in bars and pubs, and from sales packages (SP) of industrial productions, respectively. Some DF and SP samples were negative for the presence of total psychrotrophic bacteria, showing that there are no specific microbial groups associated with ice. Pseudomonads were found in the majority of ice samples analyzed. The levels of contamination of the ice samples were significantly different among the three ice cube production levels. The samples produced at domestic level and those collected from bars and pubs were characterised by the highest cell densities. The colonies representative for the different bacterial morphologies were randomly picked up from plates, purified to homogeneity and subjected to the phenotypic and genotypic characterisation. Fifty-two strains representing 31 species of eight bacterial genera were identified, with the most numerous groups included in Pseudomonas, Staphylococcus, Bacillus and Acinetobacter. A consistent percentage of the microorganisms identified from ice are known agents of human infections, and their presence indicate an environmental contamination. In order to evaluate the effectiveness of the ice cubes to transfer pathogenic agents to consumers, a bar consumption was simulated with different drink systems added with ice cubes artificially contaminated with the strains found at dominant levels (Acinetobacter lwoffii ICE100, Bacillus cereus ICE170, Pseudomonas putida ICE224 and Staphylococcus haemolyticus ICE182), and the results showed a consistent reduction of bacterial risk due to alcohol, CO 2 , pH and antibacterial ingredients of vodka, whisky, Martini, peach tea, tonic water and coke.

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“…Therefore, in this study, the standard 97% sequence identity with the closely related Bacillus was used to assign Bacillus isolates to the same species level. Based on this, extremely halotolerant Bacillus isolates screened from Dead Sea black mud were assigned to eight Bacillus species ( (Garabito et al, 1998;Palmisano et al, 2001;Roongsawang et al, 2002;Berrada et al, 2012;Zhang et al, 2012;Abbas et al, 2015;Dunlap et al, 2015) which demonstrated that those Bacillus species can tolerate increased salt concentrations. Whereas, the remained B. amyloliquefaciens was not previously defined as a halotolerant bacterium but Zar et al (2013) demonstrated that this bacterium has the ability to produce halotolerant enzymes.…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of extremely halotolerant Bacillus species from Dead Sea black mud and determination of their antimicrobial and hydrolytic activities

Obeidat¹

2017

Afr. J. Microbiol. Res.

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This is the first study that investigated the isolation of extremely halotolerant Bacillus species from Dead Sea black mud. Nine isolates obtained from black mud were considered to be extremely halotolerant Bacillus based on morphological, physiological, and biochemical properties. Most of their colonies were white to light yellow and circular to irregular. All isolates were Gram-positive rod-shaped endospore-forming bacteria, facultative anaerobes, oxidase negative, catalase positive, mesophilic, extremely halotolerant, reacted positively for tryptophan deaminase and Voges-Proskauer, hydrolyzed gelatin and aesculin, and assimilated potassium gluconate. Most of the isolates were found to hydrolyze o-nitrophenyl-beta-D-galactoside (ONPG) and p-nitrophenyl-β-D-galactopyranoside (PNPG) as well as arginine, and assimilate D-mannose, N-acetylglucosamine, D-maltose, and malic acid. All isolates were considered to be nitrate reducers, six of them were nitrite producers and three were N 2 producers, suggesting that they may play an important role in nitrification-denitrification processes and in the nitrogen cycle in soil. Based on 16S rRNA gene sequence analysis, the isolates were found to share very high identities (97-99%) with their closest phylogenetic relative and they were assigned to eight Bacillus species (B. oceanisediminis, B. subtilis, B. firmus, B. paralicheniformis, B. methylotrophicus, B. amyloliquefaciens, B. sonorensis, and B. malikii). Interestingly, several enzymatic activities were detected from nonhemolytic isolates DSM2 and DSM7 that were identified as B. paralicheniformis. It was found that only DSM2 isolate produced promising antimicrobial activities. Its aqueous extract showed the highest significant antifungal activity. Whereas, n-butanol and methanol extracts showed significant antibacterial and antifungal activities against human skin pathogens and against other frequent human pathogens.

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Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona.

Cited by 121 publications

References 29 publications

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Presence of pathogenic bacteria in ice cubes and evaluation of their survival in different systems

Isolation and characterization of extremely halotolerant Bacillus species from Dead Sea black mud and determination of their antimicrobial and hydrolytic activities

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