Characterization of plant growth-promoting alkalotolerant Alcaligenes and Bacillus strains for mitigating the alkaline stress in Zea mays.

Intensification of sodic soil due to increasing pH is an emerging environmental issue. The present study aimed to isolate and characterise alkaline stress-tolerant and plant growth-promoting bacterial strains from moderately alkaline soil (pH 8-9), strongly alkaline soil (pH 9-10), and very strongly alkaline soil (> 10). Total 68 bacteria were isolated, and screened for multiple plant growth promoting (PGP) attributes. Out of total, 42 isolates demonstrating at least three plant growth promoting PGP traits selected for further assays. Then out of 42, 15 bacterial isolates were selected based on enhanced maize plant growth under greenhouse experiment, and 16S rRNA gene sequencing revealed Bacillus spp. as a dominant genus. Furthermore, based on improved seed germination percentage and biomass of maize (Zea mays L.) under alkaline stress conditions Alcaligenes sp. NBRI NB2.5, Bacillus sp. NBRI YE1.3, and Bacillus sp. NBRI YN4.4 bacterial strains were selected, and evaluated for growth-promotion and alkaline stress amelioration under greenhouse condition. Amongst the selected 3 plant growth promoting rhizobacterial (PGPR) strains, Bacillus sp. NBRI YN4.4 significantly improved the photosynthetic pigments and soluble sugar content, and decreased proline level in inoculated maize plants as compared to uninoculated control under stress conditions. Moreover, significantly enhanced soil enzymes such as dehydrogenase, alkaline phosphatase and betaglucosidase due to inoculation of Bacillus sp. NBRI YN4.4 in maize plants grown in alkaline soil attributes to its role in improving the soil health. Therefore, alkaline stress-tolerant PGPR NBRI YN4.4 can be useful for developing strategies for the reclamation of saline/sodic soils and improving the plant growth and soil health in sustainable manner.

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

First Report of Extended-Spectrum ß-Lactamases TEM-116 and OXA-10 in Clinical Isolates of Alcaligenes Species from Kuala Lumpur, Malaysia.

There is an alarming increase in the prevalence of extended-spectrum ß-lactamases (ESBLs) present mainly in Enterobacteriaceae and other nonfermenting gram-negative bacteria, such as Alcaligenes faecalis, which is the only species in that genus that is clinically relevant. We investigated Alcaligenes species from 7 cases (6 inpatients and one outpatient) at our tertiary-care hospital. Four patients had urinary tract infections, and one each had systemic lupus erythematosus, pulmonary stenosis, and diabetic ulcer. All 7 isolates were identified as Alcaligenes spp. based on their 16S rRNA gene sequences, and antibiotic susceptibility was determined using a Vitek 2 system with AST-GN87 cards. All the strains were resistant to cefazolin; 6 were resistant to trimethoprim/sulfamethoxazole; 5 manifested resistance to ampicillin/sulbactam, cefepime, tobramycin, ciprofloxacin, and nitrofurantoin; whereas 5 had multidrug resistance profiles. All the strains (7/7) expressed ESBL activity; PCR screening and sequencing showed evidence of genes blaTEM-116 (7/7) and blaOXA-10 (4/7), and we believe that this is the first report on the presence of TEM-116 and OXA-10 in an Alcaligenes spp. A combination of the 2 genes was present in 4 strains. All 7 strains were found to harbor at least one ESBL gene probably contributing to the drug resistance.

Microbial Degradation of Nicotinamide by a Strain Alcaligenes sp. P156.

A novel Alcaligenes sp. strain P156, which can utilize nicotinamide as its sole source of carbon, nitrogen and energy, was enriched and isolated from soil in a solid waste treatment plant. Aerobic growth and degradation with nicotinamide were characterized. Seven nicotinamide degradation-related genes were obtained by sequence alignment from the genome sequence of strain P156. Four genes, designated naaA, naaD, naaE and naaF, were cloned and heterologously expressed. Nicotinamide degradation is initiated by deamination to form nicotinic acid catalyzed by the nicotinamidase NaaA, which shares highest amino acid sequence identity (27.2%) with nicotinamidase from Arabidopsis thaliana. Nicotinic acid is converted to 6-hydroxynicotinic acid, which is further oxidized to 2,5-dihydroxypyridine (2,5-DHP). 2,5-DHP is then transformed to a ring-cleavage product, N-formylmaleamic acid, by an Fe2+ dependent dioxygenase NaaD. N-formylmaleamic acid is transformed to fumaric acid through maleamic acid and maleic acid by NaaE and NaaF, respectively. To our knowledge, this is the first report of the complete microbial degradation of nicotinamide in bacteria. Nicotinamide is considered as a model compound for the study of microbial degradation of pyridinic compounds, and the nicotinamide degrading related genes in strain P156 were distributed differently from the reported similar gene clusters. Therefore, this study contribute to the knowledge on the degradation of pyridinic compounds.

Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium.

A Gram-stain-negative, rod-shaped, motile bacterium, designated AER10T, was isolated from the roots of Ammodendron bifolium collected from Takeermohuer desert in Xinjiang Uygur Autonomous Region, northwestern China. Growth was found to occur from 10 to 45 °C, at pH 5.0-9.0, and could tolerate up to 10 % (w/v) NaCl. 16S rRNA gene sequence result indicated that the strain AER10T belongs to the genus Alcaligenes and was closely related to Alcaligenes aquatilis (98.4 %), Alcaligenes faecalissubsp. parafaecalis (98.4 %), Alcaligenes faecalissubsp. faecalis (98.1 %) and Alcaligenes faecalissubsp. phenolicus (97.9 %). However, the DNA-DNA hybridization values between the strain AER10T and the above strains were less than the threshold value (below 70 %) for the delineation of genomic species. The DNA G+C content was 53.3 mol%. Ubiquinone-8 (Q-8) was the only quinone system present. The major fatty acids were summed feature 8 (C18 : 1ω7c, 25 %), C16 : 0 (24.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 19.3 %) and cyclo-C17 : 0 (10.5 %). The polar lipid profile of the strain AER10T consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids and five unknown polar lipids. On the basis of the evidence presented in this study, strain AER10T is a representative of a novel species in the genus Alcaligenes, for which the name Alcaligenes endophyticus sp. nov. is proposed. The type strain is AER10T (=DSM 100498T=KCTC 42688T).

Microaerobic degradation of 2-Mercaptobenzothiazole present in industrial wastewater.

Microaerobic degradation of 2-Mercaptobenzothiazole (2-MBT) was investigated using an isolated bacterial strain CSMB1. It was identified as Alcaligenes sp. MH146 by genomic analysis. The isolate degraded 50mg/L concentration of 2-MBT which was measured in terms of Total organic carbon (TOC) (700mg/L). A maximum degradation of 86% with a residual TOC concentration of 101mg/L was obtained after 72h, with the biomass growth of 290mg/L. The presence of specific activity of catechol 2, 3 oxygenase was observed in all the tested derivatives of benzothiazoles and the benzene ring opening was observed through meta cleavage. By analyzing the 72h incubated culture supernatant, 2-MBT, and all its biotransformed products were degraded into polar compounds. With the analytical results obtained, a possible microaerobic degradative pathway was proposed and illustrated for 2-MBT. It is concluded that microaerophilic isolate CSMB1 was able to degrade 2-MBT and its intermediates by utilizing them as sole carbon and energy.

Characteristics and metabolic pathway of Alcaligenes sp. TB for simultaneous heterotrophic nitrification-aerobic denitrification.

A novel heterotrophic nitrification-aerobic denitrification bacterium, Alcaligenes sp. TB (GenBank accession no. JQ044686), was isolated from a rotating drum biofilter for NO removal. Its characteristics and metabolic pathway for NO removal were comprehensively investigated. Experimental results showed that the nitrification and denitrification efficiency reached 99.42 and 96.44 %, respectively, after 44 h under the conditions of pH 7.2, 30 °C, and 120 rpm. The tests with the addition of Pb2+ and Na2WO4 as the reductase inhibitor revealed that nitrite was the key intermediate to produce the nitrogen gas as the final product in the simultaneous heterotrophic nitrification and denitrification by strain TB. Based on the experimental results, the metabolic pathway of strain TB has been proposed that it carries out shortcut/complete simultaneous nitrification and denitrification with nitrite as an intermediate and nitrogen gas as a final product. The two potential metabolic pathways existing in strain TB can be described as NH4+ â†’ NH2OH â†’ NO2- â†’ N2O â†’ N2 and NH4+ â†’ NH2OH â†’ NO2- â†’ NO3- â†’ NO2- â†’ N2O â†’ N2. This work indicates that the strain TB may be a good candidate for the denitrification of the sewage.

Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.

Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes.

Novel approach for the ammonium removal by simultaneous heterotrophic nitrification and denitrification using a novel bacterial species co-culture.

Agricultural activities lead excessive emission of ammonia nitrogen in the environment and can profoundly interfere the equilibrium of the natural ecosystems leading to their contamination. Actually, the biological purification of wastewaters is the most adopted technique thanks to its several advantages such as high performance and low energy consumption. For this reason, two novel strains of Alcaligenes sp. S84S3 and Proteus sp. S19 genus were isolated from an activated sludge and applied in the treatment of ammonium and nitrite in aqueous solution. Under the optimum operating conditions of temperature (30 °C), pH (7), carbon substrate (2 g/L of glucose) and duration of incubation time (69 h), the strain Alcaligenes sp. S84S3 could oxidize 65% of the ammonium as high as 272.72 mg-NH4(+)/L. Moreover, during 48 h, the nitrate reduction rate performed by the strain Proteus S19 was about 99 % without production of nitrite intermediate (negligible concentration). Moreover, the coculture of the strains Alcaligenes sp. S84S3 and Proteus sp. S19 could eliminate 65.83% of the ammonium ions without production of toxic forms of nitrogen oxides during a short time of incubation (118 h) at the same operational conditions with providing the aeration in the first treatment phase. The coculture of our isolated strains is assumed to have a good potential for nitrification and denitrification reactions applied in the treatment of wastewater containing ammonium, nitrite and nitrate. As a result, we can consider that the mixed culture is a practical method in the treatment of high-strength ammonium wastewater with reducing of sludge production.

Antimicrobial activity of Alcaligenes sp. HPC 1271 against multidrug resistant bacteria.

Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity observed. Gene expression analysis demonstrated that both NRPS and dTDP-glucose 4,6-dehydratase gene clusters are functional and could be involved in antibacterial biosynthesis.

Discovery of keratinases using bacteria isolated from marine environments.

Bacteria are important for the biodegradation of keratin. Thus, a workflow to isolate keratin-degrading bacteria utilizing an optimized azo-keratin assay was established. Deteriorated feather samples, collected in marine shoreline environments from the intertidal zone, yielded 50 unique bacterial isolates exhibiting keratin degradation when feather meal was supplied as keratin substrate. The majority of isolates, identified by 16S sequencing, belonged to genera previously reported to produce keratinases: Bacillus spp. (42%) and Stenotrophomonas spp. (40%). The remaining 18% represented the genera Alcaligenes, Chryseobacterium, Salinivibrio, Delftia, Stappia, and Microbacterium, genera not previously been associated with keratinase production. The workflow, also applied to 21 Bacilli from our in-house culture collection, additionally revealed four Bacilli with remarkable feather degradation potential. The industrial applicability of their associated keratinases was evaluated and the most active keratinase expressed in E. coli to confirm keratinase expression. Enriched keratinase fractions demonstrated activity up to 75°C and retained viability when stored lyophilized at 20°C for up to 200d.

Characterization of the novel dimethyl sulfide-degrading bacterium Alcaligenes sp. SY1 and its biochemical degradation pathway.

Recently, the biodegradation of volatile organic sulfur compounds (VOSCs) has become a burgeoning field, with a growing focus on the reduction of VOSCs. The reduction of VOSCs encompasses both organic emission control and odor control. Herein, Alcaligenes sp. SY1 was isolated from active sludge and found to utilize dimethyl sulfide (DMS) as a growth substrate in a mineral salt medium. Response surface methodology (RSM) analysis was applied to optimize the incubation conditions. The following conditions for optimal degradation were identified: temperature 27.03°C; pH 7.80; inoculum salinity 0.84%; and initial DMS concentration 1585.39 µM. Under these conditions, approximately 99% of the DMS was degraded within 30 h of incubation. Two metabolic compounds were detected and identified by gas chromatography-mass spectrometry (GC-MS): dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). The DMS degradation kinetics for different concentrations were evaluated using the Haldane-Andrews model and the pseudo first-order model. The maximum specific growth rate and degradation rate of Alcaligenes sp. SY1 were 0.17 h(-1) and 0.63 gs gx(-1)h(-1). A possible degradation pathway is proposed, and the results suggest that Alcaligenes sp. SY1 has the potential to control odor emissions under aerobic conditions.

Persistent Bordetella petrii Infection Related to Bone Fractures

No abstract available.

A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan.

Two strains, NCCP-650(T) and NCCP-667, were isolated from industrial effluent and their taxonomic positions were investigated using a polyphasic taxonomic approach. The strains were found to be Gram-stain negative, strictly aerobic, motile short rods, which are tolerant to heavy-metals (Cr(+2), As(+2), Pb(+2) and Cu(+2)). Cells were observed to grow at a temperature range of 10-37 °C (optimal 25-33 °C), pH range of 5.5-10.0 (optimal 6.5-7.5) and can tolerate 0-7 % NaCl (w/v) (optimum 0-1 %) in tryptic soya agar medium. Sequencing of the 16S rRNA gene and two housekeeping genes, gyrB and nirK, of the isolated strains revealed that both strains belong to the Betaproteobacteria showing highest sequence similarities with members of the genus Alcaligenes. The chemotaxonomic data [major quinones as Q-8; predominant cellular fatty acids as summed features 3 (C16 :1 ω7c/iso-C15 :0 2OH) and C16:0 followed by Summed features 2 (iso-C16 :1 I/C14 :0 3OH), C17:0 Cyclo and C18:1 ω7c; major polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid] also supported the affiliation of the isolated strains with the genus Alcaligenes. DNA-DNA hybridizations between the two strains and with closely related type strains of species of the genus Alcaligenes confirmed that both isolates belong to a single novel species within the genus Alcaligenes. On the basis of phylogenetic analyses, physiological, biochemical characteristics and DNA-DNA hybridization, the isolated strains can be differentiated from established Alcaligenes species and thus represent a novel species, for which the name Alcaligenes pakistanensis sp. nov. is proposed with the type strain NCCP-650(T) (=LMG 28368(T) = KCTC42083(T) = JCM 30216(T)).

[Activated Sludge Bacteria Transforming Cyanopyridines and Amides of Pyridinecarboxylic Acids].

Species diversity of bacteria from the activated sludge of Perm biological waste treatment facilities capable of transformation of cyanopyridines and amides of pyridinecarboxylic acids was investigated. Enrichment cultures in mineral media with 3-cyanopyridine as the sole carbon and nitrogen source were used to obtain 32 clones of gram-negative heterotrophic bacteria exhibiting moderate growth on solid and liquid media with 3- and 4-cyanopyridine. Sequencing of the 16S rRNA gene fragments revealed that the clones with homology of at least 99% belonged to the genera Acinetobacte, Alcaligenes, Delftia, Ochrobactrum, Pseudomonas, Stenotrophomonas, and Xanthobacter. PCR analysis showed that 13 out of 32 isolates contained the sequences (-1070 bp) homologous to the nitrilase genes reported previously in Alcaligenes faecalis JM3 (GenBank, D13419.1). Nine clones were capable of nitrile and amide transformation in minimal salt medium. Acinetobacter sp. 11 h and Alcaligenes sp. osv transformed 3-cyanopyridine to nicotinamide, while most of the clones possessed amidase activity (0.5 to 46.3 mmol/(g h) for acetamide and 0.1 to 5.6 mmol/(g h) for nicotinamide). Nicotinamide utilization by strain A. faecalis 2 was shown to result in excretion of a secondary metabolite, which was identified as dodecyl acrylate at 91% probability.

Simultaneous nitrification and denitrification by novel heterotrophs in remediation of fish processing effluent.

Three isolates viz. Lysinibacillus sp. HT13, Alcaligenes sp. HT15 and Proteus sp. HT37 isolated from fish processing effluent and having a C/N ratio of 2, removed 218, 169, and 400 µg cell(-1) day(-1) NH4(+)-N, respectively without subsequent build up of nitrite or nitrate. Ability of the selected isolates in removing NH4(+)-N, NO2(-)-N, and NO3(-)-N was checked in the presence of four commonly reported and tested effluent carbon sources viz. pyruvate, glycerol, methanol, and acetate. Further, when supplemented to fish processing wastewater containing 234 ppm total Kjeldahl's nitrogen, Lysinibacillus sp. HT13, Alcaligenes sp. HT15, and Proteus sp. HT37 could remediate 95.74, 86.17, and 76.6% nitrogen, respectively in 48 h. This is the first report of a Lysinibacillus sp. carrying out aerobically the process of simultaneous nitrification and denitrification. The results demonstrate the potential of the isolates for use in treatment of fish processing effluents and demonstrating the efficient removal of ammonia.

Scleral buckle infection with Alcaligenes xylosoxidans.

We describe a rare case of extraocular inflammation secondary to scleral buckle infection with Alcaligenes xylosoxidans. A 60-year-old female with a history of retinal detachment repair with open-book technique of scleral buckling presented with purulent discharge and irritation in the right eye that had begun 4 weeks earlier and had been treated ineffectively at another hospital. Conjunctival erosion with exposure of the scleral buckle was noted. The scleral buckle was removed and cultured. The explanted material grew gram-negative rod later identified as A. xylosoxidans. On the basis of the susceptibility test results, the patient was treated by subconjunctival injection and fortified topical ceftazidime. After 4 weeks of treatment, the infection resolved.

Development of a PCR-based method for monitoring the status of Alcaligenes species in the agricultural environment.

To analyze the status of the genus Alcaligenes in the agricultural environment, we developed a PCR method for detection of these species from vegetables and farming soil. The selected PCR primers amplified a 107-bp fragment of the 16S rRNA gene in a specific PCR assay with a detection limit of 1.06 pg of pure culture DNA, corresponding to DNA extracted from approximately 23 cells of Alcaligenes faecalis. Meanwhile, PCR primers generated a detectable amount of the amplicon from 2.2×10(2) CFU/ml cell suspensions from the soil. Analysis of vegetable phylloepiphytic and farming soil microbes showed that bacterial species belonging to the genus Alcaligenes were present in the range from 0.9×10(0) CFU per gram (or cm(2)) (Japanese radish: Raphanus sativus var. longipinnatus) to more than 1.1×10(4) CFU/g (broccoli flowers: Brassica oleracea var. italic), while 2.4×10(2) to 4.4×10(3) CFU/g were detected from all soil samples. These results indicated that Alcaligenes species are present in the phytosphere at levels 10-1000 times lower than those in soil. Our approach may be useful for tracking or quantifying species of the genus Alcaligenes in the agricultural environment.

Screening of assimilatory and dissimilatory denitrifying microbes isolated from nitrate-contaminated water and soil.

Nitrate NO(3)(-) contamination of groundwater resources is a serious problem. Such contamination in drinking water is regulated by environmental agencies around the world since at higher concentrations it can cause several health problems in infants. The aim of the present study was to identify the efficiency of the bacterial species isolated from nitrate-contaminated water and soil samples collected from Erode, Salem, Dharmapuri, and Krishnagiri districts of Tamilnadu, India. There are 74 morphologically different bacterial species were isolated and evaluated by a dissimilatory and assimilatory nitrate reduction test. Among the isolates, DW-27, DS-29, DS-31, DS-45, DS-46, and DS-47 were found to be potential dissimilatory and EW-6, ES-15, DS-39, DS-41, DS-48, DS-55, and SW-59 were potential assimilatory nitrate reducers. The results of bacterial analysis revealed that the isolated nitrate-reducing bacteria belonged to the genera Bacillus (64%) and Corynebacterium (22%), family Enterobacteriaceae (11%), and genus Alcaligenes (3%). This observation has led to the conclusion that these bacterial species showed efficiency of nitrate removal.