Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments

Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil

A Gram-stain-positive, rod-shaped, non-spore-forming, alkane degrading bacterium, designated DJM-14T, was isolated from oilfield alkali-saline soil in Heilongjiang, Northeast China. On the basis of 16 S rRNA gene sequencing, strain DJM-14T was shown to belong to the genus Nocardioides, and related most closely to Nocardioides terrigena KCTC 19,217T (95.53% 16 S rRNA gene sequence similarity). Strain DJM-14T was observed to grow at 25-35 °C, pH 7.0-11.0, in the presence of 0-6.0% (w/v) NaCl. The predominant respiratory quinone was MK-8 (H4) and LL-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were identified as iso-C16:0 and C18:1 ω9c. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The genome (3,722,608 bp), composed of 24 contigs, had a G + C content of 69.6 mol%. Out of the 3667 predicted genes, 3618 were protein-coding genes, and 49 were ncRNAs. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of strain DJM-14T against genomes of the type strains of related species in the same family ranged between 18.7% and 20.0%; 68.8% and 73.6%, respectively. According to phenotypic, genotypic and phylogenetic data, strain DJM-14T represents a novel species in the genus Nocardioides, for which the name Nocardioides limicola sp. nov. is proposed and the type strain is DJM-14T (= CGMCC 4.7593T, =JCM 33,692T). In addition, novel strains were able to grow with n-alkane (C24-C36) as the sole carbon source. Multiple copies of alkane 1-monooxygenase (alkB) gene, as well as alcohol dehydrogenase gene and aldehyde dehydrogenase gene involved in the alkane assimilation were annotated in the genome of type strain DJM-14T.

Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment

Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.

The potential application of carbazole-degrading bacteria for dioxin bioremediation

Extensive research has been conducted over the years on the bacterial degradation of dioxins and their related compounds including carbazole, because these chemicals are highly toxic and has been widely distributed in the environment. There is a pressing need to explore and develop more bacterial strains with unique catabolic features to effectively remediate dioxin-polluted sites. Carbazole has a chemical structure similar to dioxins, and the degradation pathways of these two chemicals are highly homologous. Some carbazole-degrading bacterial strains have been demonstrated to have the ability to degrade dioxins, such as Pseudomonas sp. strain CA10 và Sphingomonas sp. KA1. The introduction of strain KA1 into dioxin-contaminated model soil resulted in the degradation of 96% and 70% of 2-chlorodibenzo-p-dioxin (2-CDD) and 2,3-dichlorodibenzo-p-dioxin (2,3-DCDD), respectively, after 7-day incubation period. These degradation rates were similar to those achieved with strain CA10, which removed 96% of 2-CDD and 80% of 2,3-DCDD from the same model soil. Therefore, carbazole-degrading bacteria hold significant promise as potential candidates for dioxin bioremediation. This paper overviews the connection between the bacterial degradation of dioxins and carbazole, highlighting the potential for dioxin biodegradation by carbazole-degrading bacterial strains.

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5-97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4-97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2-77.3 % and 21.3-21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).

The Effect of Date Palm Genotypes on Rhizobacterial Community Structures under Saline Environments

Some genotypes of date palms (Phoenix dactylifera L.) are salt-tolerant; however, salinity significantly affects others. This study aimed to determine the root epiphytic bacterial contributions to the salt tolerance mechanism in the date palm and to verify if the salt-tolerant “Umsila” and the salt-susceptible “Zabad” cultivars have different bacterial communities. Therefore, the epiphytic bacterial community structures were investigated in both cultivars when grown under control and salinity conditions. The proximal soils of the roots were collected, the DNA was extracted, and a culture-independent approach using Illumina® MiSeq™ sequence analysis was carried out to identify the changes in the bacterial community structures in the soil samples due to the changes in salinity and the genotypes of the plants based on 16S rRNA gene sequencing. While salt tolerance response differences were evident between the two cultivars, the 16S rRNA gene sequencing results revealed 771 operational taxonomic units (OTUs), including 62 that were differentially accumulated in response to salinity. The ordination analysis showed significant (p = 0.001) changes among the communities in response to salinity in both cultivars. However, the results showed that the two cultivars had distinct bacterial communities when grown under controlled conditions, whereas they had a more similar bacterial community structure when grown under salinity conditions. The plant genotype does not affect the epiphyte bacterial community structure under salinity, probably because salinity affects the plant-microbe interaction similarly in both cultivars. Also, the identified rhizospheric bacteria are not directly associated with the root’s physiological processes in response to salinity.

Correlating biodegradation kinetics of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the dynamics of microbial communities originating from soil in Vietnam contaminated with herbicides and dioxins

We studied the succession of bacterial communities during the biodegradation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD). The communities originated from a mesocosm with soil from Bien Hoa airbase in Vietnam heavily contaminated with herbicides and dioxins. They were grown in defined media with different carbon and Gibbs energy sources and 2,3,7,8-TCDD. Cultures with dimethyl sulfoxide (DMSO) as the sole carbon and energy source degraded about 95% of 2,3,7,8-TCDD within 60 days of cultivation. Those with an additional 1 mM of vanillin did that in roughly 90 days. Further 16S rRNA gene amplicon sequencing showed that the increase in relative abundance of members belonging to the genera Bordetella, Sphingomonas, Proteiniphilum, and Rhizobium correlated to increased biodegradation of 2,3,7,8-TCDD in these cultures. A higher concentration of vanillin slowed down the biodegradation rate. Addition of alternative carbon and Gibbs energy sources, such as amino acids, sodium lactate and sodium acetate, even stopped the degradation of 2,3,7,8-TCDD completely. Bacteria from the genera Bordetella, Achromobacter, Sphingomonas and Pseudomonas dominated most of the cultures, but the microbial profiles also significantly differed between cultures as judged by non-metric multidimensional scaling (NMDS) analyses. Our study indicates that 2,3,7,8-TCDD degradation may be stimulated by bacterial communities preadapted to a certain degree of starvation with respect to the carbon and energy source. It also reveals the succession and abundance of defined bacterial genera in the degradation process.

Biochemical and genetic characterization comparison of four extradiol dioxygenases in Rhizorhabdus wittichii RW1

Rhizorhabdus (previously Sphingomonas) wittichii RW1 uses a diverse array of aromatic organic compounds as energy and carbon sources, including some extremely recalcitrant compounds such as dibenzo-p-dioxin and dibenzofuran. Extradiol dioxygenases play a key role in the metabolism of dibenzofuran (DBF), dibenzo-p-dioxin (DBD), PCBs, and various other aromatic compounds. In this study, a detailed kinetic analysis of four extradiol dioxygenases identified in R. wittichii RW1 (DbfB, Edo2, Edo3, and Edo4) showed all of them to be typical 2,3dihydroxybiphenyl (DHB) dioxygenases with DHB as preferred substrate (k_cat/K_m values of 0.13-188 (µM ^-1 s^-1)) and only slightly lower activity against trihydroxybiphenyl (THB) whereas monocyclic substrates were, to different extents, poor substrates due to high k_m values. All extradiol dioxygenases analyzed were subject to mechanism-based inactivation by 2,2`,3-trihydroxybiphenylether (THBE) the intermediate of DBD degradation. However, Edo4 was superior as reflected by the relatively high partition ratio and the comparably low efficiency of inactivation. Significant differences were observed with respect to their inactivation by 3-chlorocatechol. The absence of any significant mechanism-based inactivation makes Edo3 a perfect candidate for being recruited for chlorobiphenyl degradation where inactivation of extradiol dioxygenases by this intermediate creates significant metabolic problems. KEY POINTS: • Characterization of additional extradiol dioxygenases encoded by RW1 • Identification of differences in 2,2`,3-trihydroxybiphenylether transformation • Identification of differences in inhibition by 3-chlorocatechol.

Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine

From the metagenome of a carbamazepine amended selective enrichment culture the genome of a new to science bacterial species affiliating with the genus Nocardioides was reconstructed. From the same enrichment an aerobic actinobacterium, strain CBZ_1^T, sharing 99.4% whole-genome sequence similarity with the reconstructed Nocardioides sp. bin genome was isolated. On the basis of 16S rRNA gene sequence similarity the novel isolate affiliated to the genus Nocardioides, with the closest relatives Nocardioides kongjuensis DSM19082^T (98.4%), Nocardioides daeguensis JCM17460^T (98.4%) and Nocardioides nitrophenolicus DSM15529^T (98.2%). Using a polyphasic approach it was confirmed that the isolate CBZ_1^T represents a new phyletic lineage within the genus Nocardioides. According to metagenomic, metatranscriptomic studies and metabolic analyses strain CZB_1^T was abundant in both carbamazepine and ibuprofen enrichments, and harbors biodegradative genes involved in the biodegradation of pharmaceutical compounds. Biodegradation studies supported that the new species was capable of ibuprofen biodegradation. After 7 weeks of incubation, in mineral salts solution supplemented with glucose (3 g l^-1) as co-substrate, 70% of ibuprofen was eliminated by strain CBZ_1^T at an initial conc. of 1.5 mg l^-1. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain CBZ_1^T to the genus Nocardioides, for which the name Nocardioides carbamazepini sp. nov. (CBZ_1^T = NCAIM B.0.2663 = LMG 32395) is proposed. To the best of our knowledge, this is the first study that reports simultaneous genome reconstruction of a new to science bacterial species using metagenome binning and at the same time the isolation of the same novel bacterial species.

Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria ), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides . Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099T, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to Nocardioides pelophilus KACC 19192T with 98.11 % similarity. The DNA G+C content of strain BN130099T was 68.84 mol% (draft genome sequence). The genome sequence of BN130099T displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the major respiratory quinone. The predominant fatty acid was iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099T from N. pelophilus KACC 19192T. The strain represents a novel species of the genus Nocardioides , for which we propose the name Nocardioides humilatus sp. nov. The type strain is BN130099T (=KCTC 49079T=CCTCC AB 2018135T).

Separate Upper Pathway Ring Cleavage Dioxygenases Are Required for Growth of Sphingomonas wittichii Strain RW1 on Dibenzofuran and Dibenzo-p-Dioxin

Sphingomonas wittichii RW1 is one of a few strains known to grow on the related compounds dibenzofuran (DBF) and dibenzo-p-dioxin (DXN) as the sole source of carbon. Previous work by others (B. Happe, L. D. Eltis, H. Poth, R. Hedderich, and K. N. Timmis, J Bacteriol 175:7313-7320, 1993, https://doi.org/10.1128/jb.175.22.7313-7320.1993) showed that purified DbfB had significant ring cleavage activity against the DBF metabolite trihydroxybiphenyl but little activity against the DXN metabolite trihydroxybiphenylether. We took a physiological approach to positively identify ring cleavage enzymes involved in the DBF and DXN pathways. Knockout of dbfB on the RW1 megaplasmid pSWIT02 results in a strain that grows slowly on DBF but normally on DXN, confirming that DbfB is not involved in DXN degradation. Knockout of SWIT3046 on the RW1 chromosome results in a strain that grows normally on DBF but that does not grow on DXN, demonstrating that SWIT3046 is required for DXN degradation. A double-knockout strain does not grow on either DBF or DXN, demonstrating that these are the only ring cleavage enzymes involved in RW1 DBF and DXN degradation. The replacement of dbfB by SWIT3046 results in a strain that grows normally (equal to the wild type) on both DBF and DXN, showing that promoter strength is important for SWIT3046 to take the place of DbfB in DBF degradation. Thus, both dbfB- and SWIT3046-encoded enzymes are involved in DBF degradation, but only the SWIT3046-encoded enzyme is involved in DXN degradation.IMPORTANCE S. wittichii RW1 has been the subject of numerous investigations, because it is one of only a few strains known to grow on DXN as the sole carbon and energy source. However, while the genome has been sequenced and several DBF pathway enzymes have been purified, there has been very little research using physiological techniques to precisely identify the genes and enzymes involved in the RW1 DBF and DXN catabolic pathways. Using knockout and gene replacement mutagenesis, our work identifies separate upper pathway ring cleavage enzymes involved in the related catabolic pathways for DBF and DXN degradation. The identification of a new enzyme involved in DXN biodegradation explains why the pathway of DBF degradation on the RW1 megaplasmid pSWIT02 is inefficient for DXN degradation. In addition, our work demonstrates that both plasmid- and chromosomally encoded enzymes are necessary for DXN degradation, suggesting that the DXN pathway has only recently evolved.

Root-Associated Endophytic Bacterial Community Composition of Asparagus officinalis of Three Different Varieties

Asparagus (Asparagus officinalis L) is an economically important crop, rich in nutrients, and is also conducive to solving ecological and environmental problems. Plants may acquire benefits from root-associated endophytic bacteria. However, the composition of the endophytic bacterial community associated with the roots of asparagus is poorly elucidated. In this study, the nine root samples of asparagus from three different varieties including Asparagus officinalis var. Grande (GLD), A. officinalis var. Jinglvlu3 (JL3) and A. officinalis var. Jingzilu2 (JZL) were investigated by high-throughput sequencing technology of the 16S rDNA V5-V7 hypervariable region of endophytic bacteria. A total of 16 phyla, 29 classes, 90 orders, 171 families, and 312 genera were identified. Endophytic bacteria diversity and bacteria structure was different among the three varieties and was influenced by rhizosphere soil properties and varieties. In the GLD variety, the main phyla were Proteobacteria, Actinobacteria, and Firmicutes. The main phylum in JL3 and JZL varieties was Proteobacteria. The observations showed that GLD had the highest diversity of endophytes as indicated by the Shannon index (GLD > JZL > JL3). The order of the endophytes richness was GLD > JL3 > JZL. The PCA and PCoA analysis revealed the microbial communities were different between three different asparagus varieties, and the microbial composition of GLD and JZL was more similar. This report provides an important reference for the study of endophytic microorganisms of asparagus.

Supplementary information

The online version contains supplementary material available at (10.1007/s12088-021-00926-6) contains supplementary material, which is available to authorized users.

Nocardioides antri sp. nov., Isolated from Soil in a Rock Cave

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041^T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34 ^T, N. pelophilus THG-T63^T, and N. immobilis FLL521^T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27 Mb containing 424 contigs with a DNA G + C content of 70.5 mol%. The ANI value between strain BN140044^T and its closely related species N. silvaticus S-34 ^T was 82.6%. The genome sequence of BN140041^T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C_16:0 (55.3%), C_18:1ω9c (7.7%) and iso-C_17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041^T from related the Nocardioides strains. Therefore, strain BN140041^T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041^T (= KCTC 49080 ^T = CCTCC AB 2018226 ^T).

Complete Genome of Isoprene Degrading Nocardioides sp. WS12

Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.

Biodegradation of ritalinic acid by Nocardioides sp. - Novel imidazole-based alkaloid metabolite as a potential marker in sewage epidemiology

The consumption of methylphenidate, a nootropic drug used to improve mental performance, is becoming increasingly serious. Methylphenidate is metabolized in human liver to ritalinic acid, which has been commonly detected in sewage and surface waters. Additionally, ritalinic acid serves as a biomarker in sewage epidemiology studies. Thus knowledge of the stability and microbial degradation pathways of ritalinic acid is essential for proper estimation of methylphenidate consumption. In the study reported here, we describe the fast formation of a previously unknown, dead-end metabolite of ritalinic acid by Nocardioides sp. strain MW5. HRMS and 2D NMR analyses allowed precisely identification of the compound as an imidazole-based alkaloid cation with chemical formula 11-[3-(formylamino)propyl]-1,2,3,4,6,7,8,9-octahydrodipyrido[1,2-a:1',2'-c]imidazole-5-ium. In experiments, Nocardioides sp. strain MW5 transformed 34% of ritalinic acid into this metabolite, while 52% was mineralized into CO₂. Alkaloid was not biodegraded during the OECD 301 F test. This study provides new insight into the environmental fate of methylphenidate and its metabolites. The data collected are essential for assessing nootropic drug consumption by sewage epidemiology and should lead to a better understanding of microbial degradation of ritalinic acid.

Aerobic bacterial transformation and biodegradation of dioxins: a review

Waste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.

Pseudomonas humi sp. nov., isolated from leaf soil

An aerobic, Gram-negative, non-sporulating, motile, rod-shaped and lignin-degrading bacterial strain, Pseudomonas sp. CCA1, was isolated from leaf soil collected in Japan. This strain grew at 20-45 °C (optimum 20 °C), at pH 5.0-10.0 (optimum pH 5.0), and in the presence of 2% NaCl. Its major cellular fatty acids were C_16:0 and summed feature 8 (C_18:1ω6c and/or C_18:1ω7c). The predominant quinone system was ubiquinone-9. Comparative 16S rRNA gene sequence analysis showed that Pseudomonas sp. CCA1 was related most closely to P. citronellolis NBRC 103043^T (98.9%), but multilocus sequence analysis based on fragments of the atpD, gyrA, gyrB and rpoB gene sequences showed strain CCA1 to branch separately from its most closely related Pseudomonas type strains. DNA-DNA hybridization values between Pseudomonas sp. CCA1 and type strains of closely related Pseudomonas species were less than 53%. Based on its phenotypic, chemotaxonomic and phylogenetic features, we propose that Pseudomonas sp. CCA1 represents a novel species within the genus Pseudomonas, for which the name Pseudomonas humi sp. nov. is proposed. The type strain is CCA1 (= HUT 8136^T = TBRC 8616^T).

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces

In the present study, we describe two novel Gram-stain-positive, irregular rod-shaped bacterial strains, 78^T and 601, that had been isolated from the faeces of Tibetan antelopes at the Hoh Xil Nature Reserve, Qinghai-Tibet Plateau, China. The cells were aerobic, oxidase-negative and catalase-positive. When cultured on brain-heart infusion agar supplemented with 5 % sheep blood, colonies were cream in colour, circular, smooth and convex. Phylogenetic analysis based on the full-length 16S rRNA sequences revealed that type strain 78^T and strain 601 belong to the genus Nocardioides, sharing the highest similarity to Nocardioides solisilvae JCM 31492^T (98.3 %), Nocardioides gilvus XZ17^T (97.4 %) and Nocardioides daejeonensis JCM 16922^T (97.4 %). The average nucleotide identity values between the two novel strains and the three closely related type strains of the genus Nocardioides were lower than the 95-96 % threshold. The DNA G+C content of strains 78^T and 601 were 71.2 and 71.3 mol% respectively. MK-8 (H4) was the predominant respiratory quinone and ll-2,6-diaminopimelic acid was the diagnostic diamino acid in its cell-wall peptidoglycan. Its polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The main whole-cell sugars were rhamnose, xylose and galactose and the major fatty acids (>10 %) were C17 : 1ω8c, iso-C16 : 0 and C18 : 1ω9c. These data supported the affiliation of strains 78^T and 601 to genus Nocardioides. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named Nocardioideshouyundeii sp. nov. The type strain is 78^T (=CGMCC 4.7461^T=DSM 106424^T).

Diversity of cultivable bacterial endophytes in Paullinia cupana and their potential for plant growth promotion and phytopathogen control

Endophytic bacteria occupy the same niche of phytopathogens and may produce metabolites that induce the host plant systemic resistance and growth. Host and environmental variables often determine the endophytic community's structure and composition. In this study, we addressed whether the plant genotype, organ, and geographic location influence the structure, composition, and functionality of endophytic bacterial communities in Paullinia cupana. To characterize the communities and identify strains with potential application in agriculture, we analyzed two P. cupana genotypes cultivated in two cities of the State of Amazonas, Brazil. Endophytic bacteria were isolated from surface-disinfested root, leaf, and seed tissues through the fragmentation and maceration techniques. The colonization rate, number of bacteria, richness, diversity, and functional traits were determined. The plant growth-promoting ability of selected bacterial strains was assessed in Sorghum bicolor. We identified 95 bacterial species distributed in 29 genera and 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes). The colonization rate, richness, diversity, and species composition varied across the plant organs; the last parameter also varied across the plant genotype and location. Some strains exhibited relevant plant growth-promoting traits and antagonistic traits against the main phytopathogens of P. cupana, but they were not separated by functional traits. The main bacterial strains with plant growth-promoting traits induced S. bicolor growth. Altogether, our findings open opportunities to study the application of isolated endophytic bacterial strains in the bioprospection of processes and products.

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.

Nocardioides flavus sp. nov., isolated from marine sediment

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short rod-shaped actinomycete strain, Y4T, was isolated from a sediment sample collected from the Western Pacific. This isolate grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-9.0 and 4-40 °C; optimum growth was observed with 1 % (w/v) NaCl and at pH 7.0 and 35-37 °C. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain Y4T belonged to the genus Nocardioides and was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.0 %) and Nocardioides exalbidus RC825T (98.0 %), followed by Nocardioides alpinus Cr7-14T (97.9 %), Nocardioides oleivorans DSM 16090T (97.9 %), Nocardioides furvisabuli SBS-26T (97.4 %) and Nocardioides hwasunensis HFW-21T (97.4 %). Sequence similarities between strain Y4T and the other related species of the genus Nocardioides were less than 96.3 %. Strain Y4T had MK-8(H4) and MK-7(H4) as the predominant respiratory quinones and C17 : 1ω8c, iso-C16 : 0 and C17 : 0 as major fatty acids. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid, two unknown glycolipids and one unknown lipid. The DNA G+C content was 70.4 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. Strain Y4T could be differentiated from recognized Nocardioides species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. Thus, strain Y4T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides flavus sp. nov. is proposed. The type strain is Y4T (=MCCC 1A09944T=LMG 28100T=JCM 19770T=CGMCC 1.12791T).

Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan

A Gram-staining positive, non-spore forming, non-pigmented and non-motile bacterium, designated as NCCP-1340(T), was isolated from a hot water spring, Tatta Pani, Pakistan. Cells of strain NCCP-1340(T) were observed to be aerobic, rod shaped, catalase and urease positive but H2S production and oxidase negative. Growth was observed at pH 6.0-8.0 (optimum pH 7.0) and at 20-40 °C (optimum 37 °C). The strain could tolerate 0-8 % NaCl (optimum 2 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain NCCP-1340(T) belongs to the genus Nocardioides and is closely related to Nocardioides iriomotensis JCM 17985(T) (96.8 %), Nocardioides daedukensis KCTC 19601(T) (96.6 %), Nocardioides jensenii KCTC 9134(T) (96.1 %) and Nocardioides daejeonensis KCTC 19772(T) (96.1 %). The DNA-DNA relatedness values of strain NCCP-1340(T) with N. iriomotensis JCM 17985(T), N. daedukensis KCTC 19601(T) and N. jensenii KCTC 9134(T) were found to be less than 53 %. The DNA G+C content of strain NCCP-1340(T) was determined to be 71.8 mol  %. The affiliation of strain NCCP-1340(T) to the genus Nocardioides was further supported by chemotaxonomic data which showed the presence of MK-8(H4) as major menaquinone system; iso-C16:0, C17:0, C16:0 10-methyl, iso-C15:0 and C 15:0 as major cellular fatty acids; and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unidentified glycolipids and polar lipids in the polar lipids profile. The cell wall peptidoglycan contained LL-diaminopimelic acid as the diagnostic amino acid. On the basis of physiological and biochemical characteristics and the phylogenetic analyses, strain NCCP-1340(T) can be distinguished from the closely related taxa and thus represents a novel species of the genus Nocardioides, for which the name Nocardioides pakistanensis sp. nov. is proposed with the type strain NCCP-1340(T) (= DSM 29942(T) = JCM 30630(T)).

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.

Metabolic fate of the (14)C-labeled herbicide clodinafop-propargyl in a sediment-water system

The metabolic fate of (14)C-phenyl-labeled herbicide clodinafop-propargyl ((14)C-CfP) was studied for 28 days in lab assays using a sediment-water system derived from a German location. Mineralization was 5.21% of applied (14)C after 28 days exhibiting a distinct lag phase until day 14 of incubation. Portions of radioactivity remaining in water phases decreased at moderate rate to 18.48% after 28 days; 62.46% were still detected in water after 14 days. Soxhlet extraction of the sediment using acetonitrile released 35.56% of applied (14)C with day 28, while 33.99% remained as non-extractable residues. A remarkable increase of bound (14)C was observed between 14 and 28 days correlating with the distinct increase of mineralization. No correlation was found throughout incubation with microbial activity of the sediment as determined by dimethyl sulfoxide reduction. Dissolved oxygen and pH value of water phases remained almost constant for 28 days. Analyses of Soxhlet extracts of the sediment and ethyl acetate extracts of water phases by radio-TLC and radio-HPLC revealed that CfP was rapidly cleaved to free acid clodinafop (Cf), which was further (bio-) transformed. DT50 values (based on radio-HPLC) were below 1 day (CfP) and slightly above 28 days (Cf). Further metabolites were not detected. Fractionation of humic and non-humic components of the sediment demonstrated that CfP's non-extractable residues were predominantly associated with fulvic acids up to 14 days of incubation (3.36%), whereas after 28 days, the majority of radioactivity was found in the humin/mineral fraction (13.30% of applied (14)C). Due to high-performance size-exclusion chromatography of the fulvic acids fraction derived from assays incubated for 28 days, this portion of (14)C was firmly, possibly covalently bound to fulvic acids and did not consist of CfP or Cf. Using an isolation strategy comprising preincubation of sediment with CfP and mineralization of (14)C-CfP as criterion, a microorganism was isolated from the sediment examined. It grew on (14)C-CfP as sole carbon source with evolution of (14)CO2. The bacterium was characterized by growth on commonly used carbon sources and 16S rDNA sequence analysis. Its sequence exhibited high similarity with that of Nocardioides aromaticivorans strain H-1 (98.85%; DSM 15131, JCM 11674).

Raoultella electrica sp. nov., isolated from anodic biofilms of a glucose-fed microbial fuel cell

A Gram-stain-negative, non-spore-forming, rod-shaped bacterium, designated strain 1GBT, was isolated from anodic biofilms of a glucose-fed microbial fuel cell. Strain 1GBT was facultatively anaerobic and chemo-organotrophic, having both a respiratory and a fermentative type of metabolism, and utilized a wide variety of sugars as carbon and energy sources. Cells grown aerobically contained Q-8 as the major quinone, but excreted Q-9 and a small amount of Q-10 when cultured with an electrode serving as the sole electron acceptor. The G+C content of the genomic DNA of 1GBT was 54.5 mol%. Multilocus sequence typing (MLST) analysis showed that strain 1GBT represented a distinct lineage within the genus Raoultella (98.5–99.4 % 16S rRNA gene sequence similarity and 94.0–96.5 % sequence similarity based on the three concatenated housekeeping genes gyrA, rpoB and parC. Strain 1GBT exhibited DNA–DNA hybridization relatedness of 7–43 % with type strains of all established species of the genus Raoultella . On the basis of these phenotypic, phylogenetic and genotypic data, the name Raoultella electrica sp. nov. is proposed for strain 1GBT. The type strain is 1GBT ( = NBRC 109676T = KCTC 32430T).

Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant

A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5(T)) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of Nocardioides nitrophenolicus (98.6 % similarity), N. kongjuensis (98.5 %), N. caeni (98.4 %), N. simplex (98.3 %), N. aromaticivorans (98.1 %) and N. ginsengisoli (97.5 %); the phylogenetic distance from other species with validly published names within the genus Nocardioides was greater than 3 %. Strain 2C1-5(T) was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C16 : 0 and C17 : 1ω6c as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5(T) to the genus Nocardioides. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5(T) from existing species with validly published names. Therefore, strain 2C1-5(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides daeguensis sp. nov. is proposed, with the type strain 2C1-5(T) ( = JCM 17460(T) = KCTC 19799(T)).

Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6‒0.9 μm in width and 1.2‒3.0 μm in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3‒60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585T = KCTC 23252T).

Isolation and functional gene analyses of aromatic-hydrocarbon-degrading bacteria from a polychlorinated-dioxin-dechlorinating process

Aerobic aromatic-hydrocarbon-degrading bacteria from a semi-anaerobic microbial microcosm that exhibited apparent complete dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were isolated through enrichment and plating culture procedures with dibenzofuran as the model substrate. By 16S rRNA gene sequence comparisons, these dibenzofuran-degrading isolates were identified as being members of the phyla Actinobacteria, Firmicutes, and Proteobacteria, among which those of the genera Paenibacillus and Rhizobium were most abundant. All of the isolates utilized naphthalene as the sole carbon and energy source and degraded dibenzofuran metabolically or co-metabolically; however, they hardly attacked monochlorinated dibenzofuran and dibenzo-p-dioxin. By PCR cloning and sequencing, genes predicted to encode aromatic-ring-hydroxylating dioxygenase (AhDO) were detected in all test isolates. Real-time quantitative PCR assays with specific primer sets detected approximately 10⁵ copies of the AhDO large subunit genes g⁻¹ wet wt in the microcosm from which the isolates were obtained. This order of the copy number corresponded to approximately 1% of the 16S rRNA gene copies from "Dehalococcoides" and its relatives present as potent dechlorinators. These results suggest that aerobic AhDO-containing bacteria co-exist and play a role in the oxidative degradation of less chlorinated and completely dechlorinated products in the PCDD/F-dechlorinating process, thereby achieving the apparent complete dechlorination of PCDD/Fs.

Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1

Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the xenobiotic compounds dibenzodioxin and dibenzofuran (DBF). A number of genes involved in DBF degradation have been previously characterized, such as the dxn cluster, dbfB, and the electron transfer components fdx1, fdx3, and redA2. Here we use a combination of whole genome transcriptome analysis and transposon library screening to characterize RW1 catabolic and other genes implicated in the reaction to or degradation of DBF. To detect differentially expressed genes upon exposure to DBF, we applied three different growth exposure experiments, using either short DBF exposures to actively growing cells or growing them with DBF as sole carbon and energy source. Genome-wide gene expression was examined using a custom-made microarray. In addition, proportional abundance determination of transposon insertions in RW1 libraries grown on salicylate or DBF by ultra-high throughput sequencing was used to infer genes whose interruption caused a fitness loss for growth on DBF. Expression patterns showed that batch and chemostat growth conditions, and short or long exposure of cells to DBF produced very different responses. Numerous other uncharacterized catabolic gene clusters putatively involved in aromatic compound metabolism increased expression in response to DBF. In addition, only very few transposon insertions completely abolished growth on DBF. Some of those (e.g., in dxnA1) were expected, whereas others (in a gene cluster for phenylacetate degradation) were not. Both transcriptomic data and transposon screening suggest operation of multiple redundant and parallel aromatic pathways, depending on DBF exposure. In addition, increased expression of other non-catabolic genes suggests that during initial exposure, S. wittichii RW1 perceives DBF as a stressor, whereas after longer exposure, the compound is recognized as a carbon source and metabolized using several pathways in parallel.

Nocardioides hungaricus sp. nov., isolated from a drinking water supply system

Three Gram-positive, rod-shaped bacterial strains were isolated from the drinking water supply system of the Hungarian capital, Budapest. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparison revealed that the isolates represented a distinct cluster within the clade of the genus Nocardioides and were most closely related to Nocardioides pyridinolyticus OS4T, Nocardioides aquiterrae GW-9T, Nocardioides sediminis MSL-01T and N. hankookensis DS-30T. The peptidoglycan based on ll-2,6-diaminopimelic acid, the major menaquinone MK-8(H4), the cellular fatty acid profile with iso-C16 : 0 and anteiso-C17 : 0 as predominating components and the DNA G+C content of 71.4 mol% (strain 1RaM5-12T) were consistent with the affiliation of the isolates to the genus Nocardioides. Because of differences in physiological characteristics, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of protein extracts, PvuII RiboPrinter patterns and 96.1 % 16S rRNA gene sequence similarity between strain 1RaM5-12T and its closest phylogenetic neighbour, N. pyridinolyticus OS4T, a novel species, Nocardioides hungaricus sp. nov., is proposed. The type strain is 1RaM5-12T (=DSM 21673T =NCAIM 02330T).

Nocardioides sp. strain WSN05-2, isolated from a wheat field, degrades deoxynivalenol, producing the novel intermediate 3-epi-deoxynivalenol

The mycotoxin deoxynivalenol (DON) causes serious problems worldwide in the production of crops such as wheat and barley because of its toxicity toward humans and livestock. A bacterial culture capable of degrading DON was obtained from soil samples collected in wheat fields using an enrichment culture procedure. The isolated bacterium, designated strain WSN05-2, completely removed 1,000 μg/mL of DON from the culture medium after incubation for 10 days. On the basis of phylogenetic studies, WSN05-2 was classified as a bacterium belonging to the genus Nocardioides. WSN05-2 showed significant growth in culture medium with DON as the sole carbon source. High-performance liquid chromatography analysis indicated the presence of a major initial metabolite of DON in the culture supernatant. The metabolite was identified as 3-epi-deoxynivalenol (3-epi-DON) by mass spectrometry and ¹H and ¹³C nuclear magnetic resonance analysis. The amount of DON on wheat grain was reduced by about 90% at 7 days after inoculation with WSN05-2. This is the first report of a Nocardioides sp. strain able to degrade DON and of the yet unknown 3-epi-DON as an intermediate in the degradation of DON by a microorganism.

Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 346T) was isolated from the soil of a ginseng field in South Korea and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequences, strain Gsoil 346T was shown to belong to the genus Nocardioides in the family Nocardioidaceae, with the most closely related species being Nocardioides aquiterrae GW-9T (96.6 % 16S rRNA gene sequence similarity); however, the strain clustered in a distinct branch of the phylogenetic tree with Nocardioides kongjuensis A2-4T (96.2 %), Nocardioides aromaticivorans H-1T (96.1 %), Nocardioides nitrophenolicus NSP41T (96.1 %) and Nocardioides simplex ATCC 15799T (95.9 %). Strain Gsoil 346T was characterized chemotaxonomically and found to have ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, phosphatidylinositol and phosphatidylglycerol as the major polar lipids, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C18 : 1 ω9c and C17 : 1 ω8c as the major fatty acids. The G+C content of the genomic DNA of the novel strain was 73.0 mol%. These chemotaxonomic properties supported the placement of strain Gsoil 346T in the genus Nocardioides. The results of physiological and biochemical tests, along with the phylogenetic analysis, allowed strain Gsoil 346T to be differentiated genotypically and phenotypically from recognized species of the genus Nocardioides. Therefore, strain Gsoil 346T represents a novel species, for which the name Nocardioides panacisoli sp. nov. is proposed, with Gsoil 346T (=KCTC 19470T=DSM 21348T) as the type strain.

Two angular dioxygenases contribute to the metabolic versatility of dibenzofuran-degrading Rhodococcus sp. strain HA01

Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% +/- 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.

Nocardioides terrigena sp. nov., isolated from soil

A Gram-positive, rod- or coccoid-shaped bacterial strain, DS-17T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-17T grew optimally at around pH 8.0 and 30 °C in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-17T belonged to the genus Nocardioides. The chemotaxonomic properties of strain DS-17T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0, C17 : 1 ω8c and C17 : 0 were the major fatty acids. The DNA G+C content was 71.5 mol%. Strain DS-17T exhibited 16S rRNA gene sequence similarity values of 94.5–96.9 % to the type strains of recognized Nocardioides species. Strain DS-17T could be distinguished from recognized Nocardioides species by differences in phenotypic characteristics. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-17T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides terrigena sp. nov. is proposed. The type strain is DS-17T (=KCTC 19217T=JCM 14582T).

Nocardioides insulae sp. nov., isolated from soil

A Gram-positive, rod-shaped or coccoid bacterial strain, DS-51T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-51T grew optimally at pH 8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-51T forms a distinct line of descent within the radiation enclosed by the genus Nocardioides. The chemotaxonomic properties of strain DS-51T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0 was the major fatty acid. The DNA G+C content was 71.1 mol%. The 16S rRNA gene sequence of strain DS-51T had similarity levels of 92.5–95.1 % with the sequences of the type strains of Nocardioides species. Strain DS-51T could be distinguished from other Nocardioides species by differences in some phenotypic characteristics. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-51T represents a novel species of the genus Nocardioides, for which the name Nocardioides insulae sp. nov. is proposed. The type strain is DS-51T (=KCTC 19180T=DSM 17944T).

Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments

Three strains of strictly aerobic, Gram-negative, naphthalene-degrading bacteria isolated from polychlorinated-dioxin-contaminated soil and sediment were characterized. These isolates grew well with naphthalene as the sole carbon and energy source, degrading it completely within 24 h of incubation. The isolates also degraded dibenzofuran co-metabolically in the presence of naphthalene with the concomitant production of yellow intermediate metabolite(s). A 16S rRNA gene sequence analysis revealed that the isolates affiliated to the genus Novosphingobium with Novosphingobium pentaromativorans and Novosphingobium subarcticum as their nearest phylogenetic neighbors (97.4-97.5% similarity). The isolates had a genomic DNA G+C ratio of 64.5-64.6 mol% and formed a genetically coherent group distinguishable from any established species of the genus Novosphingobium at a DNA-DNA hybridization level of less than 46%. The cellular fatty acids were characterized by the predominance of 18 : 1omega7c with significant proportions of 16 : 0, 16 : 1omega7c, 17 : 1omega6c and 2-OH 14 : 0. Sphingoglycolipids were present. The major respiratory quinone was ubiquinone-10. Spermidine was detected as the major polyamine. The distinct taxonomic position of the isolates within the Novosphingobium was also demonstrated by physiological and biochemical testing. Based on these phylogenetic and phenotypic data, we propose Novosphingobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is strain TUT562(T) (DSM 18518(T), JCM 13951(T), NBRC 102051(T)).

Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium

A Gram-positive, rod- or coccoid-shaped andN-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4Tgrew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4Tis most closely related to members of the genusNocardioides. Strain A2-4Tpossessed chemotaxonomic properties indicative of members of the genusNocardioides; the cell-wall peptidoglycan type was based onll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4Twas 98.3–99.1 % similar to those of the type strains ofNocardioides simplex,Nocardioides aromaticivoransandNocardioides nitrophenolicusand 93.8–96.3 % similar to those of the type strains of otherNocardioidesspecies. Strain A2-4Tcould be distinguished from the three phylogenetic relatives,N. nitrophenolicus,N. aromaticivoransandN. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genusNocardioides, for which the nameNocardioides kongjuensissp. nov. is proposed. The type strain is A2-4T(=KCTC 19054T=JCM 12609T).

Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177

Nocardioides aromaticivorans IC177 is a gram-positive carbazole degrader. The genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. The car genes were clustered into the carAaCBaBbAcAd and carDFE gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme A, respectively. The conserved amino acid motifs proposed to bind the Rieske-type [2Fe-2S] cluster and mononuclear iron, the Rieske-type [2Fe-2S] cluster, and flavin adenine dinucleotide were found in the deduced amino acid sequences of carAa, carAc, and carAd, respectively, which showed similarities with CarAa from Sphingomonas sp. strain KA1 (49% identity), CarAc from Pseudomonas resinovorans CA10 (31% identity), and AhdA4 from Sphingomonas sp. strain P2 (37% identity), respectively. Escherichia coli cells expressing CarAaAcAd exhibited major carbazole 1,9a-dioxygenase (CARDO) activity. These data showed that the IC177 CARDO is classified into class IIB, while gram-negative CARDOs are classified into class III or IIA, indicating that the respective CARDOs have diverse types of electron transfer components and high similarities of the terminal oxygenase. Reverse transcription-PCR (RT-PCR) experiments showed that the carAaCBaBbAcAd and carDFE gene clusters are operonic. The results of quantitative RT-PCR experiments indicated that transcription of both operons is induced by carbazole or its metabolite, whereas anthranilate is not an inducer. Biotransformation analysis showed that the IC177 CARDO exhibits significant activities for naphthalene, carbazole, and dibenzo-p-dioxin but less activity for dibenzofuran and biphenyl.

Validation of publication of new names and new combinations previously effectively published outside the IJSEM

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.