Alkalihalobacillus


Alkalihalobacillus is a genus of gram-positive or gram-variable rod-shaped bacteria in the family Bacillaceae from the order Bacillales. The type species of this genus is Alkalihalobacillus alcalophilus.
This genus comprises species formerly belonging to the genus Bacillus, a genus that has been recognized as displaying extensive polyphyly and phylogenetic heterogeneity due to the vague criteria previously used to assign species to this clade. Multiple studies using comparative phylogenetic analyses have been published in an attempt to clarify the evolutionary relationships between Bacillus species, resulting in the establishment of numerous novel genera such as Alkalihalobacillus, Brevibacillus, Solibacillus, Alicyclobacillus and Virgibacillus. The genus Bacillus is now restricted to species closely related to Bacillus subtilis and Bacillus cereus.
The name Alkalihalobacillus is composed of the prefix "alkali-", the prefix "halo-" and suffixed by "-bacillus". Together, the name refers to bacillus living in salty or alkaline conditions, or salty and alkaline conditions.

Classification

Phylogeny

This genus, as of May 2021, contains a total of 44 species, 39 of which have been validly published and have established names. This genus was identified as a monophyletic clade and phylogenetically unrelated to other Bacillus species in studies examining the taxonomic relationships within Bacillus. This branching pattern is also observed in the Genome Taxonomy Database.
Two additional Bacillus species are found to group with other members of Alkalihalobacillus in phylogenetic trees as well as share the same molecular markers in the form of conserved signature indels. However, their transfer was not officially proposed due to the lack of culture strain information. Further revision of this genus is required as additional genomes and novel species are discovered and assigned.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and National Center for Biotechnology Information.

Former species

Renamed due to: Joshi et al. 2021.
current nameformer name
Alkalicoccobacillus gibsonii Joshi et al. 2022Alkalihalobacillus gibsonii Gupta et al. 2020
Alkalicoccobacillus murimartini Joshi et al. 2022Alkalihalobacillus murimartini Patel & Gupta 2020
Alkalihalobacterium alkalinitrilicus Joshi et al. 2022Alkalihalobacillus alkalinitrilicus Patel & Gupta 2020
Alkalihalobacterium bogoriensis Joshi et al. 2022Alkalihalobacillus bogoriensis Patel & Gupta 2020
Alkalihalophilus lindianensis Joshi et al. 2022Alkalihalobacillus lindianensis Patel & Gupta 2020
Alkalihalophilus marmarensis Joshi et al. 2022Alkalihalobacillus marmarensis Patel & Gupta 2020
Alkalihalophilus pseudofirmus Joshi et al. 2022Alkalihalobacillus pseudofirmus Patel & Gupta 2020
Halalkalibacter urbisdiaboli Joshi et al. 2022Alkalihalobacillus urbisdiaboli Gupta et al. 2020
Halalkalibacter kiskunsagensis Joshi et al. 2022Alkalihalobacillus kiskunsagensis Gupta et al. 2020
Halalkalibacter nanhaiisediminis Joshi et al. 2022Alkalihalobacillus nanhaiisediminis Patel & Gupta 2020
Halalkalibacter oceani Joshi et al. 2022Alkalihalobacillus oceani Gupta et al. 2020
Halalkalibacter hemicellulosilyticus Joshi et al. 2022Alkalihalobacillus hemicellulosilyticus corrig. Patel & Gupta 2020
Halalkalibacter wakoensis Joshi et al. 2022Alkalihalobacillus wakoensis Patel & Gupta 2020
Halalkalibacter okuhidensis Joshi et al. 2022Alkalihalobacillus okuhidensis Patel & Gupta 2020
Halalkalibacter krulwichiae Joshi et al. 2022Alkalihalobacillus krulwichiae Patel & Gupta 2020
Halalkalibacter akibai Joshi et al. 2022Alkalihalobacillus akibai Patel & Gupta 2020
Halalkalibacter alkalisediminis Joshi et al. 2022Alkalihalobacillus alkalisediminis Patel & Gupta 2020
Halalkalibacterium halodurans Joshi et al. 2022Alkalihalobacillus halodurans Patel & Gupta 2020
Halalkalibacterium okhensis Joshi et al. 2022Alkalihalobacillus okhensis Patel & Gupta 2020
Halalkalibacterium ligniniphilum Joshi et al. 2022Alkalihalobacillus ligniniphilus Patel & Gupta 2020
"Pseudalkalibacillus algicola" Joshi et al. 2021Alkalihalobacillus algicola Patel & Gupta 2020
Pseudalkalibacillus berkeleyi Joshi et al. 2022Alkalihalobacillus berkeleyi Patel & Gupta 2020
Pseudalkalibacillus caeni Joshi et al. 2022Alkalihalobacillus caeni Gupta et al. 2020
Pseudalkalibacillus decolorationis Joshi et al. 2022Alkalihalobacillus decolorationis Patel & Gupta 2020
"Pseudalkalibacillus hemicentroti" Joshi et al. 2021Alkalihalobacillus hemicentroti corrig. Patel & Gupta 2020
"Pseudalkalibacillus hwajinpoensis" Joshi et al. 2021Alkalihalobacillus hwajinpoensis Patel & Gupta 2020
"Pseudalkalibacillus macyae" Joshi et al. 2021Alkalihalobacillus macyae Gupta et al. 2020
"Shouchella alkalilacus" Joshi et al. 2021Alkalihalobacillus alkalilacus Gupta et al. 2020
Shouchella clausii Joshi et al. 2022Alkalihalobacillus clausii Patel & Gupta 2020
Shouchella hunanensis Joshi et al. 2022Alkalihalobacillus hunanensis Patel & Gupta 2020
Shouchella lonarensis Joshi et al. 2022Alkalihalobacillus lonarensis Patel & Gupta 2020
Shouchella miscanthi Joshi et al. 2022Alkalihalobacillus miscanthi Gupta et al. 2020
Shouchella oshimensis Joshi et al. 2022Alkalihalobacillus oshimensis Patel & Gupta 2020
Shouchella patagoniensis Joshi et al. 2022Alkalihalobacillus patagoniensis Patel & Gupta 2020
Shouchella rhizosphaerae Joshi et al. 2022Alkalihalobacillus rhizosphaerae Patel & Gupta 2020
Shouchella shaceensis Joshi et al. 2022Alkalihalobacillus shaceensis Patel & Gupta 2020
Shouchella xiaoxiensis Joshi et al. 2022Alkalihalobacillus xiaoxiensis Patel & Gupta 2020

Biochemical characteristics and molecular signatures

Most members of this genus are aerobic or facultatively anaerobic and are found in diverse locations such as hypersaline lakes, coastal regions and soil. All species, with the exception of Alkalihalobacillus okhensis, are able to produce endospores. Motility is variable, with some species possessing peritrichous flagella. The majority of species from this genus are alkaliphilic and halophilic/tolerant, and thus they are able to grow in alkaline conditions, with the optimal growth rate being in the pH range of 9–10 with 1-5% NaCl. Some species are obligately alkaliphilic and require very alkaline conditions to survive. A wide range of temperature can be conducive to growth; however, optimal growth occurs in the range of 25-37 °C. Some species are able to produce enzymes such as cellulases and proteases, which are used in laundry detergent manufacturing, xylanases for the pulp paper sector and cyclodextrin glucanotransferase for starch treatment. In addition, A. clausii is diazotrophic and able to convert atmospheric nitrogen into ammonia and it is also able to produce antimicrobial compounds for the manufacturing of probiotic.
Through genomic analysis, ten CSIs have been identified for this genus in the following proteins: RNase adapter RapZ, flagellar basal body M-ring protein FliF, 7-carboxy-7-deazaguanine synthase QueE, peptide chain release factor 3, type I glutamate-ammonia ligase, tRNA threonyl-carbamoyladenosine dehydratase, transcription-repair coupling factor, tRNA uridine-5- carboxymethylaminomethyl synthesis enzyme MnmG, 50S ribosomal protein L11 methyltransferase, and homoserine kinase. These CSIs are specific for Alkalihalobacillus and provide a novel way to molecularly differentiate this genus from other Bacillaceae genera and bacteria.