Azospirillum oleiclasticum sp. nov, a nitrogen-fixing and heavy oil degrading bacterium isolated from an oil production mixture of Yumen Oilfield.

Two nitrogen-fixing and heavy oil degrading strains, designated RWY-5-1-1T and ROY-1-1-2, were isolated from an oil production mixture from Yumen Oilfield in China. The 16S rRNA gene sequence showed they belong to Azospirillum and have less than 96.1 % pairwise similarity with each species in this genus. The average nucleotide identity and digital DNA-DNA hybridization values between them and other type strains of Azospirillum species were less than 75.69 % and 22.0 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate RWY-5-1-1T shared 2145 core gene families with other type strains in Azospirillum, and the number of strain-specific gene families was 1623, almost two times more than the number known from other species. Furthermore, genes related to nitrogenase, hydrocarbon degradation and biosurfactant production were found in the isolates' genomes. Also, this strain was capable of reducing acetylene to ethylene at a rate of 22nmol ethylene h-1 (108 cells) and degrading heavy oil at a rate of 36.2 %. The major fatty acids and polar lipids were summed feature 8 (C18:1ω7c/C18:1ω6c), and phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strains RWY-5-1-1T and ROY-1-1-2 represent a novel species, for which the name Azospirillum oleiclasticum sp. nov. is proposed. The type strain is RWY-5-1-1T (=CGMCC 1.13426T =KCTC 72259 T). Azospirillum novel strains with the ability of heavy oil degradation associated with the promotion of plant growth has never been reported to date.

Azospirillum thermophilum sp. nov., isolated from a hot spring.

A novel Gram-staining negative, aerobic, motile by flagellum, rod-shaped bacterium, designated CFH 70021T was isolated from a hot spring soil sample collected from Tengchong, Yunnan province, PR China. Growth of CFH 70021T occurred at 15-50 °C (optimum 50 °C), pH 5.0-7.0 (optimum pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum 0 %, w/v). The genome of CFH 70021T consisted of four complete circular chromosomes and five plasmids, the genomic DNA G+C content was 69.3 mol%. Comparison of the 16S rRNA gene sequences indicated that CFH 70021T represented a member of the genus Azospirillum and showed close relationship with the type strains of Azospirillum agricola CC-HIH038T (97.8 %), Azospirillum rugosum IMMIB AFH-6T (97.6 %), Azospirillum doebereinerae GSF71T (97.6 %), Azospirillum thiophilum DSM 21654T (97.4 %) and Azospirillum picis IMMIB TAR-3T (97.2 %). The polar lipids of CFH 70021T contained diphosphatidylglycerol, phosphatidylmehtylethanolamine, phosphatidylglycerol, phosphatidylcholine, two aminolipids and an unidentified phospholipid. The predominant cellular fatty acids (>10 %) included C19:0cyclo ω8c (11.4 %), C16 : 0 (27.6 %) and summed feature 8 (C18:1ω7c/C18:1ω6c, 40.9 %). The major isoprenoid quinone was Q-10. On the basis of the low ANIb result (<78 %) and different phenotypic and chemotaxonomic characters, we conclude that strain CFH 70021T represents a novel member of the genus Azospirillum, for which the name Azospirillum thermophilum sp. nov. is proposed. The type strain is CFH 70021T (=KCTC 62259T= CCTCC AB2018121T).

Azospirillum palustre sp. nov., a methylotrophic nitrogen-fixing species isolated from raised bog.

Nitrogen-fixing bacterial strain, designated B2T, was isolated from methane-oxidation enrichment originating from a Sphagnum-dominated raised peatland in Tver region, Russia, and its phenotypic, chemotaxonomic and genomic characteristics were investigated. Cells of isolate were Gram-negative, aerobic, rod or spiral-shaped, with motility provided by a single polar flagellum in liquid media and peritrichous flagella on solid media. Strain was able to grow at 15-40 °C, pH 5.5-8.5 and tolerated NaCl to 2.0 % (w/v). Strain B2T gave positive amplification for dinitrogen reductase (nifH gene) and acetylene reduction activity was recorded up to 1250 nmol ethylene h-1 (mg protein)-1. Analysis of 16S rRNA showed that B2T represents a member of the genus Azospirillum and had the highest sequence similarity with A. humicireducens SgZ-5T (97.92 %). The predominant quinone system was ubiquinone Q-10 and the major fatty acids were C18 : 1ω7, C16 : 1ω7 and C16 : 0. The strain was facultative methylotrophic and used methanol and formate for the growth. Genome sequencing revealed a genome size of 8.0 Mbp and a G+C content of 67.8 mol%. The mxaFI genes encoding methanol dehydrogenase were absent, but a homologous xoxF gene was detected. The genes encoding enzymes involved in the biosynthesis of tetrahydromethanopterin (H4MPT) (formaldehyde oxidation) and NAD-linked formate dehydrogenase (fdsABG) were identified. Pairwise determined whole genome average nucleotide identity (gANI) values confirmed that strain B2T represents a novel species, for which we propose the name Azospirillum palustre sp. nov. with the type strain B2T (VKM B-3233T, КСТС 62613Т).

Azospirillum griseum sp. nov., isolated from lakewater.

A novel Gram-stain-negative, strictly aerobic, rod-shaped, gray-pigmented bacterial strain, designated L-25-5 w-1T, was isolated from the water at Baiyang Lake, PR China. Cells of strain L-25-5 w-1T were motile, with a single polar flagellum. L-25-5 w-1T was able to grow at 15-37 °C (optimum 37 °C) and pH 5-8 (optimum pH 6) in R2A medium. 16S rRNA gene sequence analysis and phylogenetic analysis of L-25-5 w-1T showed the highest relationship to Azospirillum doebereinerae GSF71T (97.9 %), Azospirillum thiophilum DSM 21654T (97.9 %) and Azospirillum agricola CC-HIH038T (97.0 %), with other species of the genus Azospirillum showing less than 97 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids; the major cellular fatty acids were C16 : 0, C16 : 0 3-OH, C18 : 1 2-OH, iso-C18 : 0, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.9525 and/or iso-C16 : 1I and/or C14 : 0 3-OH), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c); and the major respiratory quinone was ubiquinone 10. The draft genome size of L-25-5 w-1T was 5.8 Mbp, and the DNA G+C content was 66.6 %. The average nucleotide identity value and digital DNA-DNA hybridization relatedness value between L-25-5 w-1T and related type strains were 80.2 and 24.7 % with A. doebereinerae GSF71T and 78.8 and 23.6 % with A. thiophilum DSM 21654T, respectively. According to the phylogenetic, chemotaxonomic and genotypic properties, strain L-25-5 w-1T represents a novel species in the genus Azospirillum, for which the name Azospirillum griseum sp. nov. is proposed. The type strain is L-25-5 w-1T (=CGMCC 1.13672T=KCTC 62777T).

Azospirillum ramasamyi sp. nov., a novel diazotrophic bacterium isolated from fermented bovine products.

A Gram-stain-negative, rod-shaped, aerobic bacterium, designated M2T2B2T, was isolated from fermented bovine products in Suwon, Republic of Korea. The strain displayed growth at 15-45 °C (optimum, 28-30 °C), pH 6.0-10.0 (pH 7.0) and 0-2 % (w/v) NaCl (0 %). Colonies were light pink-coloured, round and convex. The cells were positive for oxidase and weakly positive for catalase. The major fatty acids in whole cells of strain M2T2B2T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), followed by summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 2 (C12 : 0 aldehyde/unidentified 10.928/C14 : 0 3-OH/iso-C16 : 1 I), C16 : 0, C18 : 1 2-OH, C16 : 0 3-OH and C17 : 1ω6c. The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and three unidentified aminolipids. Ubiquinone 10 was the predominant ubiquinone. The DNA G+C content was 68.0 mol%. The strain could fix atmospheric nitrogen, which was evaluated by the acetylene reduction assay. Further, whole genome sequence analysis revealed the presence of a nif gene cluster. Strain M2T2B2T showed the highest 16S rRNA, rpoD and nifH gene sequence similarity to members of the genus Azospirillum, and showed 97.6 % 16S rRNA gene sequence similarity to Azospirillum oryzae COC8T. The phenotypic, phylogenetic and genomic analyses support the proposal of strain M2T2B2T as being a novel species of the genus Azospirillum, for which the name Azospirillumramasamyi sp. nov. is proposed. The type strain is M2T2B2T (=KACC 14063T=NBRC 106460T).

In vitro PGPR properties and osmotic tolerance of different Azospirillum native strains and their effects on growth of maize under drought stress.

Osmotic variations in the soil can affect bacterial growth diminishing the number of inoculated bacteria. In a scenario of water deficit having tolerant bacteria would be beneficial to achieve a better response of the plant to stress. Thus, selection of more resistant bacteria could be useful to design new inoculants to be used in arid zones. In this sense, a group of Azospirillum isolates deposited in INTA collection was characterized in order to select strains tolerant to osmotic stress. The results obtained demonstrated that Az19 strain has similar in vitro PGPR characteristics to Az39, the most used strain in Argentina for inoculants industries, with the advantage of a better tolerance to osmotic and salt stress. Inoculation of maize plants with this strain resulted in a better response against water deficit compared to Az39 strain, encouraging us to further study the behavior of this strain in greenhouse and field trials in view of developing new inoculants suitable for areas with water deficit.

Azospirillum spp. from native forage grasses in Brazilian Pantanal floodplain: biodiversity and plant growth promotion potential.

A sustainable alternative to improve yield and the nutritive value of forage is the use of plant growth-promoting bacteria (PGPB) that release nutrients, synthesize plant hormones and protect against phytopathogens (among other mechanisms). Azospirillum genus is considered an important PGPB, due to the beneficial effects observed when inoculated in several plants. The aim of this study was to evaluate the diversity of new Azospirillum isolates and select bacteria according to the plant growth promotion ability in three forage species from the Brazilian Pantanal floodplain: Axonopus purpusii, Hymenachne amplexicaulis and Mesosetum chaseae. The identification of bacterial isolates was performed using specific primers for Azospirillum in PCR reactions and partial sequencing of the 16S rRNA and nifH genes. The isolates were evaluated in vitro considering biological nitrogen fixation (BNF) and indole-3-acetic acid (IAA) production. Based on the results of BNF and IAA, selected isolates and two reference strains were tested by inoculation. At 31 days after planting the plant height, shoot dry matter, shoot protein content and root volume were evaluated. All isolates were able to fix nitrogen and produce IAA, with values ranging from 25.86 to 51.26 mg N mL-1 and 107-1038 µmol L-1, respectively. The inoculation of H. amplexicaulis and A. purpusii increased root volume and shoot dry matter. There were positive effects of Azospirillum inoculation on Mesosetum chaseae regarding plant height, shoot dry matter and root volume. Isolates MAY1, MAY3 and MAY12 were considered promising for subsequent inoculation studies in field conditions.

Molecular identification of Azospirillum spp.: Limitations of 16S rRNA and qualities of rpoD as genetic markers.

Since their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been subjected to intensive research due to their biotechnological potential as crop inoculants. Phylogenetic analysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsistencies and low confidence often arise when working with close species. In this work, it was observed that these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list of housekeeping genes, the correlation between pairwise gene and whole-genome similarities was examined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for the PCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 type strains of different species. The sequences obtained were used for inferring a phylogenetic tree of the genus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla isolated from many different locations of Argentine. In addition, several strains that might represent novel species were detected. The results indicate that the sequencing of rpoD is a suitable alternative method for a confident molecular identification in Azospirillum spp.

Genomic insights into metabolic versatility of a lithotrophic sulfur-oxidizing diazotrophic Alphaproteobacterium Azospirillum thiophilum.

Diazotrophic Alphaproteobacteria of the genus Azospirillum are usually organotrophs, although some strains of Azospirillum lipoferum are capable of hydrogen-dependent autotrophic growth. Azospirillum thiophilum strain was isolated from a mineral sulfide spring, a biotope highly unusual for azospirilla. Here, the metabolic pathways utilized by A. thiophilum were revealed based on comprehensive analysis of its genomic organization, together with physiological and biochemical approaches. The A. thiophilum genome contained all the genes encoding the enzymes of carbon metabolism via glycolysis, tricarboxylic acid cycle and glyoxylate cycle. Genes for a complete set of enzymes responsible for autotrophic growth, with an active Calvin-Benson-Bassham cycle, were also revealed, and activity of the key enzymes was determined. Microaerobic chemolithoautotrophic growth of A. thiophilum was detected in the presence of thiosulfate and molecular hydrogen, being in line with the discovery of the genes encoding the two enzymes involved in dissimilatory thiosulfate oxidation, the Sox-complex and thiosulfate dehydrogenase and Ni-Fe hydrogenases. Azospirillum thiophilum utilizes methanol and formate, producing CO2 that can further be metabolized via the Calvin cycle. Finally, it is capable of anaerobic respiration, using tetrathionate as a terminal electron acceptor. Such metabolic versatility is of great importance for adaptation of A. thiophilum to constantly changing physicochemical environment.

Azospirillum agricola sp. nov., a nitrogen-fixing species isolated from cultivated soil.

A polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated CC-HIH038T, isolated from cultivated soil in Taiwan. Cells of strain CC-HIH038T were Gram-stain-negative, facultatively aerobic and spiral-shaped, with motility provided by a single polar flagellum. The 16S rRNA gene sequence analysis of strain CC-HIH038T showed highest sequence similarity to Azospirillum doebereinerae (98.0 %), Azospirillum thiophilum (97.5 %), Azospirillum rugosum (97.4 %) and Azospirillum zeae (97.2 %) and lower sequence similarity ( < 97.0 %) to all other species of the genus Azospirillum. According to DNA-DNA association, the relatedness values of strain CC-HIH038T with A. doebereinerae, A. thiophilum, A. rugosum and A. zeae were 51.8 %, 41.2 %, 56.5 % and 37.5 %, respectively. Strain CC-HIH038T was able to grow at 20-37 °C and pH 7.0-8.0. Strain CC-HIH038T gave positive amplification for dinitrogen reductase (nifH gene); the activity was recorded as 8.4 nmol ethylene h- 1. The predominant quinone system was ubiquinone Q-10 and the DNA G+C content was 68.8 mol%. The major fatty acids found in strain CC-HIH038T were C16 : 0, iso-C18 : 0, C16 : 0 3-OH, C14 : 0 3-OH/iso-C16 : 1 and C18 : 1ω7c/C18 : 1ω6c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-HIH038T is considered to represent a novel species in the genus Azospirillum, for which the name Azospirillum agricola sp. nov. is proposed. The type strain is CC-HIH038T ( = BCRC 80909T = JCM 30827T).

Phytoremediation of Polycyclic Aromatic Hydrocarbons in Soils Artificially Polluted Using Plant-Associated-Endophytic Bacteria and Dactylis glomerata as the Bioremediation Plant.

The reaction of soil microorganisms to the contamination of soil artificially polluted with polycyclic aromatic hydrocarbons (PAHs) was evaluated in pot experiments. The plant used in the tests was cock's foot (Dactylis glomerata). Three different soils artificially contaminated with PAHs were applied in the studies. Three selected PAHs (anthracene, phenanthrene, and pyrene) were used at the doses of 100, 500, and 1000 mg/kg d.m. of soil and diesel fuel at the doses of 100, 500, and 1000 mg/kg d.m. of soil. For evaluation of the synergistic effect of nitrogen fixing bacteria, the following strains were selected: associative Azospirillum spp. and Pseudomonas stutzerii. Additionally, in the bioremediation process, the inoculation of plants with a mixture of the bacterial strains in the amount of 1 ml suspension per 500 g of soil was used. Chamber pot-tests were carried out in controlled conditions during four weeks of plant growth period. The basic physical, microbiological and biochemical properties in contaminated soils were determined. The obtained results showed a statistically important increase in the physical properties of soils polluted with PAHs and diesel fuel compared with the control and also an important decrease in the content of PAHs and heavy metals in soils inoculated with Azospirillum spp. and P. stutzeri after cock's foot grass growth. The bioremediation processes were especially intensive in calcareous rendzina soil artificially polluted with PAHs.

Azospirillum soli sp. nov., a nitrogen-fixing species isolated from agricultural soil.

An aerobic, Gram-stain-negative, rod or spiral-shaped diazotrophic bacterium (designated strain CC-LY788T), was isolated from agricultural soil in Taiwan. Strain CC-LY788T was able to grow at 25-40 °C, pH 6.0-8.0 and tolerated NaCl to 2.0% (w/v). Positive for nitrogen fixation with the activity recorded as 6.5 nmol ethylene h(-1). Strain CC-LY788T showed highest 16S rRNA gene sequence similarity to Azospirillum picis DSM 19922T (97.2%) and Azospirillum rugosum DSM 19657T (97.1%) and lower sequence similarities (<96.6%) to all other species of the genus Azospirillum. According to the DNA-DNA hybridization, the relatedness values of strain CC-LY788T with A. picis DSM 19922T and A. rugosum DSM 19657T were 51.1±5.5% and 46.8±2.1%, respectively. Strain CC-LY788T was positive for the rapid identification of the genus-specific primer set. The respiratory quinone system was ubiquinone (Q-10) and the DNAG+C content was 69.8 mol%. The major fatty acids found in strain CC-LY788T were C16 : 0, C18 : 1 2-OH, C14 : 0 3-OH/C16 : 1 iso I (summed feature 2), C16 : 1ω7c/C16 : 1ω6c (summed feature 3), C18 : 0 ante/C18 : 2ω6,9c (summed feature 5) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8). Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY788T represents a novel species of the genus Azospirillum, for which the name Azospirillum soli sp. nov. is proposed. The type strain is CC-LY788T (=BCRC 80569T=JCM 18820T).

Coexistence and survival of pathogenic leptospires by formation of biofilm with Azospirillum.

Pathogenic Leptospira spp. represent one cause of leptospirosis worldwide and have long been regarded as solitary organisms in soil and aquatic environments. However, in the present study, Leptospira interrogans was observed to be associated with environmental biofilms with 21 bacterial isolates belonging to 10 genera. All 21 isolates were examined for their coaggregation and biofilm-forming ability with leptospires in vitro. Among these, Azospirillum brasilense RMRCPB showed maximum interspecies coaggregation with leptospiral strains (>75%, visual score of +4). Other significant coaggregating isolates belonged to the genera Sphingomonas, Micrococcus, Brevundimonas, Acinetobacter and Paracoccus. Biofilms of leptospires in combination with A. brasilense RMRCPB showed high resistance to penicillin G, ampicillin and tetracycline (minimum bactericidal concentration ≥800 µg/mL) and tolerance to UV radiation and high temperature (up to 49°C). This study hypothesized that biofilm formation with A. brasilense protects the pathogenic Leptospira from adverse environmental conditions/stress. This coexistence of pathogenic Leptospira with other bacteria may be the key factor for its persistence and survival. However, the mechanism of biofilm formation by leptospires needs to be explored to help devise an appropriate control strategy and reduce transmission of leptospires.

Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter.

An aerobic, Gram-stain-negative, spiral or rod-shaped, non-spore-forming, diazotrophic bacterium (strain CC-LY743(T)) was isolated from a fermentative tank in Taiwan. Strain CC-LY743(T) was able to grow at 20-37 °C and pH 6.0-8.0 and tolerated up to 3.0 % (w/v) NaCl. It was positive for nitrogen fixation, with activity of 10.6 nmol ethylene h(-1). 16S rRNA gene sequence analysis of strain CC-LY743(T) showed highest similarity to Azospirillum picis DSM 19922(T) (96.1 %), Azospirillum oryzae JCM 21588(T) (96.0 %) and Azospirillum rugosum DSM 19657(T) (96.0 %) and lower similarity (<96.0 %) to all other Azospirillum species. Highest nifH gene sequence similarities were obtained with Azospirillum brasilense BCRC 12270(T) (92.0 %), Azospirillum formosense BCRC 80273(T) (92.3 %) and A. rugosum DSM 19657(T) (91.8 %). It was positive in the rapid identification by a genus-specific primer set. The predominant quinone system was ubiquinone 10 (Q-10) and the DNA G+C content was 69.6±0.1 mol%. The major fatty acids found in strain CC-LY743(T) were n-C16 : 0, C19 : 0 cyclo ω8c, C14 : 0 3-OH/C16 : 1 iso I, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY743(T) is considered to represent a novel species within the genus Azospirillum for which the name Azospirillum fermentarium sp. nov. is proposed. The type strain is CC-LY743(T) ( = BCRC 80505(T) = JCM 18688(T) = LMG 27264(T)).

Comparison of prominent Azospirillum strains in Azospirillum-Pseudomonas-Glomus consortia for promotion of maize growth.

Azospirillum are prominent plant growth-promoting rhizobacteria (PGPR) extensively used as phytostimulatory crop inoculants, but only few studies are dealing with Azospirillum-containing mixed inocula involving more than two microorganisms. We compared here three prominent Azospirillum strains as part of three-component consortia including also the PGPR Pseudomonas fluorescens F113 and a mycorrhizal inoculant mix composed of three Glomus strains. Inoculant colonization of maize was assessed by quantitative PCR, transcription of auxin synthesis gene ipdC (involved in phytostimulation) in Azospirillum by RT-PCR, and effects on maize by secondary metabolic profiling and shoot biomass measurements. Results showed that phytostimulation by all the three-component consortia was comparable, despite contrasted survival of the Azospirillum strains and different secondary metabolic responses of maize to inoculation. Unexpectedly, the presence of Azospirillum in the inoculum resulted in lower phytostimulation in comparison with the Pseudomonas-Glomus two-component consortium, but this effect was transient. Azospirillum's ipdC gene was transcribed in all treatments, especially with three-component consortia, but not with all plants and samplings. Inoculation had no negative impact on the prevalence of mycorrhizal taxa in roots. In conclusion, this study brought new insights in the functioning of microbial consortia and showed that Azospirillum-Pseudomonas-Glomus three-component inoculants may be useful in environmental biotechnology for maize growth promotion.

Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell.

A Gram-negative, facultative anaerobic, motile, spiral, straight-to-slightly curved rod-shaped and nitrogen-fixing strain, designated SgZ-5(T), was isolated from a microbial fuel cell (MFC) and was characterized by means of a polyphasic approach. Growth occurred with 0-1 % (w/v) NaCl (optimum 1 %) and at pH 5.5-8.5 (optimum pH 7.2) and at 25-37 °C (optimum 30 °C) in nutrient broth (NB). The strain had the ability to grow under anaerobic conditions via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS). Chemotaxonomic characteristics (main ubiquinone Q-10, major fatty acid C18 : 1ω7c/C18 : 1ω6c and DNA G+C content 67.7 mol%) were similar to those of members of the genus Azospirillum. According to the results of phylogenetic analyses, strain SgZ-5(T) belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria, and was related most closely to the type strains of Azospirillum lipoferum, Azospirillum thiophilum and Azospirillum oryzae (98.0, 97.6 and 97.1 % 16S rRNA gene sequence similarity, respectively). DNA-DNA pairing studies showed that the unidentified organism displayed reassociation values of 36.7 ± 3.7, 24.1 ± 2.2 and 22.3 ± 2.4 % to the type strains of A. lipoferum, A. thiophilum and A. oryzae, respectively. Similarities between nifH gene sequences of strain SgZ-5(T) and members of the genus Azospirillum ranged from 94.0 to 97.0 %. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SgZ-5(T) represents a novel species, for which the name Azospirillum humicireducens sp. nov. is proposed. The type strain is SgZ-5(T) ( = CCTCC AB 2012021(T) = KACC 16605(T)).

A rapid and simple PCR method for identifying isolates of the genus Azospirillum within populations of rhizosphere bacteria.

AIMS: To develop a rapid and simple genus-specific polymerase chain reaction (PCR) method for detecting and identifying isolates of the genus Azospirillum which is well-recognized as plant growth-promoting rhizobacterium. METHODS AND RESULTS: Nine pairs of PCR primers were designed based on the Azospirillum 16S rRNA, ipdC, nifA and nifH genes to assess their genus specificity by testing against 12 Azospirillum (from seven species) and 15 non-Azospirillum reference strains, as compared with the fAZO/rAZO pair reported by Baudoin et al. (J Appl Microbiol, 108, 2010, 25). Among the primer pairs assessed, the Az16S-A pair designed on the 16S rRNA gene sequence showed the highest genus specificity: it successfully yielded a single amplicon of the expected size in all the 12 Azospirillum strains and for a close relative, Rhodocista centenaria. The PCR with the Az16S-A primers generated a detectable amount of the amplicon from ≥10³ CFU ml⁻¹ of Azospirillum cell suspensions even in the presence of contaminants and accurately discriminated Azospirillum and non-Azospirillum species in both 35 Azospirillum-like and 70 unknown isolates from plant roots and rhizosphere soils. CONCLUSIONS: We developed a rapid and simple PCR method for detecting and identifying Azospirillum isolates within populations of rhizosphere bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: The method developed would serve as a useful tool for isolating a variety of indigenous Azospirillum bacteria from agricultural samples.

Identification and isolation of active N2O reducers in rice paddy soil.

Dissolved N(2)O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N(2)O is emitted to the atmosphere above these fields. This indicates the occurrence of N(2)O reduction in rice paddy fields; however, identity of the N(2)O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N(2)O reducers in rice paddy soil. In a soil microcosm, N(2)O and succinate were added as the electron acceptor and donor, respectively, for N(2)O reduction. For the stable isotope probing (SIP) experiment, (13)C-labeled succinate was used to identify succinate-assimilating microbes under N(2)O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N(2)O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N(2)O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N(2)O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N(2)O-reducing conditions, in contrast to the control sample (soil incubated with only (13)C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N(2)O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N(2)O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N(2)O reduction in rice paddy soils.

Rapid detection and identification of the free-living nitrogen fixing genus Azospirillum by 16S rRNA-gene-targeted genus-specific primers.

The modern agricultural practice utilizing plant growth promoting rhizobacteria (PGPR) has brought great benefits in the promotion of crop growth. Among PGPR, Azospirillum is considered as an important genus which is not only closely-associated with plants but also shows potential in the degradation of organic contaminants. However, lack of media for selective isolation or techniques for specific detection or identification limit the exploration of these rhizobacteria. This motivated us to design a genus-specific oligonucleotide primer pair which could assist in rapid detection of species of the genus Azospirillum by means of PCR-specific amplification. The sensitivity and specificity of the newly designed primer pair Azo494-F/Azo756-R were tested against 12 Azospirillum type strains and other closely-related genera. The Azospirillum-specific 16S rRNA gene fragment (263 bp) was successfully amplified for all the reference Azospirillum species with the designed primer pair. No amplification was noted for closely-related species from other genera. The genus specificity was validated with 18 strains including environmental isolates. Interestingly, two strains assigned earlier as Azospirillum amazonense (DSM 2787(T)) and Azospirillum irakense (DSM 11586(T)) failed to produce an Azospirillum-specific fragment with this primer pair. Further phylogenetic analysis of these two isolates based on 16S rRNA gene sequences shows that these two strains might belong to other genera rather than Azospirillum. Preliminary screening of isolates and soil samples with the Azospirillum-specific primers was successful in terms of the rapid detection of Azospirillum isolates. By using real-time PCR analysis the minimum limit of Azospirillum detection was 10(2) CFU g(-1) in the seeded soil sample. The newly designed primers can be used to study the diversity of Azospirillum in ecosystems and aid in the exploration of novel species.

Isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences.

Oligotrophic denitrifying bacteria, including those belonging to the genera Herbaspirillum, Azospirillum, and Bradyrhizobium, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N(2)O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identified Bradyrhizobium strains that harbor nirS sequences previously detected only in culture-independent studies.