Andreprevotia chitinilytica gen. nov., sp. nov., isolated from forest soil from Halla Mountain, Jeju Island, Korea

A novel endo-type chitinase possessing chitobiase activity derived from the chitinolytic bacterium, Chitiniphilus shinanonensis SAY3T

One of the chitinases (ChiG) derived from the chitinolytic bacterium Chitiniphilus shinanonensis SAY3T exhibited chitobiase activity cleaving dimers of N-acetyl-D-glucosamine (GlcNAc) into monomers, which is not detected in typical endo-type chitinases. Analysis of the reaction products for GlcNAc hexamers revealed that all the five internal glycosidic bonds were cleaved at the initial stage. The overall reaction catalyzed by chitobiases toward GlcNAc dimers was similar to that catalyzed by N-acetyl-D-glucosaminidases (NAGs). SAY3 possesses two NAGs (ChiI and ChiT) that are thought to be important in chitin catabolism. Unexpectedly, a triple gene-disrupted mutant (ΔchiIΔchiTΔchiG) was still able to grow on synthetic medium containing GlcNAc dimers or powdered chitin, similar to the wild-type SAY3, although it exhibited only 3% of total cellular NAG activity compared to the wild-type. This indicates the presence of unidentified enzyme(s) capable of supporting normal bacterial growth on the chitin medium by NAG activity compensation.

Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes

Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.

Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov

The order Neisseriales contains 37 genera harboring 122 species with validly published names, which are placed into two families, Neisseriaceae and Chromobacteriaceae. Genome sequences are now available for 35 of the 37 Neisseriales genera for reliably determining their evolutionary relationships and taxonomy. We report here comprehensive phylogenomic and comparative analyses on protein sequences from 110 Neisseriales genomes plus 3 Chitinimonas genomes using multiple approaches. In a phylogenomic tree based on 596 core proteins, Neisseriales species formed 5 strongly supported clades. In addition to the clades for Neisseriaceae and Chromobacteriaceae families, three novel species clades designated as the "Chitinibacteraceae", "Aquaspirillaceae", and "Leeiaceae" were observed. The genus Chitinimonas grouped reliably with members of the "Chitinibacteraceae" clade. The major clades within the order Neisseriales can also be distinguished based on average amino acid identity analysis. In parallel, our comparative genomic studies have identified 30 conserved signature indels (CSIs) that are specific for members of the order Neisseriales or its five main clades. One of these CSIs is uniquely shared by all Neisseriales, whereas 8, 4, 9, 3 and 5 CSIs are distinctive characteristics of the Neisseriaceae, Chromobacteriaceae, "Chitinibacteraceae", "Aquaspirillaceae" and "Leeiaceae" clades, respectively. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the three newly identified clades should be recognized as novel families (Chitinibacteraceae fam. nov., Aquaspirillaceae fam. nov. and Leeiaceae fam. nov.) within the order Neisseriales. In addition, we are also emending descriptions of the families Neisseriaceae and Chromobacteriaceae regarding their constituent genera and other distinguishing characteristics.

Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river

A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) ( = BCRC 80376(T) = LMG 26668(T) = KCTC 23712(T)).

Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov

The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).

Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil

A bacterial strain named IGB-41(T) was isolated from a soil sample from an ant hill near Stuttgart, Germany. The strain was Gram-negative, rod-shaped, motile and facultatively anaerobic. Phylogenetic analysis based on 16S rRNA grouped the strain IGB-41(T) within the class Betaproteobacteria into the family Neisseriaceae together with Silvimonas amylolytica NBRC 103189(T), Silvimonas iriomotensis NBRC 103188(T) and Silvimonas terrae KM-45(T) as the closest relatives with sequence similarities of 96.7, 96.6 and 96.1 %, respectively. The G+C content of the genomic DNA was determined to be 61.5 mol% and quinone analysis revealed Q-8 as the only detectable quinone. Major cellular fatty acids were identified as C(16 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) and C(18 : 1)ω7c . Strain IGB-41(T) was unique in harbouring phosphoaminolipids, aminolipids and glycoaminolipids when compared with Silvimonas amylolytica NBRC 103189(T) in polar lipid analysis. On the basis of the physiological, phenotypic and genotypic characteristics of strain IGB-41(T), we suggest that the novel strain should be assigned to a new genus Amantichitinum and novel species Amantichitinum ursilacus. The type species of the genus Amantichitinum is Amantichitinum ursilacus and the type strain is IGB-41(T) (=DSM 23761(T) =CIP 110167(T)).

Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake

A facultatively anaerobic, chitinolytic bacterium, strain KL-9(T), was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9(T) were gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15-40 °C (optimum, 30-37 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9(T) was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9(T) formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria, being most closely related to members of the genera Leeia, Chitinimonas, Silvimonas and Andreprevotia. Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9(T) is thus considered to represent a novel species of a new genus within the class Betaproteobacteria, for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9(T) ( = BCRC 80168(T) = LMG 25530(T)).

Chitinolyticbacter meiyuanensis SYBC-H1T, gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil

A novel aerobic mesophilic bacterial strain SYBC-H1(T) capable of degrading chitin was isolated and classified in this study. The strain exhibited strong chitinolytic activity and was a Gram-negative, curved, rod-shaped, and motile bacterium. Growth of this strain was observed between 10 and 41°C and between pH 3.5 and 9.5. The DNA G + C content of strain SYBC-H1(T) was 53.25 mol%. The cellular fatty acids (>5%) were 12:0 iso 3-OH (5.87%), 16:0 (28.16%), and 18:1ω7c (20.48%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain SYBC-H1(T) belonged to the family Neisseriaceae, and was distantly related (95.0% similarity) to the genus Chitiniphilus. Its phenotype was unique and genetic and phylogenetic analysis experiments suggested that strain SYBC-H1(T) represented the type strain (CGMCC 3438(T), ATCC BAA-2140(T)) of a novel genus, for which the name Chitinolyticbacter meiyuanensis SYBC-H1(T) gen. nov., sp. nov. was proposed. The highest enzymatic activity of chitinase (9.6 U/ml) was obtained at 72 h in 250 ml shake flasks. The 16S rRNA gene sequence of SYBC-H1(T) has been deposited in GenBank under the accession number GQ981314.

Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria

A bacterial strain capable of degrading chitin, strain SAY3T, was isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. The strain was gram-negative, curved rod-shaped, facultatively anaerobic, and motile with a single polar flagellum. It grew well with chitin as a sole carbon source. The cellular fatty acids profiles showed the presence of C16:1 omega7c and C16:0 as the major components. The G+C content of DNA was 67.6 mol% and Q-8 was the major respiratory quinone. A 16S rRNA gene sequence-based phylogenetic analysis showed the strain belonged to the family Neisseriaceae but was distantly related (94% identity) to any previously known species. Since the strain was clearly distinct from closely related genera in phenotypic and chemotaxonomic characteristics, it should be classified under a new genus and a new species. We propose the name Chitiniphilus shinanonensis gen. nov., sp. nov. The type strain is SAY3T (=NBRC 104970T=NICMB 14509T).