Multifarious characteristics of sulfur-oxidizing bacteria residing in rice rhizosphere

Sulfur-oxidizing bacteria (SOB) are versatile microorganisms known for their ability to oxidize various reduced sulfur compounds, namely, elemental sulfur (S0), hydrogen sulfide (H2S), tetrathionate (S4O62-), and trithionate (S3O62-) to sulfate (SO42-). In this study, out of twelve SOB isolates from rice rhizosphere, five were screened based on their sulfur oxidation potential, viz., SOB1, SOB2, SOB3, SOB4, and SOB5, and were identified as Ochrobactrum soli SOB1, Achromobacter xylosoxidans SOB2, Stenotrophomonas maltophilia SOB3, Brucella tritici SOB4, and Stenotrophomonas pavanii SOB5, respectively. All the isolates displayed chemolithotrophic nutritional mode by consuming thiosulfate and accumulating trithionate and tetrathionate in the growth medium which is ultimately oxidized to sulfate. The strains were authenticated with the production of thiosulfate oxidizing enzymes such as rhodanese and sulfite oxidase. Despite their tendency to oxidize reduced sulfur compounds, B. tritici SOB4 and S. pavanii SOB5 were also found to possess phosphate and zinc solubilization potential, acetic acid, and indole acetic acid (IAA) production and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The presence of sulfanyl (R-SH) groups was noticed in the A. xylosoxidans SOB2. Elemental sulfur conversion into sulfate was noted in the S. maltophilia SOB3, and hydrogen sulfide conversion into sulfate was observed in the Ochromobacter soli SOB1. Sulfur oxidation potential coupled with beneficial properties of the isolates widen the knowledge on SOB.

Gamma-induced mutants of Bacillus and Streptomyces display enhanced antagonistic activities and suppression of the root rot and wilt diseases in pulses

This study aims to increase Bacillus and Streptomyces antagonistic activity against the root rot and wilt diseases of pulses caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. udum, respectively. To increase antagonistic action, Bacillus subtilis BRBac4, Bacillus siamensis BRBac21, and Streptomyces cavourensis BRAcB10 were subjected to random mutagenesis using varying doses of gamma irradiation (0.5–3.0 kGy). Following the irradiation, 250 bacterial colonies were chosen at random for each antagonistic strain and their effects against pathogens were evaluated in a plate assay. The ERIC, BOX, and random amplified polymorphic studies demonstrated a clear distinction between mutant and wild-type strains. When mutants were compared to wild-type strains, they showed improved plant growth-promoting characteristics and hydrolytic enzyme activity. The disease suppression potential of the selected mutants, B. subtilis BRBac4-M6, B. siamensisi BRBac21-M10, and S. cavourensis BRAcB10-M2, was tested in green gram, black gram, and red gram. The combined inoculation of B. siamensis BRBac21-M10 and S. cavourensis BRAcB10-M2 reduced the incidence of root rot and wilt disease. The same treatment also increased the activity of the defensive enzymes peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase. These findings suggested that gamma-induced mutation can be exploited effectively to improve the biocontrol characteristics of Bacillus and Streptomyces. Following the field testing, a combined bio-formulation of these two bacteria may be utilised to address wilt and root-rot pathogens in pulses.

Functional characterization of cultivable gut bacterial communities associated with rugose spiralling whitefly, Aleurodicus rugioperculatus Martin

Gut symbiotic bacteria provide protection and nutrition to the host insect. A high reproductive rate and dispersal ability of the rugose spiralling whitefly help this polyphagous species to develop and thrive on many horticultural crops. In this study, we isolated the cultivable gut bacteria associated with rugose spiralling whitefly and demonstrated their role in the host insect. We also studied the influence of antibiotics on the rugose spiralling whitefly oviposition. A total of 70 gut bacteria were isolated from the second nymphal stage of rugose spiralling whitefly reared on coconut, banana, and sapota using seven growth media. From the 70 isolates, chitinase, siderophore (51), protease (44), and Glutathione-S-Transferase producers (16) were recorded. The activities of chitinase, siderophore, protease, and Glutathione-S-Transferase in the gut bacterial isolates of rugose spiralling whitefly ranged from 0.07 to 3.96 µmol^-1 min^-1 mL^-1, 10.01 to 76.93%, 2.10 to 83.40%, and 5.21 to 24.48 nmol^-1 min^-1 mL^-1 μg^-1 protein, respectively. The16S rRNA gene sequence analysis revealed that bacterial genera associated with the gut of rugose spiralling whitefly included Bacillus, Exiguobacterium, Acinetobacter, Lysinibacillus, Arthrobacter, and Pseudomonas. Based on the susceptibility of the gut bacteria to antibiotics, 11antibiotic treatments were administered to the host plant leaves infested with the nymphal stages. The antibiotics were evaluated for their effect on rugose spiralling whitefly oviposition. Among the antibiotic treatments, carbenicillin (100 µg mL^-1) + ciprofloxacin (5 µg mL^-1) significantly reduced the oviposition (13 eggs spiral^-1) and egg hatchability (61.54%) of rugose spiralling whitefly. Disruption of chitinase, siderophore, protease, and detoxification enzyme producers and elimination of these symbionts through antibiotics altered the host insect physiology and indirectly affected whitefly oviposition. In conclusion, gut bacteria-based management strategies might be used as insecticides for the effective control of whiteflies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03081-3.

Diversity and functional characterization of endophytic Methylobacterium isolated from banana cultivars of South India and its impact on early growth of tissue culture banana plantlets

AIMS

This study aimed at determining the distribution, colonization and growth promoting nature of Methylobacterium spp. in tissue culture banana plantlets.

METHODS AND RESULTS

Leaf samples from different field grown banana cultivars were used for Methylobacterium spp., isolation. Metabolic profile and functional characterization for plant growth-promoting traits of the isolates were assessed. The isolates were confirmed using 16S rRNA gene sequencing analysis, which resulted in six distinct species of Methylobacterium namely M. radiotolerans, M. salsuginis, M. thiocyanatum, M. rhodesianum, M. rhodinum and M. populi. Methylobacterium spp. inoculation experiment was conducted under hydroponic system in tissue culture banana plantlets (germ free) with eight selected isolates. A significant increase in growth parameters of Methylobacterium treated plantlets compared to uninoculated control was observed. Methylobacterium salsuginis TNMB03-gfp29 was developed and colonization micrograph was obtained using confocal laser scanning microscopy (CLSM) and scanning electron microscopy in different parts of banana plantlets (root, stem and leaves).

CONCLUSION

Field grown banana plants found to harbour diverse endophytic Methylobacterium population. Our finding suggests that endophytic Methylobacterium species may provide significant plant growth promoting compounds/nutrients to the banana plants. The experimental results demonstrated the efficacy of Methylobacterium spp. as a potential bioinoculant and can be exploited as a phyllosphere and rhizosphere based bioinoculant for the initial establishment and growth of tissue culture banana plantlets.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study extended our knowledge on the distribution of Methylobacterium spp. in banana plants and endophytic colonization nature of this particular genus in plants. In addition, efficient isolate (M. salsuginis TNMB03) identified in this study may be promoted as bio-inoculants for banana plants after field evaluation.

Endomicrobial Community Profiles of Two Different Mealybugs: Paracoccus marginatus and Ferrisia virgata

Mealybugs (Hemiptera: Coccomorpha: Pseudococcidae) harbour diverse microbial symbionts that play essential roles in host physiology, ecology, and evolution. In this study we aimed to reveal microbial communities associated with two different mealybugs, papaya mealybug (Paracoccus marginatus) and two-tailed mealybug (Ferrisia virgata) collected from the same host plant. Comparative analysis of microbial communities associated with these mealybugs revealed differences that appear to stem from phylogenetic associations and different nutritional requirements. This first report on both bacterial and fungal communities associated with these mealybugs provides a preliminary insight on factors affecting the endomicrobial communities. .

Metagenomic sequencing reveals altered bacterial abundance during coral-sponge interaction: Insights into the invasive process of coral-killing sponge Terpios hoshinota

The coral-killing invasive sponge, Terpios hoshinota, causes extensive mortality to live corals and is a potential threat to reefs at different geographical locations. However, to date, the invasive mechanism remains largely unknown. In this study, we aimed to understand the bacterial competition between sponge and coral hosted bacteria when sponge outcompetes corals. We analysed the bacterial community of Terpios-invaded coral tissue, and the adjacent healthy tissue of sponge-invaded Favites colonies from Palk bay reef (South East Asia) of the Indian Ocean by using next-generation sequencing. Comparative analysis revealed similar bacterial diversity in both healthy and sponge covered coral tissues. However, relative abundance found to be differed between the groups. Terpios covered coral tissue had higher bacterial abundance than the healthy coral tissue. Bacterial phyla such as Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia live both in sponge covered and healthy coral tissue. Notably, many of the lower abundant bacteria in healthy coral tissue (abundance <1%) became the most abundant in sponge-invaded tissue. In particular, the genus Neisseria, Bacteroides, and members of Pseudoalteromonas predominant in sponge-invaded tissue. Similar bacterial diversity between normal and and sponge-invaded coral tissues suggest that bacteria follow an exploitative competition, which might favoured sponge growth over corals.

Spatial Physiochemical and Metagenomic Analysis of Desert Environment

Investigating the bacterial diversity and their metabolic capabilities are crucial for interpreting ecological patterns in desert environment, and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physico-chemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrates a desert environment (Thar Desert, India) which face hot arid climate with very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrates. Microbial diversity of the two quadrates was studied using Illumina bar coded sequencing by targeting V3-V4 regions of 16S rDNA. As the results, 702504 high-quality sequence reads, assigned to 173 operationaltaxonomic units (OTUs) at species level. The most abundant phyla in both quadrates were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiellarepresented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrates, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physico-chemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrates, and patchy nature in local scale. Interestingly, abundance ofthe biotechnologically important phylum Actinobacteria, with large proposition of unclassified speciesin the desert suggested that this arid environment is the promising site for bioprospection.

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion

This study aimed at documenting the culturable methylotrophic bacterial diversity across different groundnut genotypes and evaluating their effect on the growth of groundnut. 80 methylotrophic bacterial isolates were obtained from the phyllosphere of 15 groundnut genotypes collected from Tamil Nadu, India. The bacterial isolates were identified through sequencing of the 16S rDNA and were tested for their plant growth-promoting properties. Groundnut seeds were inoculated with methylotrophic bacteria and their effect on growth was evaluated via in vitro and pot experiments. Molecular identification revealed that the isolates belonged to 30 different species. A higher diversity of methylotrophic bacteria at genus and species level was found in groundnut genotype TMV2. Shannon diversity index was the highest in genotype TMV7, followed by VRI2 and TMV2. Similarly, geographical location also influenced the diversity of methylotrophic bacteria. In vitro seed germination assay revealed that methylotrophic isolates enhanced root growth and improved formation of root hair. The radicle length of treated seeds ranged from 2.7 to 8.4 cm. A higher shoot length was observed in the plants from seeds treated with Methylobacterium radiotolerans VRI8-A4 (27.3 cm), followed by Pseudomonas psychrotolerans TMV13-A1 (26.3 cm) and Bacillus aryabhattai K-CO3-3 (23 cm). The findings of this study strongly suggest that beneficial methylotrophic bacteria associated with the phyllosphere of groundnut play a major role in regulating plant growth.

Biosynthetic Potential of Bioactive Streptomycetes Isolated From Arid Region of the Thar Desert, Rajasthan (India)

Acquisition of Actinobacteria, especially Streptomyces from previously underexplored habitats and the exploration of their biosynthetic potential have gained much attention in the rejuvenated antibiotics search programs. Herein, we isolated some Streptomyces strains, from an arid region of the Great Indian Thar Desert, which possess an ability to produce novel bioactive compounds. Twenty-one morphologically distinctive strains differing in their aerial and substrate mycelium were isolated by employing a stamping method. Among them, 12 strains were identified by a two-level antimicrobial screening method, exerting antimicrobial effects against a panel of indicator strains including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus species. Based on their potent antimicrobial activity, four isolates were further explored by 16S rRNA gene-based identification, genetic screening, and metabolomic analysis; and it was found that these strains belong to the genus Streptomyces. The selected strains were found to have polyketide synthase and non-ribosomal peptide synthetase systems. In addition, extracellular metabolomic screening revealed that the isolates produced analogs of doxorubicinol, pyrromycin, erythromycin, and 6-13 other putative novel metabolites. These results demonstrate the significance of Streptomyces inhabiting the arid region of Thar Desert, suggesting that similar arid environments can be considered as the reservoirs of novel Streptomyces strains that could have biotechnological significance.

Exploration of Rice Husk Compost as an Alternate Organic Manure to Enhance the Productivity of Blackgram in Typic Haplustalf and Typic Rhodustalf

The present study was aimed at using cellulolytic bacterium Enhydrobacter and fungi Aspergillus sp. for preparing compost from rice husk (RH). Further, the prepared compost was tested for their effect on blackgram growth promotion along with different levels of recommended dose of fertilizer (RDF) in black soil (typic Haplustalf) and red soil (typic Rhodustalf) soil. The results revealed that, inoculation with lignocellulolytic fungus (LCF) Aspergillus sp. @ 2% was considered as the most efficient method of composting within a short period. Characterization of composted rice husk (CRH) was examined through scanning electron microscope (SEM) for identifying significant structural changes. At the end of composting, N, P and K content increased with decrease in CO₂ evolution, C:N and C:P ratios. In comparison to inorganic fertilization, an increase in grain yield of 16% in typic Haplustalf and 17% in typic Rhodustalf soil over 100% RDF was obtained from the integrated application of CRH@ 5 t ha⁻¹ with 50% RDF and biofertilizers. The crude protein content was maximum with the combined application of CRH, 50% RDF and biofertilizers of 20% and 21% in typic Haplustalf and typic Rhodustalf soils, respectively. Nutrient rich CRH has proved its efficiency on crop growth and soil fertility.

Erratum to: Isolation, Characterization, and Use for Plant Growth Promotion Under Salt Stress, of ACC Deaminase-Producing Halotolerant Bacteria Derived from Coastal Soil

This erratum is being published to correct the error in the name of the strain in the paper by Siddikee et al. The name of the strain B. iodinum should be corrected as B. linens in title 'Isolation, Characterization, and Use for Plant Growth Promotion Under Salt Stress, of ACC Deaminase-Producing Halotolerant Bacteria Derived from Coastal Soil'.

Beneficial Soil Bacterium Pseudomonas frederiksbergensis OS261 Augments Salt Tolerance and Promotes Red Pepper Plant Growth

Soil salinity, being a part of natural ecosystems, is an increasing problem in agricultural soils throughout the world. Pseudomonas frederiksbergensis OS261 has already been proved to be an effective bio-inoculant for enhancing cold stress tolerance in plants, however, its effect on salt stress tolerance is unknown. The main aim of the present study was to elucidate P. frederiksbergensis OS261 mediated salt stress tolerance in red pepper. The plants were exposed to a salt stress using NaCl at the concentrations of 50, 100, and 150 mM after 12 days of transplantation, while plant growth and enzyme activity were estimated 50 days after sowing. The height in P. frederiksbergensis OS261 inoculated plants was significantly increased by 19.05, 34.35, 57.25, and 61.07% compared to un-inoculated controls at 0, 50, 100, and 150 mM of NaCl concentrations, respectively, under greenhouse conditions. The dry biomass of the plants increased by 31.97, 37.47, 62.67, and 67.84% under 0, 50, 100, and 150 mM of NaCl concentrations, respectively. A high emission of ethylene was observed in un-inoculated red pepper plants under salinity stress. P. frederiksbergensis OS261 inoculation significantly reduced ethylene emission by 20.03, 18.01, and 20.07% at 50, 100, and 150 mM of NaCl concentrations, respectively. Furthermore, the activity of antioxidant enzymes (ascorbate peroxidase, superoxide dismutase, and catalase) also varied in the inoculated red pepper plants. Salt stress resistance in the bacterized plants was evident from the improved antioxidant activity in leaf tissues and the decreased hydrogen ion concentration. Thus, we conclude that P. frederiksbergensis OS261 possesses stress mitigating property which can enhance plant growth under high soil salinity by reducing the emission of ethylene and regulating antioxidant enzymes.

Control of Wilt and Rot Pathogens of Tomato by Antagonistic Pink Pigmented Facultative Methylotrophic Delftia lacustris and Bacillus spp

The studies on the biocontrol potential of pink pigmented facultative methylotrophic (PPFM) bacteria other than the genus Methylobacterium are scarce. In the present study, we report three facultative methylotrophic isolates; PPO-1, PPT-1, and PPB-1, respectively, identified as Delftia lacustris, Bacillus subtilis, and Bacillus cereus by 16S rRNA gene sequence analysis. Hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicates that the isolates PPO-1, PPT-1, and PPB-1 are not pathogenic strains. Under in vitro conditions, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 showed direct antagonistic effect by inhibiting the mycelial growth of fungal pathogens; Fusarium oxysporum f. sp. lycopersici (2.15, 2.05, and 1.95 cm), Sclerotium rolfsii (2.14, 2.04, and 1.94 cm), Pythium ultimum (2.12, 2.02, and 1.92 cm), and Rhizoctonia solani (2.18, 2.08, and 1.98 cm) and also produced volatile inhibitory compounds. Under plant growth chamber condition methylotrophic bacterial isolates; D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 significantly reduced the disease incidence of tomato. Under greenhouse condition, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 inoculated tomato plants, when challenged with F. oxysporum f. sp. lycopersici, S. rolfsii, P. ultimum, and R. solani, increased the pathogenesis related proteins (β-1,3-glucanase and chitinase) and defense enzymes (phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, and catalase) on day 5 after inoculation. In the current study, we first report the facultative methylotrophy in pink pigmented D. lacustris, B. subtilis, and B. cereus and their antagonistic potential against fungal pathogens. Direct antagonistic and ISR effects of these isolates against fungal pathogens of tomato evidenced their possible use as a biocontrol agent.

Optimization of cellulase production by Enhydrobacter sp. ACCA2 and its application in biomass saccharification

Cellulase finds use in saccharification of lignocellulosic agroresidues to fermentable sugars which can be used for production of commercially important metabolites. This study reports endoglucanase (CMCase) production by Enhydrobacter sp. ACCA2. The CMCase activity of the strain ACCA2 was successively improved by optimization of range of physical and nutritional parameter in a set of non-statistical and statistical experiments. Initial non-statistical selection of carbon source, incubation time, temperature and pH resulted in 1.07 fold increase of CMCase activity. In a subsequent statistical method, response surface methodology, optimization of medium components such as carboxymethylcellulose, peptone, NaCl, MgSO4, K2HPO4, and (NH4)2SO4 yielded further increase up to 2.39 fold CMCase activity. The cellulolytic potential was evaluated in biomass saccharification with different plant materials and the results revealed that the enzyme produced by strain may have significant commercial values for industrial saccharification process. Moreover, this is the first report of cellulase production by an Enhydrobacter spp.

Evaluation of Bacillus spp. as dough starters for Adhirasam - A traditional rice based fermented food of Southern India

Adhirasam is a cereal based, doughnut shaped, deep fried dessert consumed in the southern regions of India. The dough used to prepare adhirasam is fermented and contains rice flour and jaggery. The aim of the present study was to characterize the cultivable bacteria associated with this fermented dough and to identify a suitable starter culture for the production of quality adhirasam. In total, one hundred and seventy bacterial isolates were recovered from de Man Rogosa Sharp (MRS) agar, nutrient agar, lysogeny agar and tryptic soy agar media. Out of the 170 bacterial isolates, sixteen isolates were selected based on their ability to tolerate glucose and sucrose. All the bacterial isolates tolerated 15% glucose and 30% sucrose. Analyses of 16S rDNA gene sequences of the bacterial isolates showed that the dominant cultivable bacteria were members of the genus Bacillus. These strains were further used as starters and tested for their ability to ferment rice flour with jaggery to produce adhirasam dough. Organoleptic evaluation was carried out to choose the best starter strain. Adhirasam prepared from Bacillus subtilis isolates S4-P11, S2-G2-A1 and S1-G15, Bacillus tequilensis isolates S2-H16, S3-P9, S3-G10 and Bacillus siamensis isolate S2-G13 were highly acceptable to consumers. Adhirasam prepared using these starter cultures had superior product characteristics such as softness in texture, flavor and enhanced aroma and sweet taste.

Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil

A bacterial strain, designated JS5-2(T), was isolated from soil collected from Jeju Island, Republic of Korea. The cells of the strain were Gram-negative, nonspore forming, catalase- and oxidase-positive, aerobic, nonmotile and rod-shaped. Strain JS5-2(T) exhibited 96.2-97.2, 95.1-96.3, and 95.4-95.8% 16S rRNA gene sequence similarities to the genera Herbaspirillum, Oxalicibacterium, and Herminiimonas, respectively. The highest sequence similarities were with Herbaspirillum autotrophicum IAM 14942(T) (97.2%) and Herbaspirillum frisingense GSF30(T) (97.1%). The major fatty acids of strain JS5-2(T) were C16:0 (35.0%), C17:0 cyclo (19.9%), C18:1 ω7c (11.4%), and summed feature 3 (C16:1 ω7c/C15:0 iso 2-OH) (15.2%), and the major polar lipids of strain JS5-2(T) were diphosphatidylglycerol and an unknown aminophospholipid. The strain contained Q-8 as the predominant ubiquinone. DNA-DNA relatedness values between strain JS5-2(T) and H. autotrophicum IAM 14942(T), and H. frisingense GSF30(T) were 32 and 35%, respectively. The DNA G+C content of strain JS5-2(T) was 59.0 mol%. On the basis of phenotypic, genotypic, and physiological evidence, strain JS5-2(T) represents a novel species of a new genus, for which the name Paraherbaspirillum soli gen. nov., sp. nov. is proposed. The type strain JS5-2(T) (=KACC 12633(T) =NBRC 106496(T)) is proposed.

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field

A bacterial strain, designated GR24-5(T), was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5(T) could be assigned to the family Alcaligenaceae. Strain GR24-5(T) showed the highest sequence similarities with Parapusillimonas granuli Ch07(T) (97.1%), Pusillimonas noertemannii BN9(T) (96.9%), Pigmentiphaga kullae DSM 13608(T) (96.5%), and Castellaniella defragrans 54Pin(T) (96.3%). Strain GR24-5(T) demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07(T). The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C(16:0), C(17:0) cyclo, and summed feature 1 (C(14:0) 3-OH/iso-C(16:1) I/C(12:0) aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5(T) were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245(T) represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5(T) (=KACC 13888 =DSM 24591(T)).

Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil

In total, 140 halotolerant bacterial strains were isolated from both the soil of barren fields and the rhizosphere of six naturally growing halophytic plants in the vicinity of the Yellow Sea, near the city of Incheon in the Republic of Korea. All of these strains were characterized for multiple plant growth promoting traits, such as the production of indole acetic acid (IAA), nitrogen fixation, phosphorus (P) and zinc (Zn) solubilization, thiosulfate (S2O3) oxidation, the production of ammonia (NH3), and the production of extracellular hydrolytic enzymes such as protease, chitinase, pectinase, cellulase, and lipase under in vitro conditions. From the original 140 strains tested, on the basis of the latter tests for plant growth promotional activity, 36 were selected for further examination. These 36 halotolerant bacterial strains were then tested for 1- aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Twenty-five of these were found to be positive, and to be exhibiting significantly varying levels of activity. 16S rRNA gene sequencing analyses of the 36 halotolerant strains showed that they belong to 10 different bacterial genera: Bacillus, Brevibacterium, Planococcus, Zhihengliuella, Halomonas, Exiguobacterium, Oceanimonas, Corynebacterium, Arthrobacter, and Micrococcus. Inoculation of the 14 halotolerant bacterial strains to ameliorate salt stress (150 mM NaCl) in canola plants produced an increase in root length of between 5.2% and 47.8%, and dry weight of between 16.2% and 43%, in comparison with the uninoculated positive controls. In particular, three of the bacteria, Brevibacterium epidermidis RS15, Micrococcus yunnanensis RS222, and Bacillus aryabhattai RS341, all showed more than 40% increase in root elongation and dry weight when compared with uninoculated saltstressed canola seedlings. These results indicate that certain halotolerant bacteria, isolated from coastal soils, have a real potential to enhance plant growth under saline stress, through the reduction of ethylene production via ACC deaminase activity.

Rhodocytophaga aerolata gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from air

A strictly aerobic, Gram-staining-negative, oxidase- and catalase-positive, non-motile, rod-shaped bacterium, designated strain 5416T-29T, was isolated from air and was characterized by using a polyphasic approach. Colonies were reddish pink and circular with entire margins. Flexirubin-type pigments were absent. The strain formed a distinct phylogenetic lineage within the family Cytophagaceae of the phylum Bacteroidetes. Strain 5416T-29T did not show more than 88 % 16S rRNA gene sequence similarity to the type strain of any recognized species. The major cellular fatty acids were C16 : 1 ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. The polar lipids were phosphatidylethanolamine, one unknown amino lipid and several unknown polar lipids. Menaquinone-7 (MK-7) was the major respiratory quinone. The G+C content of the DNA of strain 5416T-29T was 45.5 mol%. Results of phenotypic and phylogenetic analyses clearly indicate that strain 5416T-29T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhodocytophaga aerolata gen. nov., sp. nov. is proposed. The type strain of Rhodocytophaga aerolata is 5416T-29T (=KACC 12507T =DSM 22190T).

Tsukamurella soli sp. nov., isolated from soil

A Gram-positive, rod-shaped, catalase-positive, oxidase-negative, white-coloured bacterium, designated strain JS18-1T, was isolated from a soil sample collected from Halla mountain, Jeju island, Korea. 16S rRNA gene sequence analysis revealed that the strain was most closely related to members of the genus Tsukamurella with levels of sequence similarity of 95.4–96.5 %. Strain JS18-1T shared highest 16S rRNA gene sequence similarity with Tsukamurella strandjordii DSM 44573T (96.5 %), Tsukamurella carboxydivorans Y2T (96.4 %) and Tsukamurella tyrosinosolvens DSM 44234T (96.4 %). The G+C content of the total DNA of strain JS18-1T was 70 mol%. The cell-wall peptidoglycan type was A1γ and mycolic acids were also detected. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major quinone was menaquinone-9 (MK-9) and major cell-wall sugars were arabinose, ribose and glucose. The major fatty acids (>10 % of the total fatty acids) were C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic, biochemical and physiological characteristics indicate that strain JS18-1T represents a novel species of the genus Tsukamurella, for which the name Tsukamurella soli sp. nov. is proposed. The type strain is JS18-1T (=KACC 20764T=DSM 45046T).

Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.)

A Gram-negative, aerobic, motile, rod-shaped, thiosulfate-oxidizing bacterium, designated ATSB10(T), was isolated from rhizosphere soil of sunflower (Helianthus annuus L.). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ATSB10(T) was closely related to members of the genera Dyella (96.4-98.1 % 16S rRNA gene sequence similarity) and Luteibacter (96.4-97.0 %) and Fulvimonas soli LMG 19981(T) (96.7 %) and Frateuria aurantia IFO 3245(T) (97.8 %). The predominant fatty acids were iso-C(16 : 0), iso-C(17 : 1)ω9c and iso-C(15 : 0). The major quinone was Q-8. The G+C content of the genomic DNA was 66.0 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unknown phospholipid, unknown aminophospholipids and an unknown aminolipid. On the basis of phenotypic properties, phylogenetic distinctiveness and DNA-DNA relatedness, strain ATSB10(T) represents a novel species in the genus Dyella, for which the name Dyella thiooxydans sp. nov. is proposed. The type strain is ATSB10(T) (=KACC 12756(T) =LMG 24673(T)).

Cohnella yongneupensis sp. nov. and Cohnella ginsengisoli sp. nov., isolated from two different soils

Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14T and GR21-5T, were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14T and GR21-5T was 95.9 %. Strains 5YN10-14T and GR21-5T showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242T, 94.6 and 94.4 % to Cohnella hongkongensis HKU3T, 94.7 and 94.7 % to Cohnella laeviribosi RI-39T, and 95.4 and 94.8 % to Cohnella phaseoli GSPC1T. The major fatty acids of strain 5YN10-14T were anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (18.5 %) and C16 : 0 (13.2 %), and the major fatty acids of strain GR21-5T were anteiso-C15 : 0 (48.9 %), iso-C16 : 0 (15.0 %) and iso-C15 : 0 (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14T also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5T had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14T and GR21-5T were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella, for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14T=KACC 11768T=DSM 18998T) and Cohnella ginsengisoli sp. nov. (type strain GR21-5T=KACC 11771T=DSM 18997T) are proposed.

Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006

A novel bacterial strain, designated M2T2B15(T), was isolated from fermented bovine products and was characterized by using a polyphasic approach. Colonies were reddish pink and circular with entire margins. Cells were strictly aerobic, Gram-reaction-negative, oxidase- and catalase-positive rods that lacked flagella and were motile by gliding. Flexirubin-type pigments were absent. 16S rRNA gene sequence analysis indicated that strain M2T2B15(T) was related most closely to Larkinella insperata LMG 22510(T) (94.4 % similarity) but shared <87 % similarity with other members of the phylum Bacteroidetes. The major cellular fatty acids were C(16 : 1)ω5c, iso-C(15 : 0) and iso-C(17 : 0) 3-OH. The polar lipids were phosphatidylethanolamine, phosphatidylserine, two unidentified aminophospholipids and two unidentified polar lipids. Menaquinone 7 (MK-7) was the major respiratory quinone. The G+C content of the DNA of strain M2T2B15(T) was 52&emsp14;mol%. The phenotypic, genotypic and phylogenetic data presented clearly indicate that strain M2T2B15(T) represents a novel species of the genus Larkinella, for which the name Larkinella bovis sp. nov. is proposed. The type strain is M2T2B15(T) (=KACC 14040(T) =NBRC 106324(T)). Emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006 are also proposed.

Xenophilus aerolatus sp. nov., isolated from air

A novel aerobic, Gram-negative, motile, rod-shaped bacterial strain designated 5516S-2T was isolated from an air sample taken in Suwon, Republic of Korea. Colonies were yellow-pigmented and circular with entire margins. 16S rRNA gene sequence analysis showed that strain 5516S-2T was closely related to Xylophilus ampelinus DSM 7250T (97.6 % sequence similarity), Variovorax soli KACC 11579T (97.5 %) and Xenophilus azovorans DSM 13620T (97.1 %). However, the phylogenetic tree indicated that strain 5516S-2T formed a separate clade from Xenophilus azovorans. Strain 5516S-2T displayed 42, 31 and 30 % DNA–DNA relatedness to the type strains of Xenophilus azovorans, Xylophilus ampelinus and V. soli, respectively. The major fatty acids (>10 % of total fatty acids) were C16 : 0 (33.3 %), C17 : 0 cyclo (18.8 %), C18 : 1 ω7c (17.5 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 13.0 %). The DNA G+C content was 69 mol%. The major quinone was ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Genotypic and phenotypic characteristics clearly distinguished strain 5516S-2T from closely related species and indicated that it represents a novel species within the genus Xenophilus, for which the name Xenophilus aerolatus sp. nov. is proposed. The type strain is 5516S-2T (=KACC 12602T=DSM 19424T).

Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.)

A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16T, was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087T (96.7 % similarity), P. pulmonicola LMG 18016T (96.5 %), P. apista LMG 16407T (96.2 %), P. norimbergensis LMG 18379T (96.1 %) and P. sputorum LMG 18819T (96.0 %). Strain ATSB16T shared 96.0–96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16T were C17 : 0 cyclo (33.0 %) and C16 : 0 (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16T represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16T (=KACC 12757T =LMG 24779T).

Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples

Two Gram-negative, motile, rod-shaped bacteria (strains 5317J-18T and 5414S-25T) were isolated from air samples collected in the Jeju Island and Suwon region of Korea, respectively. Phylogenetically, strain 5317J-18T was grouped with the genus Massilia with Massilia brevitalea byr23-80T as the closest relative (98.8% sequence similarity). Strain 5414S-25T was affiliated with the genus Naxibacter with Naxibacter haematophilus CCUG 38318T as the closest relative (98.8% sequence similarity). The mean DNA-DNA relatedness values between strain 5317J-18T and M. brevitalea DSM 18925T and Massilia aurea DSM 18055T were 43 and 36%, respectively. The mean DNA-DNA hybridization values between strain 5414S-25T and N. haematophilus KACC 13771T, M. brevitalea DSM 18925T, Massilia timonae DSM 16850T, Naxibacter varians KACC 13770T, M. aurea DSM 18055T, Massilia lutea DSM 17473T and Massilia albidiflava DSM 17472T ranged from 33 to 42%. Both novel strains had ubiquinone Q-8 as the predominant isoprenoid quinone and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 omega7c) and C16:0 as the major fatty acids. Both strains also showed similar polar lipid profiles with phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The DNA G+C contents of strains 5317J-18T and 5414S-25T were 66.1 and 67.8%, respectively. On the basis of their phenotypic, chemotaxonomic and genotypic characteristics, the new strains represent novel species in the genera Massilia and Naxibacter. Strain 5317J-18T (=KACC 12634T=DSM 21309T) is proposed as the type strain of Massilia jejuensis sp. nov. and strain 5414S-25T (=KACC 12635T=DSM 21311T) is proposed as the type strain of Naxibacter suwonensis sp. nov.

Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost

Two aerobic, Gram-reaction-negative, non-spore-forming bacterial strains, 4M29T and 4M40T, were isolated from cotton composts. The two strains grew in the presence of 0-5% (w/v) NaCl (optimum growth in the absence of NaCl), at pH 6.0-8.0 (optimum, pH 7.0) and at 15-45 degrees C (optimum, 30 degrees C). The strains shared 97.1% 16S rRNA gene sequence similarity. Strains 4M29T and 4M40T showed the next highest levels of 16S rRNA gene sequence similarity to Parapedobacter koreensis Jip14T (95.6 and 94.4%, respectively) and Parapedobacter soli DCY14T (95.2 and 93.8%). The level of DNA-DNA relatedness between strains 4M29T and 4M40T was 38%. The two strains contained iso-C15:0, summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1omega7c) and iso-C17:0 3-OH as major fatty acids, MK-7 as the major respiratory quinone, homospermidine as the only polyamine and phosphatidylethanolamine as the major polar lipid. The DNA G+C contents of strains 4M29T and 4M40T were 47.6 and 48.6 mol%, respectively. On the basis of phylogenetic and phenotypic data, strains 4M29T and 4M40T are considered to represent two novel species of the genus Parapedobacter, for which the names Parapedobacter luteus sp. nov. (type strain 4M29T =KACC 10955T =JCM 15977T) and Parapedobacter composti sp. nov. (type strain 4M40T =KACC 10972T =JCM 15978T) are proposed.

Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil

Two novel strains isolated from soils, JS12-10(T) and JS14-6(T), were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10(T) and JS14-6(T) to the genus Dyella. However, chemotaxonomic data and DNA-DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10(T) and JS14-6(T) showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046(T) (98.4 %) and Dyella japonica XD53(T) (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA-DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29-38 %. Therefore, strains JS12-10(T) and JS14-6(T) represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10(T) =KACC 12747(T) =JCM 15423(T)) and Dyella terrae sp. nov. (type strain JS14-6(T) =KACC 12748(T) =JCM 15424(T)) are proposed.

Thiosulfate Oxidation and mixotrophic growth of Methylobacterium goesingense and Methylobacterium fujisawaense

The mixotrophic growth with methanol plus thiosulfate was examined in nutrient-limited mixotrophic condition for Methylobacterium goesingense CBMB5 and Methylobacterium fujisawaense CBMB37. Thiosulfate oxidation increased the growth and protein yield in mixotrophic medium that contained 150 mM methanol and 20 mM sodium thiosulfate, at 144 h. Respirometric study revealed that thiosulfate was the most preferable reduced inorganic sulfur source, followed by sulfite and sulfur. M. goesingense CBMB5 and M. fujisawaense CBMB37 oxidized thiosulfate directly to sulfate, and intermediate products of thiosulfate oxidation such as polythionates, sulfite, and sulfur were not detected in spent medium and they did not yield positive amplification for tested soxB primers. Enzymes of thiosulfate oxidation such as rhodanese and sulfite oxidase activities were detected in cell-free extracts of M. goesingense CBMB5, and M. fujisawaense CBMB37, and thiosulfate oxidase (tetrathionate synthase) activity was not observed. It indicated that both the organisms use the "non-S4 intermediate" sulfur oxidation pathway for thiosulfate oxidation. It is concluded from this study that M. goesingense CBMB5, and M. fujisawaense CBMB37 exhibited mixotrophic metabolism in medium containing methanol plus thiosulfate and that thiosulfate oxidation and the presence of a "Paracoccus sulfur oxidation" (PSO) pathway in methylotrophic bacteria are species dependant.

Thiosulfate oxidation and mixotrophic growth of Methylobacterium oryzae

Thiosulfate oxidation and mixotrophic growth with succinate or methanol plus thiosulfate was examined in nutrient-limited mixotrophic condition for Methylobacterium oryzae CBMB20, which was recently characterized and reported as a novel species isolated from rice. Methylobacterium oryzae was able to utilize thiosulfate in the presence of sulfate. Thiosulfate oxidation increased the protein yield by 25% in mixotrophic medium containing 18.5 mmol·L–1of sodium succinate and 20 mmol·L–1of sodium thiosulfate on day 5. The respirometric study revealed that thiosulfate was the most preferable reduced inorganic sulfur source, followed by sulfur and sulfite. Thiosulfate was predominantly oxidized to sulfate and intermediate products of thiosulfate oxidation, such as tetrathionate, trithionate, polythionate, and sulfur, were not detected in spent medium. It indicated that bacterium use the non-S4intermediate sulfur oxidation pathway for thiosulfate oxidation. Thiosulfate oxidation enzymes, such as rhodanese and sulfite oxidase activities appeared to be constitutively expressed, but activity increased during growth on thiosulfate. No thiosulfate oxidase (tetrathionate synthase) activity was detected.

Potential for plant growth promotion in groundnut (Arachis hypogaea L.) cv. ALR-2 by co-inoculation of sulfur-oxidizing bacteria and Rhizobium

The use of Rhizobium inoculant for groundnut is a common practice in India. Also, co-inoculation of Rhizobium with other plant growth-promoting bacteria received considerable attention in legume growth promotion. Hence, in the present study we investigated effects of co-inoculating the sulfur (S)-oxidizing bacterial strains with Rhizobium, a strain that had no S-oxidizing potential in groundnut. Chemolithotrophic S-oxidizing bacterial isolates from different sources by enrichment isolation technique included three autotrophic (LCH, SWA5 and SWA4) and one heterotrophic (SGA6) strains. All the four isolates decreased the pH of the growth medium through oxidation of elemental S to sulfuric acid. Characterization revealed that these isolates tentatively placed into the genus Thiobacillus. Clay-based pellet formulation (2.5 x 10(7) cf ug(-1) pellet) of the Thiobacillus strains were developed and their efficiency to promote plant growth was tested in groundnut under pot culture and field conditions with S-deficit soil. Experiments in pot culture yielded promising results on groundnut increasing the plant biomass, nodule number and dry weight, and pod yield. Co-inoculation of Thiobacillus sp. strain LCH (applied at 60 kg ha(-1)) with Rhizobium under field condition recorded significantly higher nodule number, nodule dry weight and plant biomass 136.9 plant(-1), 740.0mg plant(-1) and 15.0 g plant(-1), respectively, on 80 days after sowing and enhanced the pod yield by 18%. Also inoculation of S-oxidizing bacteria increased the soil available S from 7.4 to 8.43 kg ha(-1). These results suggest that inoculation of S-oxidizing bacteria along with rhizobia results in synergistic interactions promoting the yield and oil content of groundnut, in S-deficit soils.

Plant growth-promoting Methylobacterium induces defense responses in groundnut (Arachis hypogaea L.) compared with rot pathogens

This study, framed in two different phases, studied the plant-growth promotion and the induction of systemic resistance in groundnut by Methylobacterium. Seed imbibition with Methylobacterium sp. increased germination by 19.5% compared with controls. Combined inoculation of Methylobacterium sp. with Rhizobium sp. also significantly increased plant growth, nodulation, and yield attributes in groundnut compared with individual inoculation of Rhizobium sp. Methylobacterium sp. challenge-inoculated with Aspergillus niger/Sclerotium rolfsii in groundnut significantly enhanced germination percentage and seedling vigour and showed increased phenylalanine ammonia lyase (PAL), beta-1,3-glucanase, and peroxidase (PO) activities. Under pot-culture conditions, in Methylobacterium sp. seed-treated groundnut plants challenge-inoculated with A. niger/S. rolfsii through foliar sprays on day 30, the activities of enzymes PO, PAL, and beta-1,3-glucanase increased constantly from 24 to 72 hours, after which decreased activity was noted. Five isozymes of polyphenol oxidase and PO could be detected in Methylobacterium-treated plants challenged with A. niger/S. rolfsii. Induced systemic resistance activity in groundnut against rot pathogens in response to methylotrophic bacteria suggests the possibility that pink-pigmented facultative methylotrophic bacteria might be used as a means of biologic disease control.