Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater

Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae

Vibrio cholerae N16961 genome encodes 18 type II Toxin/Antitoxin (TA) systems, all but one located inside gene cassettes of its chromosomal superintegron (SI). This study aims to investigate additional TA systems in this genome. We screened for all two-genes operons of uncharacterized function by analyzing previous RNAseq data. Assays on nine candidates, revealed one additional functional type II TA encoded by the VCA0497-0498 operon, carried inside a SI cassette. We showed that VCA0498 antitoxin alone and in complex with VCA0497 represses its own operon promoter. VCA0497-0498 is the second element of the recently identified dhiT/dhiA superfamily uncharacterized type II TA system. RNAseq analysis revealed that another SI cassette encodes a novel type I TA system: VCA0495 gene and its two associated antisense non-coding RNAs, ncRNA495 and ncRNA496. Silencing of both antisense ncRNAs lead to cell death, demonstrating the type I TA function. Both VCA0497 and VCA0495 toxins do not show any homology to functionally characterized toxins, however our preliminary data suggest that their activity may end up in mRNA degradation, directly or indirectly. Our findings increase the TA systems number carried in this SI to 19, preferentially located in its distal end, confirming their importance in this large cassette array.

Polyaniline derived carbon membrane and its in-situ membrane fouling mitigation performance in MBR based on metal-free electro-Fenton

An electro-enhanced membrane bioreactor (EMBR) was constructed with polyaniline-based carbon (PAC) separation membrane as the membrane-electrode, which could realize the in-situ electro-generation and activation of H₂O₂ to ·OH depending on the graphitic and pyridinic N as active sites without metal catalyst. After the continuous operation of the bioreactor for 74 days, approximately 77.41% irreversible membrane fouling occurred on the electrochemically enhanced membrane, which was less than that on the control membrane (85.96%). The ·OH oxidation combined with electrostatic barrier formed by -1.0 V enhanced PAC membrane suppressed the extracellular polymeric substances deposition on membrane. After operation, the strength of total cell, proteins, β-polysaccharides and α-polysaccharides on the membrane without bias were 5.17, 4.32, 9.65 and 16.31, respectively. In EMBR, the corresponding strength were 2.03, 3.35, 2.15 and 6.73. After calculation, the unblocked pores accounted for 35.3% and 78.5% of the total membrane surface in MBR and EMBR, respectively, indicating the fouling was alleviated obviously. Meanwhile, the EMBR owned a satisfactory wastewater treatment effect with average effluent chemical oxygen demand and NH₄⁺-N around 18.98 mg/L and 0.68 mg/L. The successful implementation of this strategy achieved a green and metal-free method for ·OH production with electrochemical effect for membrane fouling control in MBR.

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.

Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient

Strain SN6^T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6^T exhibited 97.5% identity with Vitreoscilla stercoraria strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G + C content of the strain SN6^T was 49.4 mol %. After analysis of taxonogenomic data, phenotypic and biochemical characteristics, we concluded that strain SN6^T represents a new species of the genus Vitreoscilla for which the name Vitreoscilla massiliensis sp.nov is proposed. The type strain is SN6^T (=CSUR P2036 = LN870312 = DSM 100958).

Craterilacuibacter sinensis gen. nov. sp. nov., isolated from a crater lake in China

Two bacterial strains, designated B2N2-7^T and B2N2-12, were isolated from Buteha crater lake in the Greater Khingan Mountain of China. The two strains were Gram-stain-negative, non-spore-forming, motile with a single polar flagellum, short rod-shaped bacteria. They were catalase- and oxidase-positive. Optimal growth occurred at 20-25 ℃, at pH 7.5-8.0 and with 0-1.0 % (w/v) NaCl. Based on phylogenomic analysis, strains B2N2-7^T and B2N2-12 were assigned to the family Neisseriaceae, and their 16S rRNA gene sequences showed the highest similarities to that of Aquitalea denitrificans 5YN1-3^T (<94.2 %). The predominant cellular fatty acids were C_16 : 0 and summed feature 3 (comprising C_16 : 1ω7c/C_16 : 1 ω6c). The major respiratory quinone was ubiquinone 8 (Q-8). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), two unidentified aminophospholipids (APL) and some unidentified lipids (L). The genomic DNA G+C content of strain B2N2-7^T was 59.4 mol% according to the genomic sequencing result. Based on the phylogenetic, genotypic and chemotaxonomic analyses, the two strains are proposed to represent a novel species of a new genus in the family Neisseriaceae, named Craterilacuibacter sinensis gen. nov., sp. nov. The type strain of Craterilacuibacter sinensis is B2N2-7^T (=CGMCC 1.17189^T=KCTC 73735^T); B2N2-12 (=CGMCC 1.17190=KCTC 72734) is a second strain of the species.

Research on the enhancement of biological nitrogen removal at low temperatures from ammonium-rich wastewater by the bio-electrocoagulation technology in lab-scale systems, pilot-scale systems and a full-scale industrial wastewater treatment plant

In cold areas, nitrogen removal performance of wastewater treatment plants (WWTP) declines greatly in winter. This paper systematically describes the enhancement effect of a periodic reverse electrocoagulation technology on biological nitrogen removal at low temperatures. The study showed that in the lab-scale systems, the electrocoagulation technology improved the biomass amount, enzyme activity and the amount of nitrogen removal bacteria (Nitrosomonas, Nitrobacter, Paracoccus, Thauera and Enterobacter). This enhanced nitrification and denitrification of activated sludge at low temperatures. In the pilot-scale systems, the electrocoagulation technology increased the relative abundance of cold-adapted microorganisms (Luteimonas and Trueperaceae) at low temperatures. In a full-scale industrial WWTP, comparison of data from winter 2015 and winter 2016 showed that effluent chemical oxygen demand (COD), NH₄⁺-N, and NO₃^--N reduced by 10.37, 3.84, and 136.43 t, respectively, throughout the winter, after installation of electrocoagulation devices. These results suggest that the electrocoagulation technology is able to improve the performance of activated sludge under low-temperature conditions. This technology provides a new way for upgrading of the performance of WWTPs in cold areas.

Oryzisolibacter propanilivorax gen. nov., sp. nov., a propanil-degrading bacterium

Strain EPL6^T, a Gram-negative, motile, short rod was isolated from a propanil and 3,4-dichloroaniline enrichment culture produced from rice paddy soil. Based on the analyses of the 16S rRNA gene sequence, strain EPL6^T was observed to be a member of the family Comamonadaceae, sharing the highest pairwise identity with type strains of the species Alicycliphilus denitrificans K601^T (96.8 %) and Melaminivora alkalimesophila CY1^T (96.8 %). Strain EPL6^T was able to grow in a temperature range of 15-37 °C, pH 6-9 and in the presence of up to 4 % (w/v) NaCl and tested positive for catalase and oxidase reactions. The major respiratory quinone was Q8. The genomic DNA had a G+C content of 69.4±0.9 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and the major fatty acid methyl esters comprised C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). Comparison of the genome sequence of strain EPL6^T and of its closest neighbours, Melaminivora alkalimesophila CY1^T and Alicycliphilus denitrificans K601^T, yielded values of ANI ≤84.1 % and of AAI ≤80.3 %. Therefore, the genetic, phylogenetic, phenotypic and chemotaxonomic characteristics support the classification of this organism into a new taxon. Considering the genetic divergence of strain EPL6^T from the type strains of the closest species, which belong to distinct genera, we propose a new genus within the family Comamonadaceae, named Oryzisolibacter propanilivorax gen. nov., sp. nov., represented by the isolate EPL6^T as the type strain of the species (=LMG 28427^T=CECT 8927^T).

Phylogenetic Analysis and Antimicrobial Profiles of Cultured Emerging Opportunistic Pathogens (Phyla Actinobacteria and Proteobacteria) Identified in Hot Springs

Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial resistance of culturable emerging and opportunistic bacterial pathogens, in water and sediment of hot springs located in Limpopo, South Africa. Aerobic bacteria were cultured and identified using 16S ribosomal DNA (rDNA) gene sequencing. The presence of Legionella spp. was investigated using real-time polymerase chain reaction. Isolates were tested for resistance to ten antibiotics representing six different classes: β-lactam (carbenicillin), aminoglycosides (gentamycin, kanamycin, streptomycin), tetracycline, amphenicols (chloramphenicol, ceftriaxone), sulphonamides (co-trimoxazole) and quinolones (nalidixic acid, norfloxacin). Gram-positive Kocuria sp. and Arthrobacter sp. and gram-negative Cupriavidus sp., Ralstonia sp., Cronobacter sp., Tepidimonas sp., Hafnia sp. and Sphingomonas sp. were isolated, all recognised as emerging food-borne pathogens. Legionella spp. was not detected throughout the study. Isolates of Kocuria, Arthrobacter and Hafnia and an unknown species of the class Gammaproteobacteria were resistant to two antibiotics in different combinations of carbenicillin, ceftriaxone, nalidixic acid and chloramphenicol. Cronobacter sp. was sensitive to all ten antibiotics. This study suggests that hot springs are potential reservoirs for emerging opportunistic pathogens, including multiple antibiotic resistant strains, and highlights the presence of unknown populations of emerging and potential waterborne opportunistic pathogens in the environment.

Bordetella bronchialis sp. nov., Bordetella flabilis sp. nov. and Bordetella sputigena sp. nov., isolated from human respiratory specimens, and reclassification of Achromobacter sediminum Zhang et al. 2014 as Verticia sediminum gen. nov., comb. nov

The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.

Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India

This paper reports the draft genome sequence of the proteobacterium Gulbenkiania mobilis strain MB1, a sulfur-metabolizing thermophile isolated from a hot spring located in Pachmarhi, India. This study reports the first draft genome sequence of any species from the genus Gulbenkiania.

Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).

Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as ‘Commensalibacter intestini’, except for two isolates (R-52486 and LMG 28161T) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161T was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877T (96.5 %), which corresponded with genus level divergence in the family Acetobacteraceae . Isolate LMG 28161T was subjected to whole-genome shotgun sequencing; a 16S–23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae . The DNA G+C content of strain LMG 28161T was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161T were similar to those of established AAB species [with C18 : 1ω7c (43.1 %) as the major component], but the amounts of fatty acids such as C19 : 0 cyclo ω8c, C14 : 0 and C14 : 0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161T ( = DSM 28636T = R-52487T) as the type strain of the type species.

Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring

A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141T, was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0–10.0 (optimum, pH 8.0–9.0) and 10–55 °C (optimum, 40–50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141T belongs to the family Neisseriaceae , and strain YIM 78141T also showed low levels of 16S rRNA gene sequence similarity (below 93.4 %) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5 %) were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae , for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141T ( = BCRC 80650T = KCTC 32558T = DSM 27258T).

Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis

Five acetic acid bacteria isolates, awK9_3, awK9_4 ( = LMG 27543), awK9_5 ( = LMG 28092), awK9_6 and awK9_9, obtained during a study of micro-organisms present in traditionally produced kefir, were grouped on the basis of their MALDI-TOF MS profile with LMG 1530 and LMG 1531(T), two strains currently classified as members of the genus Acetobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences as well as on concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB indicated that these isolates were representatives of a single novel species together with LMG 1530 and LMG 1531(T) in the genus Acetobacter, with Acetobacter aceti, Acetobacter nitrogenifigens, Acetobacter oeni and Acetobacter estunensis as nearest phylogenetic neighbours. Pairwise similarity of 16S rRNA gene sequences between LMG 1531(T) and the type strains of the above-mentioned species were 99.7%, 99.1%, 98.4% and 98.2%, respectively. DNA-DNA hybridizations confirmed that status, while amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) data indicated that LMG 1531(T), LMG 1530, LMG 27543 and LMG 28092 represent at least two different strains of the novel species. The major fatty acid of LMG 1531(T) and LMG 27543 was C18 : 1ω7c. The major ubiquinone present was Q-9 and the DNA G+C contents of LMG 1531(T) and LMG 27543 were 58.3 and 56.7 mol%, respectively. The strains were able to grow on D-fructose and D-sorbitol as a single carbon source. They were also able to grow on yeast extract with 30% D-glucose and on standard medium with pH 3.6 or containing 1% NaCl. They had a weak ability to produce acid from d-arabinose. These features enabled their differentiation from their nearest phylogenetic neighbours. The name Acetobacter sicerae sp. nov. is proposed with LMG 1531(T) ( = NCIMB 8941(T)) as the type strain.

Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils

Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal-Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts.

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).

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11(T), was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11(T) were Patulibacter ginsengiterrae CECT 7603(T) (96.8 % similarity), Patulibacter minatonensis DSM 18081(T) (96.6 %) and Patulibacter americanus DSM 16676(T) (96.6 %). Phenotypic characterization supports the inclusion of strain I11(T) within the genus Patulibacter (phylum Actinobacteria). However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11(T) ( = DSM 25962(T) = CECT 8141(T)).

Pseudogulbenkiania gefcensis sp. nov., isolated from soil

A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16(T) were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5(T). Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5(T) (95.9 % similarity), Paludibacterium yongneupense 5YN8-15(T) (95.2 % similarity), Gulbenkiania mobilis E4FC31-5(T) (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1(T) (93.9 % similarity). The isolate was able to grow at 25-40 °C, 0.3-2 % NaCl and pH 5.5-7. The DNA G+C content was 65.9 ± 1.0 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and C(16:0). Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania. The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16(T) (=KCCM 90100(T) = JCM 17850(T)).

Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant

A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22T, was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15–37 °C, at pH 7–10 and with <8 % (w/v) NaCl (optimum growth: 30 °C, pH 7–8 and 1–3 % NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22T was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162T (98.5 % 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2T (97.9 %), Bacillus infantis SMC 4352-1T (97.4 %), Bacillus firmus IAM 12464T (96.8 %) and Bacillus muralis LMG 20238T (96.8 %). DNA–DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22T from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22T ( = DSM 23494T = NRRL B-59432T = LMG 25783T).

Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).

Acinetobacter rudis sp. nov., isolated from raw milk and raw wastewater

Two bacterial strains, G30(T) and A1PC16, isolated respectively from raw milk and raw wastewater, were characterized using a polyphasic approach. Chemotaxonomic characterization supported the inclusion of these strains in the genus Acinetobacter, with Q-8 and Q-9 as the major respiratory quinones, genomic DNA G+C contents within the range observed for this genus (38-47 mol%) and C(16:0), C(18:1)ω9c and C(16:1)ω7c/iso-C(15:0) 2-OH as the predominant fatty acids. The observation of 16S rRNA gene sequence similarity lower than 97% with other Acinetobacter species with validly published names led to the hypothesis that these isolates could represent a novel species. This hypothesis was supported by comparative analysis of partial sequences of the genes rpoB and gyrB, which showed that strains G30(T) and A1PC16 did not cluster with any species with validly published names, forming a distinct lineage. DNA-DNA hybridizations confirmed that the two strains were members of the same species, which could be distinguished from their congeners by several phenotypic characteristics. On the basis of these arguments, it is proposed that strains G30(T) and A1PC16 represent a novel species, for which the name Acinetobacter rudis sp. nov. is proposed. The type strain is strain G30(T) (=LMG 26107(T) =CCUG 57889(T) =DSM 24031(T) =CECT 7818(T)).

Gulbenkiania indica sp. nov., isolated from a sulfur spring

A novel bacterium, designated strain HT27T, was isolated from a sulfur spring sample collected from Athamallik, Orissa, India, and was characterized by using a polyphasic approach. Cells were Gram-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. Strain HT27T was oxidase- and catalase-positive. Growth was observed at pH 5.0–11.0 and at 15–45 °C; the highest growth yield was observed at pH 7.5–8.0 and 30–37 °C. The G+C content of the genomic DNA of strain HT27T was 63 mol%. The major cellular fatty acids were C16 : 1 ω7c (44.24 %), C16 : 0 (27.65 %), C18 : 1 ω7c (13.98 %), C12 : 0 (2.60 %) and C12 : 0 3-OH (2.22 %). 16S rRNA gene sequence analysis indicated that strain HT27T clustered with the genus Gulbenkiania and showed 99.0 % similarity to Gulbenkiania mobilis E4FC31T. However, the level of DNA–DNA relatedness between strain HT27T and G. mobilis E4FC31T was 30 %. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA hybridization data, strain HT27T is considered to represent a novel species of the genus Gulbenkiania, for which the name Gulbenkiania indica sp. nov. is proposed. The type strain is HT27T (=DSM 17901T =JCM 15969T).

Shinella fusca sp. nov., isolated from domestic waste compost

A bacterium, designated strain DC-196(T), isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196(T) was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10-40 degrees C, pH 6-9 and in NaCl concentrations as high as 3 %. Chemotaxonomically, C(18 : 1) was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196(T) was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6-96.8 % and the low DNA-DNA hybridization values of 38.2-32.2 % with the type strains of the three recognized Shinella species confirmed that strain DC-196(T) represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196(T)=CCUG 55808(T)=LMG 24714(T)).

Sphingobium vermicomposti sp. nov., isolated from vermicompost

Strain VC-230(T) was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15-37 degrees C and pH 6-8. On the basis of 16S rRNA gene sequence analysis, strain VC-230(T) was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790(T) (97.7 %) and Sphingobium herbicidovorans DSM 11019(T) (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C(18 : 1)omega7c/9t/12t, C(16 : 1)omega7c and C(16 : 0) and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA-DNA hybridization analyses verify that strain VC-230(T) represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230(T) (=CCUG 55809(T) =DSM 21299(T)).

Microbacterium invictum sp. nov., isolated from homemade compost

Strain DC-200T was isolated from homemade compost produced from kitchen refuse and characterized using a polyphasic approach. The isolate was a Gram-positive motile short rod, facultatively aerobic, catalase-positive and oxidase-negative, and was able to grow at 10-37 degrees C, pH 6.0-9.5 and with up to 5% of NaCl. The peptidoglycan was of the type B1 alpha and the muramic acid residues were glycolylated. The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The predominant respiratory menaquinones were MK-11 and MK-12. The G+C content of the genomic DNA was 70 mol%. Based on the analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain DC-200T were Microbacterium lacus A5E-52T (98.7%) and Microbacterium aoyamense KV-492T (98.2%). The phenetic characterization of the isolate supports its inclusion within the genus Microbacterium; however, its distinctive phenotypic features and the results from the 16S rRNA gene sequence analysis and the DNA-DNA hybridization study suggest that the isolate represents a novel species. The name Microbacterium invictum sp. nov. is proposed. The type strain is DC-200T (=DSM 19600T=LMG 24557T).

Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002

A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in a clade within the family Neisseriaceae in the order Nessieriales of the Betaproteobacteria 99.3% similar to Pseudogulbenkiania subflava. Similar to P. sublfava, predominant whole cell fatty acids were identified as 16:17c, 42.4%, and 16:0, 34.1%. Whole cell difference spectra of the Fe(II) reduced minus nitrate oxidized cyctochrome content revealed a possible role of c-type cytochromes in nitrate-dependent Fe(II) oxidation. Strain 2002 was unable to oxidize aqueous or solid-phase Mn(II) with nitrate as the electron acceptor. In addition to lithotrophic growth with Fe(II), strain 2002 could alternatively grow heterotrophically with long-chain fatty acids, simple organic acids, carbohydrates, yeast extract, or casamino acids. Nitrate, nitrite, nitrous oxide, and oxygen also served as terminal electron acceptors with acetate as the electron donor.

Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water

A transparent, non-pigmented, Gram-negative, rod-shaped bacterium, designated strain DS-28(T), was isolated from water samples collected from a spring located in Tainan County, Taiwan. 16S rRNA gene sequence analysis indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella; the only sole close neighbour of the novel strain was Vogesella indigofera ATCC 19706(T) (97.4 % 16S rRNA gene sequence similarity). The isolate was distinguished from V. indigofera on the basis of genotypic data, several phenotypic properties and an inability to produce characteristic blue-pigmented colonies on peptone agar. The fatty acid profile was slightly different from that reported for V. indigofera ATCC 19706(T). It was evident from the genotypic and phenotypic data that strain DS-28(T) represents a novel species of the genus Vogesella, for which the name Vogesella perlucida sp. nov. is proposed. The type strain is DS-28(T) (=BCRC 17730(T)=LMG 24214(T)).

Microbacterium luticocti sp. nov., isolated from sewage sludge compost

Strain SC-087B(T), isolated from sewage sludge compost during a study of bacterial diversity in composts, was characterized. The isolate was a Gram-positive, short rod that was motile, catalase- and oxidase-negative and able to grow at 27-45 degrees C, pH 5.5-9.7 and in up to 10 % NaCl. The peptidoglycan was of the B2beta type, containing the characteristic amino acids ornithine, homoserine and hydroxyglutamic acid. The muramic acid residues of the peptidoglycan were partially glycolylated. The major cell-wall sugar was mannose; traces of xylose were also detected. The predominant fatty acids, comprising more than 70 % of the total, were anteiso-C(17 : 0) and anteiso-C(15 : 0), the major respiratory quinone was menaquinone-12 (MK-12) and the G+C content of the genomic DNA was 72 mol%. Based on analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain SC-087B(T) were members of the family Microbacteriaceae, showing sequence similarity values of around 96 % with members of the species Microbacterium barkeri (96.0 %), Microbacterium gubbeenense (95.6 %) and Microbacterium indicum (95.7 %). The chemotaxonomic and phenotypic traits analysed supported the inclusion of this strain within the genus Microbacterium and the proposal of a novel species. The name Microbacterium luticocti sp. nov. is proposed and the type strain is SC-087B(T) (=DSM 19459(T)=CCUG 54537(T)).