Sample records for bacillaceae

  1. Short communication: Typing and tracking Bacillaceae in raw milk and milk powder using pyroprinting. (United States)

    VanderKelen, Jennifer J; Mitchell, Ryan D; Laubscher, Andrea; Black, Michael W; Goodman, Anya L; Montana, Aldrin K; Dekhtyar, Alexander M; Jimenez-Flores, Rafael; Kitts, Christopher L


    Contamination of fluid and processed milk products with endospore-forming bacteria, such as Bacillaceae, affect milk quality and longevity. Contaminants come from a variety of sources, including the dairy farm environment, transportation equipment, or milk processing machinery. Tracking the origin of bacterial contamination to allow specifically targeted remediation efforts depends on a reliable strain-typing method that is reproducible, fast, easy to use, and amenable to computerized analysis. Our objective was to adapt a recently developed genotype-based Escherichia coli strain-typing method, called pyroprinting, for use in a microbial source-tracking study to follow endospore-forming bacillus bacteria from raw milk to powdered milk. A collection of endospores was isolated from both raw milk and its finished powder, and, after germination, the vegetative cells were subject to the pyroprinting protocol. Briefly, a ribosomal DNA intergenic transcribed spacer present in multiple copies in Bacillaceae genomes was amplified by the PCR. This multicopy locus generated a mixed PCR product that was subsequently subject to pyrosequencing, a quantitative real-time sequencing method. Through a series of enzymatic reactions, each nucleotide incorporation event produces a photon of light that is quantified at each nucleotide dispensation. The pattern of light peaks generated from this mixed template reaction is called a pyroprint. Isolates with pyroprints that match with a Pearson correlation of 0.99 or greater are considered to be in the same group. The pyroprint also contains some sequence data useful for presumptive species-level identification. This method identified groups with isolates from raw milk only, from powdered milk only, or from both sources. This study confirms pyroprinting as a rapid, reproducible, automatically digitized tool that can be used to distinguish bacterial strains into taxonomically relevant groups and, thus, indicate probable origins of bacterial

  2. Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut

    Directory of Open Access Journals (Sweden)

    M. Tidjani Alou


    Full Text Available Numidum massiliense gen. nov., sp. nov., strain mt3T is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3755739 bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes.

  3. Surface antigens of Xenorhabdus nematophila (F. Enterobacteriaceae) and Bacillus subtilis (F. Bacillaceae) react with antibacterial factors of Malacosoma disstria (C. Insecta: O. Lepidoptera) hemolymph. (United States)

    Giannoulis, Paschalis; Brooks, Cory L; Dunphy, Gary B; Niven, Donald F; Mandato, Craig A


    Previous research established different interactions of the insect pathogen, Xenorhabdus nematophila and nonpathogen, Bacillus subtilis, with antimicrobial hemocytes and humoral factors of larval Malacosoma disstria [Giannoulis, P., Brooks, C.L., Dunphy, G.B., Mandato, C.A., Niven, D.F., Zakarian, R.J., 2007. Interaction of the bacteria Xenorhabdus nematophila (Enterobacteriaceae) and Bacillus subtilis (Bacillaceae) with the hemocytes of larval Malacosoma disstria (Insecta: Lepidoptera: Lasicocampidae). J. Invertebr. Pathol. 94, 20-30]. The antimicrobial systems were inhibited by X. nematophila and stimulated by B. subtilis. The bacterial surface antigens participating in these reactions were unknown. Thus, herein the effects of lipopolysaccharide (endotoxin) from X. nematophila and lipoteichoic acid from B. subtilis on the larval M. disstria immune factors, the hemocytes and phenoloxidase, were determined. Endotoxin elevated the level of damaged hemocytes limiting the removal of X. nematophila from the hemolymph and enhancing the rapid release of bacteria trapped by nodulation. Similar effects were observed with the lipid A moiety of the endotoxin. The effects of lipopolysaccharide and lipid A on the hemocyte activities were abrogated by polymyxin B (an antibiotic that binds to lipid A) confirming lipopolysaccharide as the hemocytotoxin by virtue of the lipid A moiety. Lipoteichoic acid elicited nodulation and enhanced phenoloxidase activation and/or activity. Although lipoidal endotoxin and lipid A inhibited phenoloxidase activation they enhanced the activity of the enzyme. Apolipophorin-III precluded the effects of lipopolysaccharide, lipid A, and lipoteichoic acid on the hemocytes and prophenoloxidase until the antigens exceeded a critical threshold.

  4. Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group

    Directory of Open Access Journals (Sweden)

    Dyer David W


    Full Text Available Abstract Background The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis. While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing suggests that these organisms should be classified as a single species (thus, we will refer to these organisms collectively as the Bc species-group. How do we account for the underlying similarity of these phenotypically diverse microbes? It has been established for some time that the most rapidly evolving and evolutionarily flexible portions of the bacterial genome are regulatory sequences and transcriptional networks. Other studies have suggested that the sigma factor gene family of these organisms has diverged and expanded significantly relative to their ancestors; sigma factors are those portions of the bacterial transcriptional apparatus that control RNA polymerase recognition for promoter selection. Thus, examining sigma factor divergence in these organisms would concurrently examine both regulatory sequences and transcriptional networks important for divergence. We began this examination by comparison to the sigma factor gene set of B. subtilis. Results Phylogenetic analysis of the Bc species-group utilizing 157 single-copy genes of the family Bacillaceae suggests that several taxonomic revisions of the genus Bacillus should be considered. Within the Bc species-group there is little indication that the currently recognized species form related sub-groupings, suggesting that they are members of the same species. The sigma factor gene family encoded by the Bc species-group appears to be the result of a dynamic gene-duplication and gene-loss process that in previous analyses underestimated the true heterogeneity of the sigma factor content in the Bc species-group. Conclusions Expansion of the sigma factor gene family

  5. Enterotoxin Production in Natural Isolates of Bacillaceae outside the Bacillus cereus Group


    Phelps, Rebecca J.; McKillip, John L.


    Thirty-nine Bacillus strains obtained from a variety of environmental and food sources were screened by PCR for the presence of five gene targets (hblC, hblD, hblA, nheA, and nheB) in two enterotoxin operons (HBL and NHE) traditionally harbored by Bacillus cereus. Seven isolates exhibited a positive signal for at least three of the five possible targets, including Bacillus amyloliquefaciens, B. cereus, Bacillus circulans, Bacillus lentimorbis, Bacillus pasteurii, and Bacillus thuringiensis su...

  6. Enterotoxin production in natural isolates of Bacillaceae outside the Bacillus cereus group. (United States)

    Phelps, Rebecca J; McKillip, John L


    Thirty-nine Bacillus strains obtained from a variety of environmental and food sources were screened by PCR for the presence of five gene targets (hblC, hblD, hblA, nheA, and nheB) in two enterotoxin operons (HBL and NHE) traditionally harbored by Bacillus cereus. Seven isolates exhibited a positive signal for at least three of the five possible targets, including Bacillus amyloliquefaciens, B. cereus, Bacillus circulans, Bacillus lentimorbis, Bacillus pasteurii, and Bacillus thuringiensis subsp. kurstaki. PCR amplicons were confirmed by restriction enzyme digest patterns compared to a positive control strain. Enterotoxin gene expression of each strain grown in a model food system (skim milk) was monitored by gene-specific reverse transcription-PCR and confirmed with the Oxoid RPLA and Tecra BDE commercial kits. Lecithinase production was noted on egg yolk-polymyxin B agar for all strains except B. lentimorbis, whereas discontinuous beta hemolysis was exhibited by all seven isolates grown on 5% sheep blood agar plates. The results of this study confirm the presence of enterotoxin genes in natural isolates of Bacillus spp. outside the B. cereus group and the ability of these strains to produce toxins in a model food system under aerated conditions at 32 degrees C.

  7. Field evaluation of the synergistic effects of neem oil with Beauveria bassiana (Hypocreales: Clavicipitaceae) and Bacillus thuringiensis var. kurstaki (Bacillales: Bacillaceae)

    NARCIS (Netherlands)

    Togbe, C.E.; Zannou, E.; Gbehounou, G.; Kossou, D.; Huis, van A.


    In the present study, the synergistic effects of Beauveria bassiana (Bals.-Criv. Vuill.) (isolate Bb11) and Bacillus thuringiensis var. kurstaki (Berliner) with neem oil were evaluated in three agroecological zones in Be´nin. Four bioinsecticide treatments (neem oil, neem oil and B. bassiana used se

  8. Interaction of the bacteria Xenorhabdus nematophila (Enterobactericeae) and Bacillus subtilis (Bacillaceae) with the hemocytes of larval Malacosoma disstria (Insecta: Lepidoptera: Lasiocampidae). (United States)

    Giannoulis, Paschalis; Brooks, Cory L; Dunphy, Gary B; Mandato, Craig A; Niven, Donald F; Zakarian, Robert J


    Malacosoma disstria larvae are a pest of deciduous trees. Little is known on the interaction of bacteria with the immediate hemocytic antimicrobial responses of these insects. Incubating dead Xenorhabdus nematophila and Bacillus subtilis with a mixture of serum-free granular cells and plasmatocytes in vitro revealed differential bacterial-hemocyte adhesion and differential discharge of lysozyme and phenoloxidase but not total protein. Although active phenoloxidase adhered equally to both bacterial species, X. nematophila limited enzyme activation whereas B. subtilis enhanced activation. Serum with active phenoloxidase (as opposed to tropolone-inhibited phenoloxidase) and purified insect lysozyme increased bacterial-hemocyte adhesion of both bacterial species. An apolipophorin-III-like protein when incubated with hemocytes, limited their responses to glass slides and bacterial adhesion. However, initial binding of the protein to both bacteria increased granular cell levels with bacteria while lowering the plasmatocyte levels with adhering procaryotes. The protein also increased lysozyme and phenoloxidase activities. Although B. subtilis in vivo elicited a nodulation-based decline in total hemocyte counts and did not affect hemocyte viability, dead X. nematophila elevated hemocyte counts and damaged the hemocytes as lipopolysaccharide levels increased and X. nematophila emerged into the hemolymph. Apolipophorin-III-like protein once bound to the bacteria slowed their removal from the hemolymph.

  9. Mortalidad en larvas de Culex quinquefasciatus y Anopheles albimanus (díptera: culicidae, causada con un producto de Bacillus sphaericus (bacteria: bacillaceae en presentación granulada en condiciones experimentales

    Directory of Open Access Journals (Sweden)

    Estrella Cárdenas Castro


    Full Text Available El objetivo de este estudio fue ensayar una serie de concentraciones de un producto granulado preparado con Bacillus sphaericus, sobre larvas de Culex quinquefasciatus y Anopheles albimanus en condiciones de laboratorio. Se utilizaron once concentraciones (20, 40, 60, 80, 100, 120, 140, 160, 180, 200 y 500 ppm sobre larvas de An. albimanus, y ocho concentraciones diez veces menores (2, 4, 6, 8, 10, 12, 14 y 16 ppm sobre larvas de Cx. quinquefasciatus. Se utilizaron 60 larvas y un control con 20 larvas por concentración. El tiempo de exposición fue de 48 h, a una temperatura de 28 ± 2 ºC. Para estimar las concentraciones letales 50 y 95 se utilizó la prueba Probit. Se encontró una CL95 de B. sphaericus entre 6,45 y 7,28 ppm para larvas de Cx. quinquefasciatus; mientras que en larvas de An. albimanus se observó una CL95 entre 450,56 y 466,76 ppm.

  10. A mixed-species microarray for identification of food spoilage bacilli

    NARCIS (Netherlands)

    Caspers, M.P.M.; Schuren, F.H.J.; Zuijlen, van A.C.M.; Brul, S.; Montijn, R.C.; Abee, T.; Kort, R.


    Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus su

  11. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium. (United States)

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter; Vangronsveld, Jaco


    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations.

  12. The bacterial diversity in the Mogao Grottoes, Dunhuang, China%敦煌莫高窟中细菌多样性的研究

    Institute of Scientific and Technical Information of China (English)

    张昺林; 唐德平; 张楠; 王婉如; 张东明; 武发思; 薛林贵


    [目的]通过对敦煌莫高窟内细菌多样性及生理生化特征的分析,为壁画微生物病害防治提供试验依据.[方法]采用纯培养与16S rDNA等技术对莫高窟245#窟内空气样品、壁画样品进行分析,并在培养基中添加壁画颜料测试其对细菌生长的影响.[结果]分离出可培养细菌76株,分属于8个属.其中空气中有6个属,分别为Bacillus、Arthrobacter、Pseudomonas、Acinetobacter、Enterobacter、Kocuria,优势菌为Bacillus、Arthrobacter.壁画上有Bacillus、Arthrobacter、Paenibacillus、Erythrobacter 4个属,优势菌为Bacillus、Arthrobacter;并发现DHXJ05 (Enterobacteriaceae)、DHXJ08 (Bacillaceae)、DHXJ15 (Erythrobacteraceae)、DHXJ16 (Bacillaceae)和DHXJ17 (Bacillaceae)能在含有铁红、铅丹、朱砂的环境中良好生长.[结论]为后期研究壁画颜料的变色机理及选择相应的细菌防治制剂提供了条件.%[Objective] Analyzing the bacterial diversity, physiological and biochemical characteristics in the mogao grottoes can provide an experimental basis for microbial disease prevention and treatment of Mogao murals. [Methods] Both the air and mural samples collected from Mogao Grottoes 245# are analyzed by means of pure culture techniques, and testing effect of mural paint on bacterial growth. [Results] 76 bacteria belonging to eight different genera are identified and characterized. Six genera are revived form the air, they are Bacillus, Ar-throbacter, Pseudomonas, Acinetobacter, Enterobacter, Kocuria, Among them, Bacillus and Arthrobacter are dominant. Four genera are revived from the mural, they are Bacillus, Ar-throbacter, Paenibacillus, Erythrobacter, among them, Bacillus and Arthrobacter are dominant; and it is found that some bacteria, such as DHXJ05 (Enterobacteriaceae), DHXJ08 (Bacillaceae), DHXJ15 (Erythrobacteraceae), DHXJ16 (Bacillaceae) and DHXJ17 (Bacilla-ceae) can grow well in environment containing red ferric oxide, red lead, and cinnabar

  13. Enemigos naturales de Macrodactylus murinus Bates (Coleoptera; Scarabaeidae en San Miguel, Sierra de Manantlán, Jalisco, México

    Directory of Open Access Journals (Sweden)

    S. Hernández


    Full Text Available Para conocer los enemigos naturales del «frailecillo» Macrodactylus murinus en la comunidad de San Miguel, Sierra de Manantlán, Jalisco, se realizaron muestreos mensuales de julio de 1991 a junio de 1992, excepto febrero y marzo, sobre terrenos sembrados con maíz (Zea mays L.. Entre los enemigos naturales de larvas del «frailecillo» se encontraron: Thiphia sp. (Hymenoptera: Tiphidae, Metarhizium anisopliae (Moniliales: Moniliaceae y Clostridium sp. (Bacillaceae: Bacillaceae. De los enemigos naturales asociados a la etapa adulta del «frailecillo», se encontraron: Stenopoda sp. (Hemiptera: Reduviidae, Saclodxia lambels (Diptera: Sarcophagidae, Paucetia viridans (Araneida: Oxyopidae, Sitticus sp. y Eris sp. (Araneida: Salticidae

  14. S-layer nanoglycobiology of bacteria


    Messner, Paul; Steiner, Kerstin; Zarschler, Kristof; Schäffer, Christina


    Cell surface layers (S-layers) are common structures of the bacterial cell envelope with a lattice-like appearance that are formed by a self-assembly process. Frequently, the constituting S-layer proteins are modified with covalently linked glycan chains facing the extracellular environment. S-layer glycoproteins from organisms of the Bacillaceae family possess long, O-glycosidically linked glycans that are composed of a great variety of sugar constituents. The observed variations already exc...

  15. Permeability and charge-dependent adsorption properties of the S-layer lattice from Bacillus coagulans E38-66.


    Sára, M; Pum, D; Sleytr, U B


    We investigated the permeability properties of the oblique S-layer lattice from Bacillus coagulans E38-66 after depositing cell wall fragments on a microfiltration membrane, cross-linking the S-layer protein with glutaraldehyde, and degrading the peptidoglycan with lysozyme. Comparative permeability studies on such multilayered S-layer membranes and suspended S-layer vesicles from thermophilic members of the family Bacillaceae with use of the space technique (M. Sára and U. B. Sleytr, J. Bact...

  16. Bacillus rubiinfantis sp. nov. strain mt2T, a new bacterial species isolated from human gut

    Directory of Open Access Journals (Sweden)

    M. Tidjiani Alou


    Full Text Available Bacillus rubiinfantis sp. nov. strain mt2T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes.

  17. Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut

    Directory of Open Access Journals (Sweden)

    M. Tidjani Alou


    Full Text Available Bacillus niameyensis sp. nov. strain SIT3T (= CSUR P1266 = DSM 29725 is the type strain of B. niameyensis sp. nov. This Gram-positive strain was isolated from the digestive flora of a child with kwashiorkor and is a facultative anaerobic rod and a member of the Bacillaceae family. This organism is hereby described alongside its complete genome sequence and annotation. The 4  286  116 bp long genome (one chromosome but no plasmid contains 4130 protein-coding and 66 RNA genes including five rRNA genes.

  18. Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences Relações filogenéticas entre espécies de Bacillus e gêneros relacionados baseadas em sequencias 16S rDNA

    Directory of Open Access Journals (Sweden)

    Mi Sun Wei Wang


    Full Text Available Neigh-borjoining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups.Árvores utilizando os métodos de neighbor-joining, máxima parcimônia, evolução mínima, máxima verossimilhança e bayesiana, construídas baseadas em seqüências de rDNA 16S de 181 linhagens-tipo de espécies de Bacillus e taxa relacionados, mostraram a formação de nove grupos filogenéticos. A análise filogenética mostrou que Bacillus não é um grupo monofilético. B. subtilis se colocou no Grupo 1. Grupos 4, 6 e 8, respectivamente, consistiram de bacilos termofílicos, halofílicos ou halotolerantes e alcalifílicos. Grupos 2, 4 e 8 consistindo de espécies de Bacillus e gêneros relacionados demonstraram que o sistema taxonômico corrente não concorda perfeitamente com as árvores evolucionárias por rDNA 16S. A posição de Caryophanaceae e Planococcaceae no Grupo 2 sugere

  19. Supplemental control of lepidopterous pests on Bt transgenic sweet corn with biologically-based spray treatments. (United States)

    Farrar, Robert R; Shepard, B Merle; Shapiro, Martin; Hassell, Richard L; Schaffer, Mark L; Smith, Chad M


    Biologically-based spray treatments, including nucleopolyhedroviruses, neem, and spinosad, were evaluated as supplemental controls for the fall armyworm, Spodoptera frugiperda (J. E. Smith), and corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), on transgenic sweet corn, Zea mays (L.) (Poales: Poaceae), expressing a Cry1Ab toxin from Bacillus thuringiensis Berliner (Bacillales: Bacillaceae) (Bt). Overall, transgenic corn supported lower densities of both pests than did nontransgenic corn. Control of the fall armyworm was improved in both whorl-stage and tassel-stage corn by the use of either a nucleopolyhedrovirus or neem, but the greatest improvement was seen with spinosad. Only spinosad consistently reduced damage to ears, which was caused by both pest species. In general, efficacy of the spray materials did not differ greatly between transgenic and nontransgenic corn.

  20. Pesquisa de proteínas citotóxicas e nematicidas em isolados Bacillus thuringiensis dos Açores


    Raimundo, Natacha Sofia Rodrigues


    Dissertação de Mestrado, Ciências Biomédicas, 25 de Maio de 2016, Universidade dos Açores. Bacillus thuringiensis (Bt), pertencente à família Bacillaceae, é classificado como gram-positiva e tem despertado elevado interesse em várias áreas, destacando-se a aplicações na agricultura e na saúde. Os isolados de Bt são caracterizados pela sua capacidade de produzir inclusões cristalinas de origem proteica durante a fase de esporulação, as quais são conhecidas como proteínas δ-endotoxinas ou pr...

  1. The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. (United States)

    More, Ravi P; Purohit, Hemant J


    The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classification of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a regular expression that is specific to each particular taxon. Our main goal was to identify discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We applied combined composite vector and multiple sequence alignment approaches to generate gene-specific signatures. Further, we mapped all the patterns into the different hypervariable regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as V3-V4 for targeted taxa. We also examined the evolution in discriminating patterns of signatures across taxonomic levels. We assessed the comparative classification accuracy of signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity close to 0.99. We developed signature-based software DNA Barcode Identification (DNA BarID) for taxonomic classification that is available at website . This pattern-based study provides a deeper understanding of taxon-specific discriminating patterns in 16S rRNA gene with respect to taxonomic classification.

  2. Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, Li; Tang, Jia; Wang, Yueqiang; Hu, Min; Zhou, Shungui, E-mail:


    Highlights: • Paddy soil contaminated with benzoate incubated with hematite and magnetite. • Iron oxides addition enhanced methanogenic benzoate degradation by 25–53%. • The facilitated syntrophy might involve direct interspecies electron transfer. • Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved. - Abstract: Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89–94% of the electrons released from benzoate oxidation were recovered in CH{sub 4} production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.

  3. Biological mechanisms associated with triazophos (TAP) removal by horizontal subsurface flow constructed wetlands (HSFCW)

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Juan; Feng, Yuqin; Dai, Yanran; Cui, Naxin [State Key Laboratory of Pollution Control and ResourceReuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China); Anderson, Bruce [Department of Civil Engineering, Queen' s University, Kingston K7L3N6 (Canada); Cheng, Shuiping, E-mail: [State Key Laboratory of Pollution Control and ResourceReuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China)


    Triazophos (TAP) is a widely used pesticide that is easily accumulated in the environment due to its relatively high stability: this accumulation from agricultural runoff results in potential hazards to aquatic ecosystems. Constructed wetlands are generally considered to be an effective technology for treating TAP polluted surface water. However, knowledge about the biological mechanisms of TAP removal is still lacking. This study investigates the responses of a wetland plant (Canna indica), substrate enzymes and microbial communities in bench-scale horizontal subsurface-flow constructed wetlands (HSCWs) loaded with different TAP concentrations (0, 0.1, 0.5 and 5 mg·L{sup −1}). The results indicate that TAP stimulated the activities of superoxide dismutase (SOD) and peroxidase (POD) in the roots of C. indica. The highest TAP concentrations significantly inhibited photosynthetic activities, as shown by a reduced effective quantum yield of PS II (Φ{sub PSII}) and lower electron transport rates (ETR). However, interestingly, the lower TAP loadings exhibited some favorable effects on these two variables, suggesting that C. indica is a suitable species for use in wetlands designed for treatment of low TAP concentrations. Urease and alkaline phosphatase (ALP) in the wetland substrate were activated by TAP. Two-way ANOVA demonstrated that urease activity was influenced by both the TAP concentrations and season, while acidphosphatase (ACP) only responded to seasonal variations. Analysis of high throughput sequencing of 16S rRNA revealed seasonal variations in the microbial community structure of the wetland substrate at the phylum and family levels. In addition, urease activity had a greater correlation with the relative abundance of some functional microbial groups, such as the Bacillaceae family, and the ALP and ACP may be influenced by the plant more than substrate microbial communities. - Highlights: • Physiological responses of the wetland plant to triazophos

  4. Heterotrophic bacteria from brackish water of the southern Baltic Sea: biochemical and molecular identification and characterisation

    Directory of Open Access Journals (Sweden)

    Agnieszka Cabaj


    Full Text Available Six bacterial strains isolated from the surface water of thesouthern Baltic Sea were described on the basis of their morphological,physiological and biochemical features, and were classified onthe basis of 16S rDNA sequence analysis. Comparative analysesof the 16S rDNA sequences of five of the six bacterial strainsexamined displayed a ≥98% similarity to the sequences availablein the NCBI GenBank. The 16S rDNA sequence of strain 2 sharedonly a 96% similarity with other published sequences, whichsuggests that this is a new, hitherto unknown species. The isolatedheterotrophic bacteria belong to the families Bacillaceae(strain 1, Flexibacteriaceae (strain 2, Sphingomonadaceae(strains 3, 5, Micrococcaceae (strain 4 and Aurantimonadaceae(strain 6.    This is the first study in which the polyphasic approach hasbeen applied to the identification of heterotrophic bacteriafrom the brackish waters of the Gulf of Gdańsk and Gdańsk Deep.

  5. Analysis of raw goat milk microbiota: impact of stage of lactation and lysozyme on microbial diversity. (United States)

    McInnis, Elizabeth A; Kalanetra, Karen M; Mills, David A; Maga, Elizabeth A


    To protect infants from infection, human milk contains high levels of the enzyme lysozyme, unlike the milk of dairy animals. We have genetically engineered goats to express human lysozyme (hLZ milk) in their milk at 68% the amount found in human milk to help extend this protection. This study looked at the effect of hLZ on bacteria in raw milk over time. As the microbial diversity of goats' milk has yet to be investigated in depth using next-generation sequencing (NGS) technologies, we applied NGS and clone library sequencing (CLS) to determine the microbiota of raw goat milk (WT milk) and hLZ milk at early, mid and late lactation. Overall, in WT milk, the bacterial populations in milk at early and mid lactation were similar to each other with a shift occurring at late lactation. Both methods found Proteobacteria as the dominant bacteria at early and mid lactation, while Actinobacteria surged at late lactation. These changes were related to decreases in Pseudomonas and increases in Micrococcus. The bacterial populations in hLZ milk were similar to WT milk at early and mid lactation with the only significant differences occurring at late lactation with the elevation of Bacillaceae, Alicyclobacillaceae, Clostridiaceae and Halomonadaceae.

  6. Biofouling characteristics and identification of preponderant bacteria at different nutrient levels in batch tests of a recirculating cooling water system. (United States)

    Liu, Fang; Zhao, Chao-Cheng; Xia, Lu; Yang, Fei; Chang, Xin; Wang, Yong-Qiang


    Understanding the influence of nutrient levels on biofouling control is an important requirement for management strategies in a recirculating cooling water system. Nutrient limitation may be one way to control biofouling development without increasing biocide dosing. Therefore, this study was carried out to investigate the effects of nutrient levels on biofouling characteristics and to identify the preponderant bacteria in the batch tests with a simulated cooling water system. The biofouling characteristics were assessed by varying the biofoulant mass and the bacteria respiratory activity, which was estimated by measuring oxygen uptake rates. According to the results obtained in nutrient factor experiments, the biofouling could be better controlled at carbon, nitrogen and phosphorus concentrations of 30 mg N/L, 8 mg N/L and 1.0 mg P/L, respectively. Increasing carbon concentrations shortened the biofouling initial growth period and resulted in higher biofoulant mass. The preponderant bacteria strains involved in biofouling under two culture conditions were identified by applying both physiological and biochemical tests and further molecular biology techniques with phylogenetic affiliation analysis. Enterobacter (family Enterobacteriaceae), Staphylococcus (family Micrococcaceae), Bacillus (family Bacillaceae), Proteus (family Enterobacteriaceae), Neisseria (family Neisseriaceae) and Pseudomonas (family Pseudomonadaceae) were dominant in the conditions of lower carbon concentration (30 mg/L). Enterobacter are autotrophs, but the other five bacteria are all heterotrophs. In the conditions of higher carbon concentration (70 mg/L), Klebsiella (family Enterobacteriaceae), Enterobacter and Microbacterium (family Microbacteriaceae) were dominant; Enterobacter and Microbacterium are heterotrophs.

  7. Screening and identification of newly isolated cellulose-degrading bacteria from the gut of xylophagous termite Microcerotermes diversus (Silvestri). (United States)

    Pourramezan, Z; Ghezelbash, G R; Romani, B; Ziaei, S; Hedayatkhah, A


    The aim of the present study was to isolate and characterize the cellulose-degrading bacteria from the gut of the local termite, Microcerotermes diversus (Silvestri), inhabiting the Khuzestan province of Iran. The microorganisms capable of growing in the liquid medium containing cellulose as the only source of carbon were isolated and their cellulolytic activity on CMC-containing media was confirmed by the congo red clearing zone assay. The isolates were identified based on biochemical characteristics and the phylogenetic analysis of 16S rRNA gene fragments. The results of the present study show that three cellulose-degrading bacteria isolated from local termite guts belonged to the genera Acinetobacter, Pseudomonas and Staphylococcus and four cellulose-degrading bacteria belonged to Enterobacteriaceae and Bacillaceae families. Several isolates recovered from separate termite Microcerotermes diversus samples closely clustered in phylogenetic trees indicating high similarity and the abundance of particular cellulolytic strains. Bacillus B5B and Acinetobacter L9B hydrolyzed cellulose faster than the other isolates (with CMCase activity of 1.47 U/mL and 1.22 U/mL, respectively). The stability of CMCase produced by Bacillus B5B over a broad range of pH and high temperature indicated that the enzyme may be of great commercial value.

  8. Bioprospecting for secondary metabolites in the entomopathogenic bacterium Photorhabdus luminescens subsp. sonorensis. (United States)

    Orozco, Rousel A; Molnár, István; Bode, Helge; Stock, S Patricia


    Crude extracts of in vitro and in vivo cultures of two strains of Photorhabdus l. sonorensis (Enterobacteriaceae) were analyzed by TLC, HPLC-UV and LC-MS. Nine unique compounds with mass/charge ratios (m/z) ranging from 331.3 to 713.5 were found in MS analyses. Bioactivity of extracts was assessed on a selection of plant pathogens/pests and non-target species. Caborca strain extracts showed the highest activity against Helicoverpa zea (Lepidoptera: Noctuidae) neonates at all concentrations tested. Mortality ranged from 11% (at 10μg/ml) to 37% (at 40μg/ml). Strain CH35 extracts showed the highest nematicidal activity on Meloidogyne incognita (Tylenchida: Meloidogynidae) at 40μg/ml. Low to no nematicidal activity was observed against the non-target species Steinernema carpocapsae (Rhabditida: Steinernematidae) and Caenorhabditis elegans (Rhabditida: Rhabditidae). Caborca extracts exhibited a strong antibiotic effect on Pseudomonas syringae (Pseudomonadales: Pseudomonadacedae) at 40μg/ml, while both Caborca and CH35 extracts inhibited the growth of Bacillus subitillis (Bacillales: Bacillaceae) at 40μg/ml. All extracts strongly inhibited the growth of the fungus Fusarium oxysporum (Hypocreales: Nectriceae) but not that of Alternaria alternata (Pleosporales: Pleosporaceae). Contrastingly, a moderate to high inhibitory effect was denoted on the non-target biocontrol fungus Beauveria bassiana (Hypocreales: Clavivipitaceae).

  9. Antimicrobial activities of novel cultivable bacteria isolated from marine sponge Tedania anhelans

    Institute of Scientific and Technical Information of China (English)

    ZENG Zhen; ZHAO Jing; KE Caihuan; WANG Dexiang


    Marine sponge Tedania anhelans distributes throughout the intertidal zone of Fujian,southeastern China,and is a potential source of natural bioactive products.The sponge harbors a large number of bacterial groups that have been identified using various techniques,including fluorescent in situ hybridization (FISH).Fractionation of dissociated sponge allowed isolation of 25 bacterial species.Based on 16S rRNA gene sequencing,phylogenetic analysis attributed most of these eubacteria to a-Proteobacteria,γ-Proteobacteria,Cytophaga/Flavobacterium/Bacteroidetes (CFB group),and the family Bacillaceae of Gram-positive bacteria.In sequence similarity,five putatively novel species were identified with less than 98% similarity to other strains in the NCBI database.Tests for antimicrobial activities were performed against Gram-positive bacteria,Gram-negative bacteria,fungi,antitumor indicators Escherichia coli 343/591 (with DNA repair deficiency),regular E.coli 343/636 (with different DNA repair capacity),and 10 bacterial isolates exhibited inhibitory bioactivities.Among these strains,three isolates were detected involving function gene NRPS-A domains,which were most closely related to the amino acid sequences of linear gramicidin synthetase and pyoverdine synthetase.These results contribute to our knowledge of the microbes associated with marine sponges and further reveal novel bacterial resources for the screening of bioactive marine natural products.

  10. Чутливість до протимікробних засобів мікрофлори статевих органів корів при ендометриті




    З патологічного матеріалу від корів хворих на різні форми ендометриту були виділені монокультури Streptococcaceae, Staphylococcaceae, Enterobacteriaceae, Micrococcaceae, Bacillaceae, Lactobacilus та іх асоціації. Виділені культури перевірялися на чутливість до 18 антибіотиків, ефірних олій та спиртових і водних розчинів прополісу....

  11. Microcosm-based interaction studies between members of two ecophysiological groups of bioemulsifier producer and a hydrocarbon degrader from the Indian intertidal zone. (United States)

    Markande, A R; Nerurkar, A S


    Isolates were obtained from intertidal zone site samples from all five western and one eastern coastal states of India and were screened. These ecophysiological groups of aerobic, mesophilic, heterotrophic, sporulating, and bioemulsifier-producing bacteria were from Planococcaceae and Bacillaceae. This is the first report of bioemulsifier production by Sporosarcina spp., Lysinibacillus spp., B. thuringiensis, and B. flexus. In this group, Solibacillus silvestris AM1 was found to produce the highest emulsification activity (62.5 %EI) and the sample that yielded it was used to isolate the ecophysiological group of non-bioemulsifier-producing, hydrocarbon-degrading bacteria (belonging to Chromatiales and Bacillales). These yielded hitherto unreported degrader, Rheinheimera sp. CO6 which was selected for the interaction studies (in a microcosm) with bioemulsifier-producing S. silvestris AM1. The gas chromatographic study of these microcosm experiments revealed increased degradation of benzene, toluene, and xylene (BTX) and the growth of Rheinheimera sp. CO6 in the presence of bioemulsifier produced by S. silvestris AM1. Enhancement of the growth of S. silvestris AM1 in the presence of Rheinheimera sp. CO6 was observed possibly due to reduced toxicity of BTX suggesting mutualistic association between the two. This study elucidates the presence and interaction between enhancers and degraders in a hydrocarbon-contaminated intertidal zone and contributes to the knowledge during application of the two in remediation processes.

  12. Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests

    Directory of Open Access Journals (Sweden)

    Anaïs Castagnola


    Full Text Available This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae and Bacillus (Firmicutes: Bacillaceae. Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol.

  13. pGIAK1, a heavy metal resistant plasmid from an obligate alkaliphilic and halotolerant bacterium isolated from the Antarctic Concordia station confined environment.

    Directory of Open Access Journals (Sweden)

    Suxia Guo

    Full Text Available pGIAK1 is a 38-kb plasmid originating from the obligate alkaliphilic and halotolerant Bacillaceae strain JMAK1. The strain was originally isolated from the confined environments of the Antarctic Concordia station. Analysis of the pGIAK1 38,362-bp sequence revealed that, in addition to its replication region, this plasmid contains the genetic determinants for cadmium and arsenic resistances, putative methyltransferase, tyrosine recombinase, spore coat protein and potassium transport protein, as well as several hypothetical proteins. Cloning the pGIAK1 cad operon in Bacillus cereus H3081.97 and its ars operon in Bacillus subtilis 1A280 conferred to these hosts cadmium and arsenic resistances, respectively, therefore confirming their bona fide activities. The pGIAK1 replicon region was also shown to be functional in Bacillus thuringiensis, Bacillus subtilis and Staphylococcus aureus, but was only stably maintained in B. subtilis. Finally, using an Escherichia coli - B. thuringiensis shuttle BAC vector, pGIAK1 was shown to display conjugative properties since it was able to transfer the BAC plasmid among B. thuringiensis strains.

  14. Microbial hitchhikers on intercontinental dust: catching a lift in Chad (United States)

    Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A


    Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes—Bacillaceae, (b) Actinobacteria—Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria—Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes—Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516

  15. Diversity, Bacterial Symbionts and Antibacterial Potential of Gut-Associated Fungi Isolated from the Pantala flavescens Larvae in China. (United States)

    Shao, Ming-Wei; Lu, Yi-Hui; Miao, Shuang; Zhang, Yun; Chen, Ting-Ting; Zhang, Ying-Lao


    The diversity of fungi associated with the gut of Pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. In total, 48 fungal isolates were obtained from P. flavescens larvae. Based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. Fourteen bacterial 16S rDNA sequences derived from total genomic DNA extractions of fungal mycelia were obtained. The majority of the sequences were associated with Proteobacteria (13/14), and one Bacillaceae (1/14) was included. Leclercia sp., Oceanobacillus oncorhynchi and Methylobacterium extorquens, were reported for the first time as bacterial endosymbionts in fungi. High-performance liquid chromatography (HPLC) analysis indicated that bacterial symbionts produced specific metabolites and also exerted an inhibitory effect on fungal metabolites. The biological activity of the fungal culture extracts against the pathogenic bacteria Staphylococcus aureus (ATCC 6538), Bacillus subtilis (ATCC 6633) and Escherichia coli (ATCC 8739) was investigated, and 20 extracts (42%) exhibited antibacterial activity against at least one of the tested bacterial strains. This study is the first report on the diversity and antibacterial activity of symbiotic fungi residing in the gut of P. flavescens larvae, and the results show that these fungi are highly diverse and could be exploited as a potential source of bioactive compounds.


    Directory of Open Access Journals (Sweden)

    Gabi-Mirela Matei


    Full Text Available Favorability for microbial life of litic and mixic regosols from different urban areas in Iassy municipium was assessed using methods for monitoring the level of soil respiration, microbial density of bacterial and fungal microflora as well as taxonomic composition and species frequency. All soils presented urbic horinzons (U, destroyed structure and carbonates of anthropogenic origin even in topsoil layer. In conditions of neutral-alkaline reaction of urban soil, a moderate content of humus, good conditions for organic matter mineralization processes, rich supply with total nitrogen and mobile phosphorus and potassium and levels of loading with heavy metals below maximum allowable limits, microbial activity was moderate with an average value of 46,443 mg CO2x100g-1 soil. Bacterial community has moderate to high numbers of representatives, dominated by Bacillaceae and Pseudomonadaceae. Fungal microflora is moderately developed and strongly dependent on local soil conditions from the point of view of species composition, with a slight dominance of cosmopolitan Fusarium species. In highly anthropic disturbed soils microbial numbers and activity arelower than in soils less affected by urbanization.

  17. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure. (United States)

    Lim, Jia Chun; Thevarajoo, Suganthi; Selvaratnam, Chitra; Goh, Kian Mau; Shamsir, Mohd Shahir; Ibrahim, Zaharah; Chong, Chun Shiong


    Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L(-1) of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.

  18. Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub-glacial lakes of NW Indian Himalayas. (United States)

    Yadav, Ajar Nath; Sachan, Shashwati Ghosh; Verma, Priyanka; Kaushik, Rajeev; Saxena, Anil Kumar


    The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes.

  19. The lumazine synthase/riboflavin synthase complex: shapes and functions of a highly variable enzyme system. (United States)

    Ladenstein, Rudolf; Fischer, Markus; Bacher, Adelbert


    The xylene ring of riboflavin (vitamin B2 ) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogs of lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.

  20. Diversity and functional significance of cellulolytic microbes living in termite, pill-bug and stem-borer guts. (United States)

    Bashir, Zeenat; Kondapalli, Vamsi Krishna; Adlakha, Nidhi; Sharma, Anil; Bhatnagar, Raj K; Chandel, Girish; Yazdani, Syed Shams


    Arthropods living on plants are able to digest plant biomass with the help of microbial flora in their guts. This study considered three arthropods from different niches - termites, pill-bugs and yellow stem-borers - and screened their guts for cellulase producing microbes. Among 42 unique cellulase-producing strains, 50% belonged to Bacillaceae, 26% belonged to Enterobacteriaceae, 17% belonged to Microbacteriaceae, 5% belonged to Paenibacillaceae and 2% belonged to Promicromonosporaceae. The distribution of microbial families in the three arthropod guts reflected differences in their food consumption habits. Most of the carboxymethylcellulase positive strains also hydrolysed other amorphous substrates such as xylan, locust bean gum and β-D-glucan. Two strains, A11 and A21, demonstrated significant activity towards Avicel and p-nitrophenyl-β-D-cellobiose, indicating that they express cellobiohydrolase. These results provide insight into the co-existence of symbionts in the guts of arthropods and their possible exploitation for the production of fuels and chemicals derived from plant biomass.

  1. Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods (United States)

    Keisam, Santosh; Romi, Wahengbam; Ahmed, Giasuddin; Jeyaram, Kumaraswamy


    Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9–52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods. PMID:27669673

  2. Relationship between honeybee nutrition and their microbial communities. (United States)

    Saraiva, Miriane Acosta; Zemolin, Ana Paula Pegoraro; Franco, Jeferson Luis; Boldo, Juliano Tomazzoni; Stefenon, Valdir Marcos; Triplett, Eric W; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Wurdig


    The microbiota and the functional genes actively involved in the process of breakdown and utilization of pollen grains in beebread and bee guts are not yet understood. The aim of this work was to assess the diversity and community structure of bacteria and archaea in Africanized honeybee guts and beebread as well as to predict the genes involved in the microbial bioprocessing of pollen using state of the art 'post-light' based sequencing technology. A total of 11 bacterial phyla were found within bee guts and 10 bacterial phyla were found within beebread. Although the phylum level comparison shows most phyla in common, a deeper phylogenetic analysis showed greater variation of taxonomic composition. The families Enterobacteriaceae, Ricketsiaceae, Spiroplasmataceae and Bacillaceae, were the main groups responsible for the specificity of the bee gut while the main families responsible for the specificity of the beebread were Neisseriaceae, Flavobacteriaceae, Acetobacteraceae and Lactobacillaceae. In terms of microbial community structure, the analysis showed that the communities from the two environments were quite different from each other with only 7 % of species-level taxa shared between bee gut and beebread. The results indicated the presence of a highly specialized and well-adapted microbiota within each bee gut and beebread. The beebread community included a greater relative abundance of genes related to amino acid, carbohydrate, and lipid metabolism, suggesting that pollen biodegradation predominantly occurs in the beebread. These results suggests a complex and important relationship between honeybee nutrition and their microbial communities.

  3. Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust. (United States)

    Sylvan, Jason B; Hoffman, Colleen L; Momper, Lily M; Toner, Brandy M; Amend, Jan P; Edwards, Katrina J


    A facultatively anaerobic bacterium, designated strain 1MBB1T, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1-3 μm long, that occurred singly and in chains. Strain 1MBB1T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C16:1ω11c (26.5 %), anteiso-C15:0 (19.5 %), C16:0 (18.7 %) and iso-C15:0 (10.4 %), and the cell-wall diamino acid was meso-diaminopimelic acid. Endospores of strain 1MBB1T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1T was a member of the family Bacillaceae, with Bacillus foraminis CV53T and Bacillus novalis LMG 21837T being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1T ( = NCMA B78T = LMG 28275T).

  4. Cloning and Tissue-Specific Expression of a Chitin Deacetylase Gene from Helicoverpa armigera (Lepidoptera: Noctuidae) and Its Response to Bacillus thuringiensis (United States)

    Han, Guoying; Li, Xiumin; Zhang, Ting; Zhu, Xiaoting


    Chitin deacetylases (CDAs) convert chitin into chitosan, the N-deacetylated form of chitin, which influences the mechanical and permeability properties of structures such as the cuticle and peritrophic matrices. In this article, a new CDA encoding gene, Hacda2, was cloned by reverse transcription-polymerase chain reaction method in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), with an open reading frame of 1,611 bp. The deduced protein composed of 536 amino acid residues with a signal peptide, a chitin-binding domain, a low-density lipoprotein receptor class A domain, and a polysaccharide deacetylase-like catalytic domain. The highest expression level of Hacda2 was detected in fat body among tissues tested in the fifth-instar larvae using real-time quantitative polymerase chain reaction method. Feeding of Bacillus thuringiensis (Bt) (Bacillales: Bacillaceae) diet changed the expression level of Hacda1, Hacda2, Hacda5a, and Hacda5b significantly and differentially in the third-instar larvae. Hacda5a and Hacda5b expression were initially down-regulated and then up-regulated, whereas, the expression level of Hacda1 and Hacda2 was suppressed constantly postfeeding on Bt diet. These results suggested that HaCDAs may be involved in the response of H. armigera larvae to Bt and may be helpful to elucidate the roles of HaCDAs in the action of Bt cry toxin. The potential of HaCDAs to be used as synergists of Bt insecticidal protein needs to be further tested. PMID:26163665

  5. Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni. (United States)

    Lee, Jae-Bong; Jeon, Seon Hwa; Choi, Seok-Gwan; Jung, Hee-Young; Kim, Myung Kyum; Srinivasan, Sathiyaraj


    In this paper, a new bacterial strain designated as 16MFT21(T) is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21(T) is a Gram-staining-positive, catalase-oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21(T) revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21(T) is with Bacillus licheniformis ATCC 14580(T) (96.6%) and Bacillus sonorensis NBRC 101234(T) (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone-7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21(T) (=KCTC 18866(T) =JCM 31664(T)) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

  6. Individual and Combined Effects of Bacillus Thuringiensis and Azadirachtin on Plodia Interpunctella Hübner (Lepidoptera: Pyralidae). (United States)

    Nouri-Ganbalani, Gadir; Borzoui, Ehsan; Abdolmaleki, Arman; Abedi, Zahra; George Kamita, Shizuo


    The Indianmeal moth, Plodia interpunctella Hübner (Lepidoptera: Pyralidae), is a major stored product pest that is found throughout the world. In this study, the effect of oral exposure to Bacillus thuringiensis (Berliner) subsp. kurstaki (Bacillales: Bacillaceae) and azadirachtin was evaluated in third instar P. interpunctella under laboratory conditions. The median lethal concentration (LC50) of Bt and azadirachtin on third instars was 490 and 241 μg a.i./ml, respectively. The median lethal time (LT50) of these insecticides was the same (4.5 d following exposure to 750 or 400 μg a.i./ml of Bt or azadirachtin, respectively). When the larvae fed on diet containing LC30 concentrations of both Bt and azadirachtin an additive interaction in terms of mortality was found. A synergistic interaction was found when the larvae fed on diet containing LC50 concentrations of both insecticides. Larvae that fed on insecticide-containing diet (either Bt or azadirachtin at an LC30 concentration, or both insecticides at LC30 or LC50 concentrations) showed lower glycogen and lipid levels, and generally lower protein content in comparison to control larvae. Larvae that fed on diet containing both Bt and azadirachtin showed reduced weight gain and nutritional indices in comparison to control larvae or larvae fed on the diet containing only one of the insecticides. Finally, exposure to both insecticides, either individually or in combination, reduced the level of digestive enzymes found in the midgut. Our findings indicate that both Bt and azadirachtin, either individually or in combination have significant potential for use in controlling of P. interpunctella.

  7. Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism.

    Directory of Open Access Journals (Sweden)

    Kian Mau Goh

    Full Text Available Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.

  8. Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core

    Directory of Open Access Journals (Sweden)

    Vanya Miteva


    Full Text Available The 2537-m-deep North Greenland Eemian Ice Drilling (NEEM core provided a first-time opportunity to perform extensive microbiological analyses on selected, recently drilled ice core samples representing different depths, ages, ice structures, deposition climates and ionic compositions. Here, we applied cultivation, small subunit (SSU rRNA gene clone library construction and Illumina next-generation sequencing (NGS targeting the V4–V5 region, to examine the microbial abundance, viability and diversity in five decontaminated NEEM samples from selected depths (101.2, 633.05, 643.5, 1729.75 and 2051.5 m deposited 300–80 000 years ago. These comparisons of the indigenous glacial microbial populations in the ice samples detected significant spatial and temporal variations. Major findings include: (a different phylogenetic diversity of isolates, dominated by Actinobacteria and fungi, compared to the culture-independent diversity, in which Proteobacteria and Firmicutes were more frequent; (b cultivation of a novel alphaproteobacterium; (c dominance of Cyanobacteria among the SSU rRNA gene clones from the 1729.75-m ice; (d identification of Archaea by NGS that are rarely detected in glacial ice; (e detection of one or two dominant but different genera among the NGS sequences from each sample; (f finding dominance of Planococcaceae over Bacillaceae among Firmicutes in the brittle and the 2051.5-m ice. The overall beta diversity between the studied ice core samples examined at the phylum/class level for each approach showed that the population structure of the brittle ice was significantly different from the two deep clathrated ice samples and the shallow ice core.

  9. Bacillus oleivorans sp. nov., a diesel oil-degrading and solvent-tolerant bacterium. (United States)

    Azmatunnisa, M; Rahul, K; Subhash, Y; Sasikala, Ch; Ramana, Ch V


    Two Gram-stain-positive, diesel oil-degrading, solvent-tolerant, aerobic, endospore-forming, rod-shaped bacteria were isolated from a contaminated laboratory plate. Based on 16S rRNA gene sequence analysis, strains JC228(T) and JC279 were identified as belonging to the genus Bacillus within the family Bacillaceae of the phylum Firmicutes and were found to be most closely related to Bacillus carboniphilus JCM 9731(T) (98.1% 16S rRNA gene sequence similarity) and shared Bacillus . The DNA-DNA hybridization value between the two strains was 88±2%. Strain JC228(T) showed 23.4±1% reassociation (based on DNA-DNA hybridization) with B. carboniphilus LMG 18001(T). The DNA G+C content of strains JC228(T) and JC279 was 39 and 38.4 mol%, respectively. Both strains were positive for catalase and oxidase activities, and negative for hydrolysis of starch and Tween 80. Strains JC228(T) and JC279 grew chemoorganoheterotrophically with optimum growth at pH 7 (range pH 7-9.5) and 35 °C (range 25-40 °C). Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid (PL2) were the major polar lipids. Major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), iso-C(17 : 0) and C(16 : 0). Whole-cell hydrolysates contained l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. Both strains utilized diesel oil as sole carbon and energy source. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed clear differentiation of strains JC228(T) and JC279 from their closest phylogenetic neighbours. Therefore strains JC228(T) and JC279 represent a novel species of the genus Bacillus , for which the name Bacillus oleivorans sp. nov. is proposed. The type strain is JC228(T) ( = LMG 28084(T) = CCTCC AB 2013353(T)).

  10. Thermolongibacillus altinsuensis gen. nov., sp. nov. and Thermolongibacillus kozakliensis sp. nov., aerobic, thermophilic, long bacilli isolated from hot springs. (United States)

    Cihan, Arzu Coleri; Koc, Melih; Ozcan, Birgul; Tekin, Nilgun; Cokmus, Cumhur


    Two novel endospore-forming, aerobic bacilli, strains E173a(T) and E265(T), were isolated from soil and sediment samples from Kozakli and Altinsu hot springs, Nevsehir (Turkey). Their young cells in the exponential phase of growth were motile, Gram-stain-positive, straight rods, 0.6-1.1×3.0-8.0 µm in size, but they became strikingly long, approximately 0.6-1.2 by 9.0-35.0 µm, after the stationary phase of growth. Cells varied in tests for oxidase, and had a weakly positive reaction for catalase. Both strains could grow between 40 and 70 °C, with optimal growth at 60 °C (E173a(T)) and 55 °C (E265(T)). Growth occurred within the range pH 5.0-11.0 with optimal growth at pH 9.0 (E173a(T)) and pH 8.5 (E265(T)). Strain E173a(T) grew within a salinity range from 0 to1.5 % (w/v) NaCl with optimal growth at 0.5 %, while strain E265(T) grew within the range 0-5.0 % (w/v), with an optimum at 3.0 %. The new isolates differed from each other in some phenotypic and chemotaxonomic characters as well as repetitive extragenic palindromic element PCR (rep-PCR) fingerprints. 16S rRNA gene sequence similarities suggested distant relationships with other members of the family Bacillaceae (60 %), iso-C17 : 0 and C16 : 0] supported the consideration of these isolates as members of a novel genus. Based upon phenotypic, phylogenetic and chemotaxonomic characteristics, it is proposed that new isolates represent a novel genus, Thermolongibacillus gen. nov., with two novel species: Thermolongibacillus altinsuensis sp. nov. (type strain E265(T) = DSM 24979(T) = NCIMB 14850(T)) and Thermolongibacillus kozakliensis sp. nov. (type strain E173a(T) = DSM 24978(T) = NCIMB 14849(T)).

  11. Análise fenotípica e genotípica de bactérias heterotróficas e fixadoras de nitrogênio em sedimento na bacia do Rio Cuiabá-MT

    Directory of Open Access Journals (Sweden)

    Fernanda Viana da Cunha


    Full Text Available Os sedimentos apresentam-se como um sistema complexo, que são afetados por parâmetros geológicos, hidrodinâmicos, químicos e biológicos, caracterizado por uma interação entre o ambiente sedimentar de cada região. O presente estudo consistiu em caracterizar a diversidade de bactérias heterotróficas totais e fixadores de nitrogênio em sedimentos do rio Cuiabá utilizando técnicas convencionais de microbiologia e de biologia molecular. As amostras de sedimento foram coletadas com periodicidade bimestral, em quatro pontos sendo estes: Cuiabazinho, Passagem da Conceição, Ribeirão dos Cocais e Barão de Melgaço. As amostras foram processadas através de diluições seriadas (10-2 a 10-7 em solução salina 0,85%. Em seguida cultivadas em placa de Petri através da técnica de Spreed Plate, em meio de cultivo Trypic Soy Agar (TSA para bactérias heterotróficas totais e para bactérias nitrificantes foram utilizados meios seletivos (NFB, JMV e Meio 79 incubadas a 35°C. Posteriormente as estirpes bacterianas foram reisoladas em Agar Nutriente (AN a fim de obter cultura pura para análise morfotintorial de Gram. Este teste permitiu verificar que dos 202 isolados bacterianos, 59% eram bastonetes positivos, sendo que, a maior quantificação bacteriana obtida foi no meio de cultivo TSA, comparado aos outros meios de cultura. O perfil da comunidade bacteriana apresentou na sua maioria bactérias da família Bacillaceae com 28%, sendo que as mesmas foram utilizadas para a análise molecular por Box-PCR, que apresentou uma riqueza de espécies. Esses resultados indicam a importância de pesquisas sobre diversidade microbiana de sedimentos no Estado de Mato Grosso que utilizam técnicas moleculares.

  12. Effect of Ultra-high Pressure on Microbial Population and Shelf Life of Vacuum-packaged Frankfurters during 4 ~C Storage%鳌高压处理对法兰克福香肠中主要微生物的影响及其变化规律

    Institute of Scientific and Technical Information of China (English)

    高杨; 周国兴; 王洋; 郑海涛; 李平兰


    Vacuum-packaged frankfurters were subjected to ultra-high pressure treatments at (20±5) ℃ and different pressure levels: 200, 400 MPa and 600 MPa for 5 or 10 min before storage at 4 ℃ for 60 days with the aim of investigating the effect of ultra-high pressure on the microbial population and shelf life of vacuum-packaged frankfurters. Compared with control samples without receiving any sterilization treatment, ultra-high pressure treatment could dramatically reduce initial microbial count in frankfurters, and inhibit the growth of dominant spoilage bacteria including total bacteria, lactic acid bacteria, psychrophiles, enterobacteriaceae and bacillaceae, which was positively related to pressure and length of treatment time. Ultra-high pressure treatment at 600 MPa for 10 min could prolong the shelf-life of vacuum-packaged frankfurters from 9 to over 60 days during 4 ℃ storage.%为探讨超高压处理对真空包装法兰克福香肠微生物货架期的影响,在(20±5)℃对真空包装法兰克福香肠进行200MPa(5min与1Omin)、400MPa(5min与1Omin)和600MPa(5min与1Omin)的超高压处理。样品处理后于4℃保藏60d,每隔1Od取样分析,直至样品微生物数量达到峰值并趋于稳定为止。与空白对照组(不进行二次灭菌的法兰克福香肠)相比,超高压处理能显著降低法兰克福香肠初始微生物数量,并对保藏过程中的腐败微生物:嗜冷菌、乳酸菌和大肠菌群的生长有显著抑制作用,抑制程度与压力(200

  13. Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river. (United States)

    Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao


    Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on

  14. [Phylogenetic diversity of culturable bacteria in the ancient salt deposits of the Yipinglang Salt Mine, P. R. China]. (United States)

    Chen, Yi-guang; Li, Hui-ming; Li, Qin-yuan; Chen, Wei; Cui, Xiao-long


    The microbial diversity of cultivable bacteria, isolated from the ancient salt deposits from the Yipinglang Salt Mine (YPL) in the Yunnan Province, P. R. China,was investigated by using conventional culture-dependent method and phylogenetic analyses based on 16S rRNA gene sequence comparisons. 38 bacteria strains were isolated from the brine, halite and saline soil samples on MBA (marine broth agar 2216, Difco) and ISP 2 (International Streotomyces Project medium 2) media supplemented with 0.5-3.5 mol/L NaCl. The genomic DNAs of the isolates were extracted and their 16S rRNA genes were amplified by PCR using bacterial universal primers. The resulting 16S rRNA gene sequences were compared with sequences obtained from public databases to find the most closely related species. Phylogenetic analyses were performed using the software packages MEGA after multiple alignment of sequence data by CLUSTAL X. The evolutional instances (corrected by Kimura's 2-parameter model) were calculated and clustering was performed with the neighbor-joining method. The results showed that the isolates are members of twenty-four genera (Acinetobacter, Agromyces, Arthrobacter, Bacillus, Brevundimonas, Chromohalobacter, Dietzia, Erythrobacter, Exiguobacterium, Halomonas, Idiomarina, Kocuria, Marinobacter, Micrococcus, Paracoccus, Planomicrbium, Porphyrobacter, Pseudomonas, Psychrobacter, Roseivivax, Saccharospirillum, Salegentibactor, Salinicoccus, Streptomyces) of seventeen families (Alteromonadaceae, Bacillaceae, Caulobacteraceae, Flavobacteriaceae, Halomonadaceae, Idiomarinaceae, Microbacteriaceae, Micrococcaceae, Moraxellaceae, Planococcaceae, Pseudomonadaceae, Rhodobacteraceae, Dietziaceae, Saccharospirillaceae, Sphingomonadaceae, Staphylococcaceae, Streptomycetaceae) in four major phylogenetic groups (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria). The most abundant and diverse isolates were within the phyla of Proteobacteria (47.3%; Gamma-Proteobacteria, 31.5%; Alpha

  15. S-layer nanoglycobiology of bacteria. (United States)

    Messner, Paul; Steiner, Kerstin; Zarschler, Kristof; Schäffer, Christina


    Cell surface layers (S-layers) are common structures of the bacterial cell envelope with a lattice-like appearance that are formed by a self-assembly process. Frequently, the constituting S-layer proteins are modified with covalently linked glycan chains facing the extracellular environment. S-layer glycoproteins from organisms of the Bacillaceae family possess long, O-glycosidically linked glycans that are composed of a great variety of sugar constituents. The observed variations already exceed the display found in eukaryotic glycoproteins. Recent investigations of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools, indicated that the S-layer glycoprotein glycan biosynthesis pathway utilizes different modules of the well-known biosynthesis routes of lipopolysaccharide O-antigens. The genetic information for S-layer glycan biosynthesis is usually present in S-layer glycosylation (slg) gene clusters acting in concert with housekeeping genes. To account for the nanometer-scale cell surface display feature of bacterial S-layer glycosylation, we have coined the neologism 'nanoglycobiology'. It includes structural and biochemical aspects of S-layer glycans as well as molecular data on the machinery underlying the glycosylation event. A key aspect for the full potency of S-layer nanoglycobiology is the unique self-assembly feature of the S-layer protein matrix. Being aware that in many cases the glycan structures associated with a protein are the key to protein function, S-layer protein glycosylation will add a new and valuable component to an 'S-layer based molecular construction kit'. In our long-term research strategy, S-layer nanoglycobiology shall converge with other functional glycosylation systems to produce 'functional' S-layer neoglycoproteins for diverse applications in the fields of nanobiotechnology and vaccine technology. Recent advances in the field of

  16. Bacillus luteus sp. nov., isolated from soil. (United States)

    Subhash, Y; Sasikala, Ch; Ramana, Ch V


    Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 27257T).

  17. Bacillus crescens sp. nov., isolated from soil. (United States)

    Shivani, Y; Subhash, Y; Dave Bharti, P; Sasikala, Ch; Ramana, Ch V


    Two bacterial strains (JC247T and JC248) were isolated from soil samples collected from Rann of Kutch, Gujarat, India. Colonies of both strains were creamy white. Cells were Gram-stain-positive, rods-to-curved rods (crescent-shaped), and produced centrally located oval-shaped endospores. Major (>5 %) fatty acids of both strains were iso-C16  :  0, iso-C14  :  0, iso-C15  :  0, C16  :  1ω11c and C16  :  0, with minor ( 1 %) amounts of anteiso-C15  :  0, anteiso-C17  :  0, iso-C16  :  1 H, iso-C17  :  0, iso-C18  :  0, C14  :  0, C17  :  0, C18  :  0, C18  :  1ω9c, iso-C17  :  1ω10c and anteiso-C17  :  0B/isoI. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell-wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The genomic DNA G+C content of strains JC247T and JC248 was 48.2 and 48.1 mol%, respectively. Both strains were closely related with mean DNA-DNA hybridization >90 %. 16S rRNA gene sequence analysis of both strains indicated that they are members of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a 16S rRNA gene sequence similarity of 96.93 % with Bacillus firmus NCIMB 9366T and Bacillus. Sequence similarity between strain JC247T and JC248 was 100 %. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strains JC247T and JC248 as representatives of a novel species of the genus Bacillus, for which the name Bacilluscrescens sp. nov. is proposed. The type strain is JC247T ( = KCTC 33627T = LMG 28608T).

  18. Pyrosequencing evidence for iron-cycling microbial communities in sediments of the Skagerrak and Bothnian Bay (United States)

    Reyes, Carolina; Dellwig, Olaf; Noriega-Ortega, Beatriz; Dähnke, Kirstin; Gehre, Matthias; Böttcher, Michael E.; Friedrich, Michael W.


    reduction, while cryptic Fe-S-cycling can be largely excluded. 16S rRNA gene sequences indicate Proteobacteria dominated both sites. Beta diversity, i.e. diversity differences between sites, were attributed to Chloroflexi, δ-, γ-Proteobacteria, candidate division OP8, Acidobacteria, Euryarchaeota YLA114 and Thermoplasmata E2 in SK. Unclassified Archaea, Acidobacteria, Chlorobi, α-, γ- and δ-Proteobacteria were taxa that showed significant values of Spearman correlation with Fe2+ concentrations. In the BB β-Proteobacteria and Cenarchaeaceae contributed to β-diversity and Spearman correlations showed that β-Proteobacteria correlated with Mn2+ concentrations. Potential Fe and Mn reducers including Desulfobacteraceae, Desulfuromonadaceae, Desulfobulbaceae, Geobacteraceae, Pelobacteraceae, Clostridiaceae, and Bacillaceae (between ≤0.1-12% relative abundance) as well as the archaeal Methanosarcinaceae were detected. Fe oxidation occurring near the sediment surface was supported by the presence of Fe oxidising Mariprofundus in SK and Gallionella in the brackish BB sediments reflecting their adaptation to the prevailing salinity. Although Spearman correlations showed several groups correlate with Fe/Mn, specific microorganisms could not be determined. Thus, an unclassified and abundant microbial community may carry out Fe/Mn cycling or alternatively, microorganisms that are known for Fe/Mn cycling, but are less abundant, could be involved.

  19. Diversity of culturable bacteria associated with the sea urchin Hemicentrotus pulcherrimus from Naozhou Island%硇洲岛海胆可培养细菌的多样性

    Institute of Scientific and Technical Information of China (English)

    黄苛; 张丽; 刘祝祥; 陈奇辉; 彭清忠; 李文均; 崔晓龙; 陈义光


    [Objective] To investigate the diversity of culturable bacteria isolated from the sea urchin Hemicentrotus pulcherrimus collected from a tidal flat of Naozhou Island(20°52'N~20°56'N 110°33'E~110°38'E),Leizhou Bay,South China Sea,China. [Methods] Bacteria were isolated from the sample by using conventional culture-dependent method and then investigated by using phylogenetic analysis based on 16S rRNA gene sequence comparisons.[Results ]We isolated 106 bacterial strains from the sample on media (Difco marine 2216;International Streotomyces Project medium 2;nutrient;sea water and humic acid agars) supplemented with 0~2 mol/L NaCl.On the basis of morphological;physiological and biochemical characteristics;we selected 34 strains to perform a phylogenetic analysis based on 16S rRNA gene sequences.Our results showed that 34 isolates represented 21 species; belonging to 17 genera (Alteromonas, Bacillus, Brachybacterium , Brevibacterium, Halobacillus,Halomonas, Nocardiopsis , Oceanobacillus, Piscibacillus, Planococcus, Pontibadllus, Pseudoalteromonas, Pseudonocardia,Sahnicoccus, Sahnwibrio, Staphylococcus, Vibrio, Virgibacillus) of 10 families (Alteromonadaceae, Bacillaceae,Brevibactenaceae, Dermabacteraceae,Halomonadaceae,Planococcaceae,Pseudoalteromonadaceae,Pseudonocardiaceae;Nocardiopsaceae,Staphylococcaceae,Vibnonaceae)in three phylogenetic groups (Actinobactena,Firmicutes,GammaProteobactena).The most abundant and diverse isolates were within the phylum Firmicutes (58.8%)and the subphylum Gamma-Proteobactena (26.5% ).The phylogenetic distance matrix results suggested that there were obvious genetic divergences between most isolates and their closestly related type strains (16S rRNA gene sequence similarities ranged from 99.6 to 99.9%), and that, out of 34 isolates, at least 5 strains (JSM 076033, JSM 076056, JSM 076093, JSM 078063, JSM 078169) could represent 5 potential new species within 5 characterized genera (Jeotgalicoccus

  20. Biodiversity of culturable bacteria associated with Crassostrea hongkongensis from the tidal flat of Naozhou Island in the South China Sea%硇洲岛潮汐带牡蛎相关可培养细菌多样性

    Institute of Scientific and Technical Information of China (English)

    肖建青; 朱泓溢; 刘祝祥; 刘荷; 贺建武; 李洪军; 钟小娟; 李文均; 陈义光


    [Objective] To investigate the diversity of cultivable bacteria isolated from Crassostrea hongkongensis collected from the tidal flat of Naozhou Island (20°52′-20°56′ N,110°33′-110°38′ E) in the South China Sea.[Methods] Bacteria strains were isolated from homogenates of the sample by using conventional culture-dependent method,and then the isolated strains were investigated by using a phylogenetic analysis based on the 16S rRNA gene sequences.[Results] We isolated 102 bacteria strains from the sample on a number of media [MA (marine agar 2216),MH (moderate halophilic medium agar),NA (nutrient agar)] supplemented with 0-25% (W/V) NaCl.On the basis of the results of some morphological,physiological and biochemical tests,we selected 74 strains to perform a further phylogenetic analysis.Our results showed that the 74 isolates represented 38 species,belonging to 18 genera (Idiomarina,Morganella,Proteus,Halomonas,Paracoccus,Wohlfahrtiimonas,Marinobacter,Vibrio,Pseudoalteromonas,Shewanella,Oceanimonas,Nitratireductor,Myroides,Bacillus,Virgibacillus,Staphylococcus,Enterococcus,Trichococcus) of 16 families (Idiomarinaceae,Enterobacteriaceae,Halomonadaceae,Rhodobacteraceae,Xanthomonadaceae,Alteromonadaceae,Vibrionaceae,Pseudoalteromonadaceae,Shewanellaceae,Aeromonadaceae,Phyllobacteriaceae,Flavobacteriaceae,Bacillaceae,Staphylococcaceae,Enterococcaceae,Carnobacteriaceae) in 4 phylogenetic groups (Gamma-Proteobacteria,Alpha-Proteobacteria,Bacteroidetes,Firmicutes).The most of isolates were within the subphylum Gamma-Proteobacteria (45strains,60.8%),followed by Firmicutes (12 strains,16.2%),Bacteriodetes (11 strains,14.9%) and Alpha-Proteobacteria (6 strains,8.1%).The phylogenetic analysis results suggested that there were obvious genetic divergences between most isolates and their closest type strains (16S rRNA gene sequence similarities ranged from 94.3% to 99.8%).The results also showed that,out of the 74 isolates,at least 6 strains could