Novel Bacterium Strain Research Articles

Sphingomonas Immobilis sp. nov., and Sphingomonas natans sp. nov. bacteria isolated from soil.

Two novel strains of bacteria, CA1-15T and BIUV-7T, were isolated from soil samples gathered in Cheonan-si, Republic of Korea, and Inje-gun, Republic of Korea, respectively. These bacteria are Gram-negative, aerobic, and non-motile. Phylogenetic evaluations, using the sequence of the 16S rRNA gene, showed that strains CA1-15T and BIUV-7T belong to a distinctive clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest similarity in their genetic makeup with representatives of the genus Sphingomonas. Strain CA1-15T was closely related to Sphingomonas echinoides NRRL B-3126T (97.8% similarity in 16S rRNA gene sequence), Sphingomonas oligophenolica JCM 12,082T (97.8%), Sphingomonas glacialis C16yT (97.6%) and Sphingomonas psychrolutea MDB1-AT (97.3%). Strain BIUV-7T was closely related to Sphingomonas nostoxanthinifaciens AK-PDB1-5T (97.0%), Sphingomonas vulcanisoli SN6-13T (96.3%), Sphingomonas naphthae DKC-5-1T (96.2%), and Sphingomonas prati W18RDT (95.7%). The optimal growth conditions for strains CA1-15T and BIUV-7T were determined to be at pH 7.0 and a temperature of 25°C. Analysis of the cellular fatty acids of strain CA1-15T and BIUV-7T revealed that summed feature 8 (C18:1ω7c/C18:1ω6c) (60.4%), summed feature 8 (C18:1ω7c/C18:1ω6c) (62.9%) were the major component, respectively. Additionally, both strains exhibited ubiquinone Q-10 as their major respiratory quinone, and diphosphatidylglycerol (DPG), glycosphingolipid (SGL), and phosphatidylethanolamine (PE) as the major polar lipid. The genome of strain CA1-15T measures 4,133,944bp, comprising 4,026 coding sequences (CDSs) and 46 tRNA genes. Similarly, the genome of strain BIUV-7T is 4,563,252bp, characterized by 4,226 CDSs and 44 tRNA genes. The average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization (dDDH) values between strain CA1-15T and other Sphingomonas species range from 73.2 to 79.9% and 19.4-22.9%, respectively. Comparatively, ANI and dDDH values between strain BIUV-7T and other Sphingomonas species are in the range of 72.9-76.5% and 19.3-20.9%, respectively. Based on the biochemical, chemotaxonomic, and phylogenetic analyses, it is evident that strains CA1-15T and BIUV-7T represent two novel bacterial species within the genus Sphingomonas. Accordingly, the names Sphingomonas immobilis sp. nov. and Sphingomonas natans sp. nov. are proposed. also, CA1-15T(= KCTC 92960T = NBRC 116547T) is the type strain of Sphingomonas immobilis and BIUV-7T(= KCTC 92961T = NBRC 116546T) is the type strain of Sphingomonas natans.

Asymptomatic Bacteriuria in Post Renal Transplant Patients: To Treat or Not?

Urinary tract infections (UTIs) can commonly occur within the first few weeks following kidney transplantation procedures. Although the management of asymptomatic bacteriuria and acute graft pyelonephritis is important to reduce the risk of graft rejections following kidney transplantation, the efficacy of antibiotics administration remains controversial among studies in the literature. The aim of this review is to elaborate more on asymptomatic bacteriuria following kidney transplantation and try to formulate proper evidence about the efficacy of antibiotics administration on eliminating the frequency of infections and enhancing the quality of care for patients. Most studies in the literature are observational, which are usually biased in the interventions. However, the current evidence regarding the management and screening of asymptomatic bacteriuria seems to discourage such an approach. Almost all of the included studies reported that antibiotic administration did not significantly lower the rates of secondary symptomatic UTIs or enhance the functions of the graft. In addition, there is no significant impact on mortality and other clinical outcomes. Lastly, the frequent administration of antibiotics can significantly increase the risk of recurrence due to the emergence of novel strains of bacteria that are resistant to the currently administered antibiotics making it unfavorable.

Emergence of β-rhizobia as new root nodulating bacteria in legumes and current status of the legume–rhizobium host specificity dogma

Recent developments in the legume rhizobium symbiotic interaction particularly those related to the emergence of novel strains of bacteria that nodulate and fix nitrogen in legumes is gaining momentum. These novel strains of bacteria were mostly isolated from the root nodules of indigenous and invasive legumes belonging to the sub families Papilionoideae and Mimosoideae in South Africa, South America and South East China. These rhizobia are phylogenetically and taxonomically different from the traditional 'alpha rhizobia' and are termed 'β-rhizobia' as they belong to the β-sub class of Proteobacteria. There are also new reports of novel species of root nodulating bacteria from the α-Proteobacteria, not known for several decades since the discovery of rhizobia. However, in this review focus is given to the emerging β-rhizobia isolated from the indigenous Papilionoid legumes in the Cape Floristic regions in South Africa and the indigenous and invasive Mimosoid legumes in South America and South East Asia respectively. The nodulation of the indigenous South African Papilionoid legumes including that of Aspalathus linearis (rooibos) is discussed in a bit detail. Previous reports indicated that A. linearis is very specific in its rhizobium requirement and was reported to be nodulated by the slow growing Bradyrhizobium spp. This review however summarizes that the bacteria associated with the root nodules of A. linearis belong to members of both the alpha (α) Proteobacteria that include Mesorhizobium, Rhizobium and Bradyrhizobium spp. and the beta (β) Proteobacteria represented by the genus Burkholderia (now reclassified as Paraburkholderia). In addition, the occurrence of Paraburkholderia as the newly emerging root nodule symbionts of various other legumes has been discussed. In doing so, the review highlights that nodulation is no longer restricted to the traditional 'rhizobia' group following the emergence of the new beta rhizobia as potential nodulators of various indigenous legumes. It thus provides some insights on the status of the legume-rhizobium host specificity concept and the loss of this specificity in several symbiotic associations that puts the long held dogma of host specificity of the legume rhizobium symbiosis in a dilemma.

Membrane technology in bioconversion of lignocellulose to motor fuel components

The use of lignocellulosic biomass is one of the promising technologies for the production of energy carriers (bioalcohols, biosyngas) and valuable chemicals. Lignocellulosic biofuels may be thought of as a material capable of substantially replacing oil to provide an efficient consumption of natural energy resources and an improvement of the environment. In the “bioreactor–membrane separator–catalytic reactor (converter)" circuit, all stages are considered to be key: (1) the pretreatment of lignocellulose and the development of fermentation, particularly the cultivation of novel strains of bacteria; (2) the design of energyefficient vapor/gas-phase membrane systems for (a) concentrating bioalcohols and (b) controlling the biosyngas composition; and (3) the development of catalyst systems for the conversion of bioalcohols to motor fuel components. The following sequential tasks are discussed in this brief review: (i) basic approaches to the pretreatment of lignocellulosic biomass aimed at preparing it for fermentation and enzymatic processing of lignocellulose, particularly the cultivation of novel strains of bacteria and their communities, to produce bioalcohols— ethanol and butanol—and thermochemical methods of lignocellulose conversion to products in the form of complex mixtures; (ii) the development of energy-efficient membrane concentrating of bioalcohols using hydrophilic and/or organophilic polymer membranes and the control of the composition of synthesis gas in the form of a multicomponent gas mixture using commercial gas-separation membranes; and (iii) the development of catalyst systems exhibiting high selectivity in the ethanol conversion to alkane and aromatic hydrocarbons (high-quality additives to motor fuels) and valuable olefins, particularly ethylene, propylene, and linear alpha-olefins up to C10.

Sampling and Selection Factors that Enhance the Diversity of Microbial Collections: Application to Biopesticide Development.

Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bio-prospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential.

Identification, Purification and Characterization of Laterosporulin, a Novel Bacteriocin Produced by Brevibacillus sp. Strain GI-9

BackgroundBacteriocins are antimicrobial peptides that are produced by bacteria as a defense mechanism in complex environments. Identification and characterization of novel bacteriocins in novel strains of bacteria is one of the important fields in bacteriology.Methodology/FindingsThe strain GI-9 was identified as Brevibacillus sp. by 16 S rRNA gene sequence analysis. The bacteriocin produced by strain GI-9, namely, laterosporulin was purified from supernatant of the culture grown under optimal conditions using hydrophobic interaction chromatography and reverse-phase HPLC. The bacteriocin was active against a wide range of Gram-positive and Gram-negative bacteria. MALDI-TOF experiments determined the precise molecular mass of the peptide to be of 5.6 kDa and N-terminal sequencing of the thermo-stable peptide revealed low similarity with existing antimicrobial peptides. The putative open reading frame (ORF) encoding laterosporulin and its surrounding genomic region was fished out from the draft genome sequence of GI-9. Sequence analysis of the putative bacteriocin gene did not show significant similarity to any reported bacteriocin producing genes in database.ConclusionsWe have identified a bacteriocin producing strain GI-9, belonging to the genus Brevibacillus sp. Biochemical and genomic characterization of laterosporulin suggests it as a novel bacteriocin with broad spectrum antibacterial activity.

Isolation and characterization of novel bacterial taxa from extreme alkali-saline soil

In northeast China there are large areas of nearly bare soda saline-alkali soil, in which plant survival is exteremely difficult because the land has a pH greater than 10.5. In order to obtain resistant microbial resources able to grow in such conditions, we analyzed environmental microbial samples from this extreme saline-alkali soil region. Through selective culture conditions, 8 bacterial strains were isolated from medium with no less than 1.5 M NaCl, 12 were isolated in the medium with a pH value of no less than 11.0, and 8 were isolated in the medium with of no less than 200 mM Na(2)CO(3). Based on 16S rRNA gene sequence analysis 20 novel strains of bacteria were identified and classified into four groups: 8 group I strains belong to the genus Bacillus; three group II belong to genus Nesterenkonia (2 strains) and genus Zhihengliuella (1 strain); eight group III strains belong to the genera Halomonas (6), Stenotrophomonas (1) and Alkalimonas (1); one group IV strain belongs to genus Litoribacter. These four groups belong to the phylum Firmicutes, phylum Actinobacteria, phylum Gamma-Proteobacteria and phylum Bacteroidetes, respectively. The sequence homology of 16S rRNA in strains ANESC-S, H.sp.C4 and H.sp.C6 with that of known strains was 93.2, 96.5 and 96.5%, respectively. Based on the 97.0% identity cutoff commonly used to discriminate bacterial species, our data suggest that H. sp.C4 and H.sp.C6 may be new species, and ANESC-S may be belong to a new genus of classified into order Cytophagales. The morphological characteristics by scanning electron microscopy (SEM) showed that, in addition to the coccal N.sp.N3, the majority (19) of the isolates are bacilli of various lengths. In culture the colonies appeared red, orange, yellow, light yellow, and milk-white, with milk-white being predominant. Based on the resistance to NaCl and pH, the 20 novel strains were classified into obligate alkaliphilic and halophilic bacteria, obligate alkaliphilic halotolerant bacteria, and facultative alkalophilic salt-tolerant bacteria. This is the first study reporting the isolation and characterization of bacterial resources from extreme saline-alkali soils from northeast China.

Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter.

Dimethylsulfone is a major product of the chemical oxidation in the atmosphere of the principal biogenic sulfur gas, dimethylsulfide, but no studies have been reported on the mechanisms for its microbiological degradation. Three novel strains of bacteria have been isolated from enrichment cultures provided with dimethylsulfone as the only carbon and energy substrate. These are novel facultatively methylotrophic species of Hyphonmicrobium and Arthobacter, capable of growth on a range of one-carbon substrates. Cell-free extracts contained activities of enzymes necessary for a reductive/oxidative pathway for dimethylsulfone degradation: membrane-bound-dimethylsulfone and dimethylsulfoxide reductases, dimethylsulfide monooxygenase, and methanethiol oxidase. Enzymatic evidence is also presented for the subsequent oxidation of formaldehyde by formaldehyde and formate dehydrogenases in the Hyphomicrobium strain and by a dissimilatory ribulose monophosphate cycle in the Arthrobacter strains. The strains also grew on dimethylsulfoxide and dimethylsulfide, and dimethylsulfide-grown bacteria oxidized dimethylsulfide and dimethylsulfoxide but not dimethylsulfone. Formaldehyde assimilation was effected in the Hyphomicrobium strain by the serine pathway, but enzymes of the ribulose monophosphate cycle for formaldehyde assimilation were present in the Arthrobacter strains grown on dimethylsulfone. In contrast, one of the Arthrobacter strains was shown to switch to the serine pathway during growth on methanol. Growth yields on dimethylsulfone and formaldehyde were consistent with the occurrence of the serine pathway in Hyphomicrobium strain S1 and the ribulose monophosphate cycle in Arthrobacter strain TGA, and with the proposed reductive pathway for dimethylsulfone degradation in both.