Description of the Gram-Negative, Obligately Aerobic, Nitrilotriacetate (NTA)-Utilizing Bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus asaccharovorans, gen. nov., sp. nov

Chelatococcus albus sp. nov., a bacterium isolated from hot spring microbial mat

A Gram-stain-negative, non-endospore-forming, motile, short rod-shaped strain, designated SYSU G07232T, was isolated from a hot spring microbial mat, sampled from Rehai National Park, Tengchong, Yunnan Province, south-western China. Strain SYSU G07232T grew at 25-50 °C (optimum, 37 °C), at pH 5.5-9.0 (optimum, pH 6.0) and tolerated NaCl concentrations up to 1.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SYSU G07232T showed closest genetic affinity with Chelatococcus daeguensis K106T. The genomic features and taxonomic status of this strain were determined through whole-genome sequencing and a polyphasic approach. The predominant quinone of this strain was Q-10. Major cellular fatty acids comprised C19 : 0 cyclo ω8c and summed feature 8. The whole-genome length of strain SYSU G07232T was 4.02 Mbp, and the DNA G+C content was 69.26 mol%. The average nucleotide identity (ANIm ≤84.85 % and ANIb ≤76.08  %) and digital DNA-DNA hybridization (≤ 21.9 %) values between strain SYSU G07232T and the reference species were lower than the threshold values recommended for distinguishing novel prokaryotic species. Thus, based on the provided phenotypic, phylogenetic, and genetic data, it is proposed that strain SYSU G07232T (=KCTC 8141T=GDMCC 1.4178T) be designated as representing a novel species within the genus Chelatococcus, named Chelatococcus albus sp. nov.

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications

The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA-DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95-96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, "Bartonella mastomydis," and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) "Bartonella vinsonii" subsp. arupensis and "B. vinsonii" subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 ("Mesorhizobium loti LMG 6,125T"), GCF_003024595.1 ("Mesorhizobium plurifarium LMG 11,892T"), GCF_003096615.1 ("Methylobacterium organophilum DSM 760T"), and GCF_000373025.1 ("R. gallicum R-602 spT") are not from the genuine type strains used for the respective species descriptions; and v) "Xanthobacter autotrophicus" Py2 and "Aminobacter aminovorans" KCTC 2,477T represent cases of misuse of the term "type strain". Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust ("Prokaryotic Clusters"), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped, and aerobic bacterial strain (designated L72^T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong Province, PR China). Strain L72^T grew between 25 and 40 °C (optimum growth at 30 °C). The pH range for growth was between 6.0 and 8.0 (optimum growth at pH 7.0). The range of NaCl concentrations for the growth of strain L72^T was 0-3.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). The major cellular fatty acids of strain L72^T were C_19:0cyclo ω8c, C_18:1ω7c, iso-C_15:0, and anteiso-C_15:0. Strain L72^T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of Phosphatidylcholine, Glycolipid, Aminophospholipid, Phosphatidylethanolamine, Phosphatidylserine, Phosphatidyldimethylethanolamine, one unknown lipid (L) and two unidentified Phospholipids (PL). Genome sequencing revealed a genome size of 4,703,686 bp and a G + C content of 69.0 mol%. The 16S rRNA gene sequence similarities of strain L72^T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain L72^T formed a distinct phylogenetic lineage within the order Hyphomicrobiales, separating them from members of all families. Strain L72^T showed 70.7% average nucleotide identity and 18.6% digital DNA-DNA hybridization identity with the closely related species Rhodoligotrophos defluvii. Based on the phenotypic, phylogenetic and chemotaxonomic data, a new family Propylenellaceae fam. nov. comprising the genus Propylenella gen. nov. and species Propylenella binzhouense sp. nov. is proposed. The type strain is L72^T (=  CCTCC AB 2019081^T  =  KCTC 72254^T).

Coupled Microbiological–Isotopic Approach for Studying Hydrodynamics in Deep Reservoirs: The Case of the Val d’Agri Oilfield (Southern Italy)

The studies upstream of the petroleum industry include oil and gas geological exploration and are usually focused on geological, structural, geophysical, and modeling techniques. In this research, the application of a coupled microbiological–isotopic approach was explored to assess its potential as an adequate characterization and monitoring tool of geofluids in oilfield areas, in order to expand and refine the information acquired through more consolidated practices. The test site was selected within the Val d’Agri oilfield, where some natural hydrocarbon springs have been documented since the 19th century in the Tramutola area. Close to these springs, several tens of exploration and production wells were drilled in the first half of the 20th century. The results demonstrated the effectiveness of the proposed approach for the analysis of fluid dynamics in complex systems, such as oilfield areas, and highlighted the capacity of microbial communities to “behave” as “bio-thermometers”, that is, as indicators of the different temperatures in various subsurface compartments.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Aestuariivirga litoralis gen. nov., sp. nov., a proteobacterium isolated from a water sample, and proposal of Aestuariivirgaceae fam. nov

A Gram-stain-negative, non-motile, short rod and aerobic bacterium, designated strain SYSU M10001^T, was isolated from a water sample collected from the coastal region of Pearl River Estuary, Guangdong Province, PR China. Strain SYSU M10001^T showed optimal growth at 28 °C, pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and concatenation of 20 protein markers revealed a distinct lineage for strain SYSU M10001^T in the order Rhizobiales. Strain SYSU M10001^T showed highest 16S rRNA gene sequence similarities to Hyphomicrobium nitrativorans NL23^T (91.1 %) and Hyphomicrobium hollandicum IFAM KB-677^T (91.1 %). The respiratory ubiquinone was Q-8. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and three unidentified lipids. The predominant cellular fatty acids identified were C19 : 0cyclo ω8c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content was determined to be 65.5 % (genome). On the basis of differences in the phenotypic, physiological and biochemical characteristics, and results of the phylogenetic analyses, strain SYSU M10001^T is proposed to represent a novel species in a novel genus for which the name Aestuariivirga litoralis gen. nov., sp. nov. The type strain of the type species Aestuariivirga litoralis is SYSU M10001^T (=NBRC 112960^T=KCTC 52945^T). Besides, the distinct phylogenetic lineage and the distinct chemotaxonomic profile among the families in the order Rhizobiales indicated that strain SYSU M10001^T should represent a new family for which the name Aestuariivirgaceae fam. nov. is proposed.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae

There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109^T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109^T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109^T (=JCM 31876^T=DSM 102886^T). In addition, examination of the phylogenetics of strain HL-109^T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).

Complete Genome Sequence of Nitrilotriacetate-Degrading Aminobacter aminovorans KCTC 2477T

Aminobacter aminovorans is a Gram-negative, pleomorphic rod-shaped, flagellated, and obligately aerobic bacterium that was isolated from soil. Here, we report the complete genome sequence of A. aminovorans KCTC 2477^T, which degrades nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of nitrilotriacetate.

Chelatococcus composti sp. nov., isolated from penicillin fermentation fungi residue with pig manure co-compost

A novel Gram-stain-negative bacterium, designated strain PC-2^T, was isolated from penicillin fermentation fungi residue with pig manure co-compost in China. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that strain PC-2^T should be assigned to the genus Chelatococcus and that it had 98.9 % similarity with Chelatococcus daeguensis, 98.8 % with Chelatococcus sambhunathii, 98.4 %, with Chelatococcus caeni and 96.0 % with Chelatococcus asaccharovorans. The G+C content of genomic DNA was 70.9 mol%. On the basis of the phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data, strain PC-2 ^T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus composti sp. nov. is proposed. The type strain is PC-2^T (=DSM 101465^T=CGMCC 1.15283^T).

Chelatococcus thermostellatus sp. nov., a new thermophile for bioplastic synthesis: comparative phylogenetic and physiological study

The poly(3-hydroxybutyrate), PHB, accumulating thermophilic strain MW9^T, isolated from an aerobic organic waste treatment plant, was characterized by detailed physiological and phylogenetic studies. The strain is a Gram-stain-negative, rod shaped, non-spore forming member of Alphaproteobacteria. It shows optimum growth at 50 °C. Based on 16S rRNA gene sequence similarity, the strain together with five very similar isolates, was affiliated to the genus Chelatococcus (Ibrahim et al. in J Appl Microbiol 109:1579–1590, 2010). Rep-PCR genomic fingerprints and partial dnaK gene sequence also revealed that these isolates are very similar, but differ from other Chelatococcus type strains. The major fatty acids were similar to those of other strains of the genus Chelatococcus. DNA–DNA hybridization of strain MW9^T with Chelatococcus species type strains revealed 11.0–47.7 % relatedness. G+C content of DNA was 67.1 mol%, which is comparable with the other strains of Chelatococcus species. The physiological and phenotypic characteristics of the new strain MW9^T are sufficient to differentiate it from previously described species in the genus Chelatococcus. Strain MW9^T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus thermostellatus is proposed. The type strain is MW9^T (=LMG 27009^T = DSM 28244^T). Compared to known Chelatococcus strains, strain MW9^T could be a potent candidate for bioplastic production at elevated temperature.

Chelatococcus reniformis sp. nov., isolated from a glacier

A Gram-stain-negative, non-motile, reniform bacterial strain, B2974T, was isolated from an ice core of the Muztagh Glacier, on the Tibetan Plateau, China. Strain B2974T grew optimally at pH 7.0-7.5 and 25-30 °C in the presence of 0-2.0 % (w/v) NaCl. 16S rRNA gene sequence similarity analysis indicated that strain B2974T was closely related to Chelatococcus asaccharovorans LMG 25503T at a level of 97.1 %. The major quinone of strain B2974T was ubiquinone Q10. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. sym-Homospermidine was the major polyamine. The genomic DNA G+C content of the strain was 64 mol%. In DNA-DNA hybridization tests, strain B2974T shared 49.32 % DNA-DNA relatedness with the type strain of Chelatococcus asaccharovorans LMG 25503T. Based on the results of phenotypic and chemotaxonomic characteristics, strain B2974T was considered as a novel species of the genus Chelatococcus, for which the name Chelatococcus reniformis sp. nov. is proposed. The type strain is B2974T (=JCM 30308T=CGMCC 1.12919T).

Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory

Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).

Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample

A polyphasic taxonomic study was carried out on strain EBR-4-1T, which was isolated from a biofilm reactor in the Republic of Korea. The cells of the strain were Gram-stain-negative, non-spore-forming, motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain to the Alphaproteobacteria , and it was most closely related to Chelatococcus daeguensis CCUG 54519T, Chelatococcus sambhunathii HT4T, and Chelatococcus asaccharovorans DSM 6462T with 16S rRNA gene sequence similarities to the type strains of these species of 98.8 %, 98.7 %, and 96.3 %, respectively. The G+C content of the genomic DNA of strain EBR-4-1T was 68.7 mol%. Phenotypic and chemotaxonomic data [Q-10 as the major ubiquinone; C19 : 0cycloω8c, C18 : 1 2-OH, and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids] supported the affiliation of strain EBR-4-1T to the genus Chelatococcus . On the basis of the polyphasic evidence, it is proposed that strain EBR-4-1T should be assigned to a new species, Chelatococcus caeni sp. nov. The type strain is EBR-4-1T ( = KCTC 32487T = JCM 30181T).

Pseudochelatococcus lubricantis gen. nov., sp. nov. and Pseudochelatococcus contaminans sp. nov. from coolant lubricants

Two Gram-negative, rod-shaped, non-spore-forming bacteria, isolated from metal working fluids were investigated to determine their taxonomic positions. On the basis of 16S rRNA gene sequence phylogeny, both strains (MPA 1113T and MPA 1105T) formed a distinct cluster with 97.7 % sequence similarity between them, which was in the vicinity of members of the genera Methylobacterium , Camelimonas , Chelatococcus , Bosea , Salinarimonas and Microvirga to which they showed low sequence similarities (below 94 %). The predominant compounds in the polyamine pattern and in the quinone system of the two strains were spermidine and ubiquinone Q-10, respectively. The polar lipid profiles were composed of the major compounds: phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, major or moderate amounts of diphosphatidylglycerol, two unidentified glycolipids and three unidentified aminolipids. Several minor lipids were also detected. The major fatty acids were either C19 : 0 cyclo ω8c or C18 : 1ω7c. The results of fatty acid analysis and physiological and biochemical tests allowed both, the genotypic and phenotypic differentiation of the isolates from each other, while the chemotaxonomic traits allowed them to be differentiated from the most closely related genera. In summary, low 16S rRNA gene sequence similarities and marked differences in polar lipid profiles, as well as in polyamine patterns, is suggestive of a novel genus for which the name Pseudochelatococcus gen. nov. is proposed. MPA 1113T ( = CCM 8528T = LMG 28286T = CIP 110802T) and MPA 1105T ( = CCM 8527T = LMG 28285T) are proposed to be the type strains representing two novel species within the novel genus, Pseudochelatococcus gen. nov., for which the names Pseudochelatococcus lubricantis sp. nov. and Pseudochelatococcus contaminans sp. nov. are suggested, respectively.

Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga , with ≥96.1 % sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6T and WSM3557T was Microvirga flocculans TFBT, with 97.6–98.0 % similarity, while WSM3693T was most closely related to Microvirga aerilata 5420S-16T, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) and cellular fatty acid profiles confirmed the placement of Lut6T, WSM3557T and WSM3693T within the genus Microvirga . DNA–DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6T, WSM3557T and WSM3693T from each other and from other Microvirga species with validly published names. The nodA sequence of Lut6T was placed in a clade that contained strains of Rhizobium , Mesorhizobium and Sinorhizobium , while the 100 % identical nodA sequences of WSM3557T and WSM3693T clustered with Bradyrhizobium , Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that the sequences of Lut6T, WSM3557T and WSM3693T were most closely related to that of Rhizobium etli CFN42T nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini sp. nov. (type strain Lut6T  = LMG 26460T  = HAMBI 3236T), Microvirga lotononidis sp. nov. (type strain WSM3557T  = LMG 26455T  = HAMBI 3237T) and Microvirga zambiensis sp. nov. (type strain WSM3693T  = LMG 26454T  = HAMBI 3238T).

Camelimonas lactis gen. nov., sp. nov., isolated from the milk of camels

Three strains of Gram-negative, rod-shaped, non-spore-forming bacteria (M 2040T, M 1973 and M 1878-SK2), isolated from milk of camels at a camel-milk production farm in the United Arab Emirates, were investigated for their taxonomic allocation. On the basis of 16S rRNA gene sequence similarities, all three strains were shown to belong to the Alphaproteobacteria and were most closely related to Chelatococcus asaccharovorans and Chelatococcus daeguensis (95.1 and 95.2 % sequence similarity to the respective type strains). meso-Diaminopimelic acid was detected as the characteristic peptidoglycan diamino acid. The predominant compound in the polyamine pattern was spermidine, and sym-homospermidine was not detectable. The quinone system was ubiquinone Q-10. The polar lipid profile included the major compounds phosphatidylcholine and diphosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and two unidentified aminolipids. Minor lipids were also detected. The major fatty acid profile, consisting of C19 : 0 cyclo ω8c and C18 : 1 ω7c, with C18 : 0 3-OH as the major hydroxylated fatty acid, was similar to those of the genus Chelatococcus. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolates from described Chelatococcus species. Isolates M 2040T, M 1973 and M 1878-SK2 were closely related on the basis of DNA–DNA reassociation and therefore represent a single novel species. In summary, low 16S rRNA gene sequence similarities of 95 % with Chelatococcus asaccharovorans and marked differences in polar lipid profiles as well as in polyamine patterns support the description of a novel genus and species to accommodate these strains, for which the name Camelimonas lactis gen. nov., sp. nov. is proposed. The type strain of Camelimonas lactis is M 2040T (=CCUG 58638T =CCM 7696T).

Sneathiella chinensis gen. nov., sp. nov., a novel marine alphaproteobacterium isolated from coastal sediment in Qingdao, China

The taxonomic position of strain LMG 23452(T), which was isolated from coastal sediment from an aquaculture site near Qingdao, China, in 2000, was determined. Strain LMG 23452(T) comprised Gram-negative, non-spore-forming, motile rods and was found to be a halotolerant, aerobic, chemoheterotroph that produces catalase and oxidase. Comparative 16S rRNA gene sequence analysis revealed that strain LMG 23452(T) shared approximately 89 % sequence similarity with members of the genera Devosia, Hyphomonas, Ensifer and Chelatococcus, which belong to two different orders within the Alphaproteobacteria. Further phylogenetic analysis of the 16S rRNA gene sequence showed that strain LMG 23452(T) formed a separate branch within the order Rhizobiales, falling between the genera Devosia and Ensifer of the families Hyphomicrobiaceae and Rhizobiaceae, respectively. Strain LMG 23452(T) could be differentiated from its closest phylogenetic neighbours on the basis of several phenotypic features, including hydrolysis of the substrates starch and casein and assimilation of the carbohydrates d-glucose, d-mannose, mannitol, maltose and l-arabinose, and chemotaxonomically by the presence of the fatty acids C(14 : 0) 3-OH, C(16 : 1)omega11c, C(16 : 1)omega5c and C(18 : 1)omega5c. The major fatty acids detected in strain LMG 23452(T) were C(18 : 1)omega7c, C(16 : 0), C(19 : 0) cyclo omega8c, C(16 : 1)omega7c and C(17 : 1)omega6c and the G+C content of the genomic DNA was 57.1 mol%. Therefore, the polyphasic data support the placement of strain LMG 23452(T) within a novel genus and species, for which the name Sneathiella chinensis gen. nov., sp. nov. is proposed. The type strain is LMG 23452(T) (=CBMAI 737(T)).

Nitrilotriacetic acid degradation under microbial fuel cell environment

The removal of nitrilotriacetic acid (NTA) was studied under anaerobic conditions using oligotrophic and copiotrophic microbial fuel cells (MFCs) as a novel wastewater treatment process. Over 85% of NTA was removed from oligotrophic MFCs enriched and maintained with fuel containing NTA, whilst the value was around 20% in oligotrophic MFCs fed with NTA-free fuel, and in copiotrophic MFCs enriched with NTA containing fuel. The oligotrophic MFCs generated current with concomitant utilization of NTA when served as the sole organic compound, suggesting that NTA is oxidized its suitability as fuel in the MFCs.

Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments

The bacterial strains IMB-1(T) and CC495(T), which are capable of growth on methyl chloride (CH(3)Cl, chloromethane) and methyl bromide (CH(3)Br, bromomethane), were isolated from agricultural soil in California fumigated with CH(3)Br, and woodland soil in Northern Ireland, respectively. Two pesticide-/herbicide-degrading bacteria, strains ER2 and C147, were isolated from agricultural soil in Canada. Strain ER2 degrades N-methyl carbamate insecticides, and strain C147 degrades triazine herbicides widely used in agriculture. On the basis of their morphological, physiological and genotypic characteristics, these four strains are considered to represent two novel species of the genus Aminobacter, for which the names Aminobacter ciceronei sp. nov. (type strain IMB-1(T)=ATCC 202197(T)=CIP 108660(T)=CCUG 50580(T); strains ER2 and C147) and Aminobacter lissarensis sp. nov. (type strain CC495(T)=NCIMB 13798(T)=CIP 108661(T)=CCUG 50579(T)) are proposed.

The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov

Phylogenetic analysis of the class 'Alphaproteobacteria', including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class 'Alphaproteobacteria' were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class 'Alphaproteobacteria' were subdivided into five major clusters, which were compared with the taxonomic outline of Bergey's Manual of Systematic Biology and the arb tree. Based on this phylogenetic tree, three novel families are proposed: Hyphomonadaceae fam. nov. to accommodate the bacterial genera Hyphomonas, Hirschia, Maricaulis and Oceanicaulis, Xanthobacteraceae fam. nov. to include the genera Xanthobacter, Azorhizobium, Ancylobacter, Labrys and Starkeya, and Erythrobacteraceae fam. nov. to accommodate the genera Erythrobacter, Porphyrobacter and Erythromicrobium. The phylogenetic tree of 16S rRNA gene sequences established in this study may provide a sound basis for future taxonomic reconstruction of the class 'Alphaproteobacteria'.

Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences

Molecular ecological techniques were applied to analyze the bacterial diversity of two oligotrophic microbial fuel cells (MFCs) enriched using river water or artificial wastewater (AWW) as fuel. Denaturing gradient gel electrophoresis (DGGE) of the PCR amplified 16S rDNA showed that different microbial communities were present in the two MFCs and these were different from the river sediment used to initiate the enrichment. Nearly complete 16S rDNA was amplified and sequenced. Over 80% of the clones were Proteobacteria. Betaproteobacteria were the dominant clones (46.2%) in MFCs fed with river water, and about 64.4% of the clones in MFCs fed with AWW were Alphaproteobacteria. Actinobacteria were found only in the MFC fed with AWW, and Deltaproteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia in the MFC fed with river water. Many clones were related to uncultured bacteria, some with homology less than 95%, indicating that many novel bacteria were enriched in the oligotrophic MFCs.

Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer

A strictly aerobic bacterium, strain Fail4T, was isolated from free-flowing geothermal waters of a bore (bore register no. 3768) tapping the Great Artesian Basin of Australia. The non-sporulating, Gram-negative cells of strain Fail4T produced light-pink colonies, were rod-shaped (1 x 1.5-4 microm) and were motile by a single polar flagellum. Strain Fail4T grew optimally at 41 degrees C at a pH of 7.0 and had an absolute requirement for yeast extract. The strain grew on casein hydrolysate, tryptone, gelatin, xylose and acetate in a medium supplemented with 0.06 or 0.006% yeast extract. Weak acid production was detected from glucose and arabinose. Catalase was produced. Nitrite was produced from nitrate. Strain Fail4T was sensitive to antibiotics that inhibit growth of bacteria. The G + C content was 63.5 +/- 0.5 mol%. Strain Fail4T was a member of the class 'Alphaproteobacteria', phylum Proteobacteria, placed almost equidistantly between Methylobacterium species, Chelatococcus asaccharovorans and Bosea thiooxidans (similarity value of 93%) as its nearest phylogenetic relatives. Phylogenetic and phenotypic evidence suggest that strain Fail4T (=ATCC BAA-295T = DSM 14364T) should be placed as the type strain of a species in a newly created genus, for which the name Microvirga subterranea gen. nov., sp. nov. is proposed.

Iminodiacetate and nitrilotriacetate degradation by Kluyveromyces marxianus IMB3

The thermotolerant yeast Kluyveromyces marxianus IMB3 was capable of utilising either iminodiacetate or nitrilotriacetate as a sole source of nitrogen for growth. Cell extracts contained iminodiacetate dehydrogenase and nitrilotriacetate monooxygenase activities, suggesting the presence in the yeast of orthologues of these bacterial enzymes. The activities were not detectable in complete medium-growth cells, nor in nitrogen-starved cells, suggesting an inducible biodedgradation pathway for biodegradation of these xenobiotics, which has not been previously reported in a eukaryotic cell system. This observation emphasises the hitherto unrealised importance of yeast strains in the biodegradation of xenobiotics in the environment.

Identification, purification, and characterization of iminodiacetate oxidase from the EDTA-degrading bacterium BNC1

Microbial degradation of synthetic chelating agents, such as EDTA and nitrilotriacetate (NTA), may help immobilizing radionuclides and heavy metals in the environment. The EDTA- and NTA-degrading bacterium BNC1 uses EDTA monooxygenase to oxidize NTA to iminodiacetate (IDA) and EDTA to ethylenediaminediacetate (EDDA). IDA- and EDDA-degrading enzymes have not been purified and characterized to date. In this report, an IDA oxidase was purified to apparent homogeneity from strain BNC1 by using a combination of eight purification steps. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein band of 40 kDa, and by using size exclusion chromatography, we estimated the native enzyme to be a homodimer. Flavin adenine dinucleotide was determined as its prosthetic group. The purified enzyme oxidized IDA to glycine and glyoxylate with the consumption of O2. The temperature and pH optima for IDA oxidation were 35 degrees C and 8, respectively. The apparent Km for IDA was 4.0 mM with a kcat of 5.3 s(-1). When the N-terminal amino acid sequence was determined, it matched exactly with that encoded by a previously sequenced hypothetical oxidase gene of BNC1. The gene was expressed in Escherichia coli, and the gene product as a C-terminal fusion with a His tag was purified by a one-step nickel affinity chromatography. The purified fusion protein had essentially the same enzymatic activity and properties as the native IDA oxidase. IDA oxidase also oxidized EDDA to ethylenediamine and glyoxylate. Thus, IDA oxidase is likely the second enzyme in both NTA and EDTA degradation pathways in strain BNC1.

Environmental fate and microbial degradation of aminopolycarboxylic acids

Aminopolycarboxylic acids (APCAs) have the ability to form stable, water-soluble complexes with di- and trivalent metal ions. For that reason, synthetic APCAs are used in a broad range of domestic products and industrial applications to control solubility and precipitation of metal ions. Because most of these applications are water-based, APCAs are disposed of in wastewater and reach thus sewage treatment plants and the environment, where they undergo abiotic and/or biotic degradation processes. Recently, also natural APCAs have been described which are produced by plants or micro-organisms and are involved in the metal uptake by these organisms. For the two most widely used APCAs, nitrilotriacetate (NTA) and ethylenediaminetetraacetate (EDTA), transformation and mineralisation processes have been studied rather well, while for other xenobiotic APCAs and for the naturally occurring APCAs little is known on their fate in the environment. Whereas NTA is mainly degraded by bacteria under both oxic and anoxic conditions, biodegradation is apparently of minor importance for the environmental fate of EDTA. Photodegradation of iron(III)-complexed EDTA is supposed to be mostly responsible for its elimination. Isolation of a number of NTA- and EDTA-utilising bacterial strains has been reported and the spectrum of APCAs utilised by the different isolates indicates that some of them are able to utilise a range of different APCAs whereas others seem to be restricted to one compound. The two best characterised obligately aerobic NTA-utilising genera (Chelatobacter and Chelatococcus) are members of the alpha-subgroup of Proteobacteria. There is good evidence that they are present in fairly high numbers in surface waters, soils and sewage treatment plants. The key enzymes involved in NTA degradation in Chelatobacter and Chelatococcus have been isolated and characterised. The two first catabolic steps are catalysed by a monooxygenase (NTA MO) and a membrane-bound iminodiacetate dehydrogenase. NTA MO has been cloned and sequenced and its regulation as a function of growth conditions has been studied. Under denitrifying conditions, NTA catabolism is catalysed by a NTA dehydrogenase. EDTA breakdown was found to be initiated by a MO also which shares many characteristics with NTA MO from strictly aerobic NTA-degrading bacteria. In contrast, degradation of [S,S]-ethylenediaminedisuccinate ([S,S]-EDDS), a structural isomer of EDTA, was shown to be catalysed by an EDDS lyase in both an EDTA degrader and in a NTA-utilising Chelatococcus strain. So far, transport of APCAs into cells has only been studied for EDTA and the results obtained give strong evidence for an energy-dependent carrier system and Ca(2+) seems to be co-transported with EDTA. Due to their metal-complexing capacities, APCAs occur in the environment mostly in the metal-complexed form. Hence, the influence of metal speciation on various degradation processes is of utmost importance to understand the environmental behaviour of these compounds. In case of biodegradation, the effect of metal speciation is rather difficult to assess at the whole cell level and therefore only limited good data are available. In contrast, the influence of metal speciation on the intracellular enzymatic breakdown of APCAs is rather well documented but no generalising pattern applicable to all enzymes was found.

Defluvibacter lusatiae gen. nov., sp. nov., a new chlorohenol-degrading member of the alpha-2 subgroup of proteobacteria

The two Gram-negative bacterial strains S1 and S4 were isolated from activated sludge of an industrial waste water treatment plant and exhibited a stable capability to degrade 2,4-dichlorophenol, 4-chloro-2-methylphenol, 4-chlorophenol and phenol. The cells were short rods with a polar flagellum, being mesophilic, strictly aerobic, oxidase-positive, and chemoorganotrophic. They utilized a range of amino acids, but only a restricted number of carbohydrates. Reassociation experiments with DNA from strains S1 and S4 revealed high interstrain similarity, indicating, that both strains belong to the same species. The phylogenetic position was determined by comparison of the almost complete 16S rDNA sequence of strain S1 with sequences of related bacteria. Strain S1 clustered with members of the alpha-2 subgroup of the Proteobacteria by forming a separate lineage within the radiation of Mesorhizobium, Phyllobacterium and Sinorhizobium. Both strains can be differentiated from members of related taxa by a set of physiological and chemotaxonomic properties including the ability to grow with norvaline, L-tryptophan, putrescine, glutarate and malonate, and by the presence of spermidine as major polyamine and of 12:0 3OH as fatty acid. Strain S1 is described as type strain of a new species and assigned to a new genus with the proposed name Defluvibacter lusatiae.

Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH:flavin mononucleotide oxidoreductase

Nitrilotriacetate (NTA) is an important chelating agent in detergents and has also been used extensively in processing radionuclides. In Chelatobacter heintzii ATCC 29600, biodegradation of NTA is initiated by NTA monooxygenase that oxidizes NTA to iminodiacetate and glyoxylate. The NTA monooxygenase activity requires two component proteins, component A and component B, but the function of each component is unclear. We have cloned and sequenced a gene cluster encoding components A and B (nmoA and nmoB) and two additional open reading frames, nmoR and nmoT, downstream of nmoA. Based on sequence similarities, nmoR and nmoT probably encode a regulatory protein and a transposase, respectively. The NmoA sequence was similar to a monooxygenase that uses reduced flavin mononucleotide (FMNH2) as reductant; NmoB was similar to an NADH:flavin mononucleotide (FMN) oxidoreductase. On the basis of this information, we tested the function of each component. Purified component B was shown to be an NADH:FMN oxidoreductase, and its activity could be separated from that of component A. When the Photobacterium fischeri NADH:FMN oxidoreductase was substituted for component B in the complete reaction, NTA was oxidized, showing that the substrate specificity of the reaction resides in component A. Component A is therefore an NTA monooxygenase that uses FMNH2 and O2 to oxidize NTA, and component B is an NADH:FMN oxidoreductase that provides FMNH2 for NTA oxidation.

Cloning and characterization of the genes encoding nitrilotriacetate monooxygenase of Chelatobacter heintzii ATCC 29600

A 6.2-kb DNA fragment containing the genes for the nitrilotriacetate (NTA) monooxygenase of Chelatobacter heintzii ATCC 29600 was cloned and characterized by DNA sequencing and expression studies. The nucleotide sequence contained three major open reading frames (ORFs). Two of the ORFs, which were oriented divergently with an intergenic region of 307 bp, could be assigned to the NTA monooxygenase components A and B. The predicted N-terminal amino acid sequences of these ORFs were identical with those determined for the purified components. We therefore named these genes ntaA (for component A of NTA monooxygenase) and ntaB (for component B). The ntaA and ntaB genes could be expressed in Escherichia coli DH5alpha, and the gene products were visualized after Western blotting (immunoblotting) and incubation with polyclonal antibodies against component A or B. By mixing overproduced NtaB from E. coli and purified component A from C. heintzii ATCC 29600, reconstitution of a functional NTA monooxygenase complex was possible. The deduced gene product of ntaA showed only significant homology to SoxA (involved in dibenzothiophene degradation) and to SnaA (involved in pristamycin synthesis); that of ntaB shared weak homologies in one domain with other NADH:flavine mononucleotide oxidoreductases. These homologies provide no conclusive answer as to the possible evolutionary origin of the NTA monooxygenase. The deduced gene product of the third ORF (ORF1) had homology in the N-terminal region with the GntR class of bacterial regulator proteins and therefore may encode a regulator protein, possibly involved in regulation of ntaA and ntaB expression.

Dynamics of Substrate Consumption and Enzyme Synthesis in Chelatobacter heintzii during Growth in Carbon-Limited Continuous Culture with Different Mixtures of Glucose and Nitrilotriacetate

Regulation of nitrilotriacetate (NTA) degradation and expression of NTA monooxygenase (NTA-MO) in the NTA-degrading strain Chelatobacter heintzii ATCC 29600 in continuous culture at a dilution rate of 0.06 h(sup-1) under transient growth conditions when the feed was switched between media containing NTA, glucose, or different mixtures thereof as the sole carbon and energy sources was investigated. A transition from NTA to glucose was accompanied by a rapid loss of NTA-MO. A transition from glucose to NTA resulted in a lag phase of some 25 h until NTA-MO expression started, and approximately 100 h was needed before a steady state for NTA-MO specific activity was reached. This transient lag phase was markedly shortened when mixtures of NTA plus glucose were supplied instead of NTA only; for example, when a mixture of 90% glucose and 10% NTA was used, induction of NTA-MO was detected after 30 min. This suggests a strong positive influence of alternative carbon substrates on the expression of other enzymes under natural environmental conditions. Regulation of NTA-MO expression and the fate of NTA-MO were also studied during starvation of both glucose-grown and NTA-grown cultures. Starvation of NTA-grown cells led to a loss of NTA-MO protein. No synthesis of NTA-MO (derepression) was observed when glucose-grown cells were starved.

Anaerobic degradation of nitrilotriacetate (NTA) in a denitrifying bacterium: purification and characterization of the NTA dehydrogenase-nitrate reductase enzyme complex

The initial step in the anoxic metabolism of nitrilotriacetate (NTA) was investigated in a denitrifying member of the gamma subgroup of the Proteobacteria. In membrane-free cell extracts, the first step of NTA oxidation was catalyzed by a protein complex consisting of two enzymes, NTA dehydrogenase (NTADH) and nitrate reductase (NtR). The products formed were iminodiacetate and glyoxylate. Electrons derived from the oxidation of NTA were transferred to nitrate only via the artificial dye phenazine methosulfate, and nitrate was stoichiometrically reduced to nitrite. NTADH activity could be measured only in the presence of NtrR and vice versa. The NTADH-NtrR enzyme complex was purified and characterized. NTADH and NtrR were both alpha 2 dimers and had molecular weights of 170,000 and 105,000, respectively. NTADH contained covalently bound flavin cofactor, and NtrR contained a type b cytochrome. Optimum NTA-oxidizing activity was achieved at a molar ratio of NTADH to NtrR of approximately 1:1. So far, NTA is the only known substrate for NTADH. This is the first report of a redox enzyme complex catalyzing the oxidation of a substrate and concomitantly reducing nitrate.