Science.gov

Sample records for mesophilic bacterial species

  1. Bacterial gene import and mesophilic adaptation in archaea.

    PubMed

    López-García, Purificación; Zivanovic, Yvan; Deschamps, Philippe; Moreira, David

    2015-07-01

    It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.

  2. Bacterial gene import and mesophilic adaptation in archaea

    PubMed Central

    López-García, Purificación; Zivanovic, Yvan; Deschamps, Philippe; Moreira, David

    2015-01-01

    It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages — including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) — independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles. PMID:26075362

  3. Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion.

    PubMed

    Stiborova, Hana; Wolfram, Jan; Demnerova, Katerina; Macek, Tomas; Uhlik, Ondrej

    2015-11-01

    Stabilized sewage sludge is applied to agricultural fields and farmland due to its high organic matter content. The aim of this study was to investigate the effects of two types of sludge stabilization, mesophilic anaerobic digestion (MAD) and thermophilic anaerobic digestion (TAD), on bacterial communities in sludge, including the presence of pathogenic microorganisms. Bacterial community structure and phylogenetic diversity were analyzed in four sewage sludge samples from the Czech Republic. Analysis of 16S ribosomal RNA (rRNA) genes showed that investigated sludge samples harbor diverse bacterial populations with only a few taxa present across all samples. Bacterial diversity was higher in sludge samples after MAD versus TAD treatment, and communities in MAD-treated sludge shared the highest genetic similarities. In all samples, the bacterial community was dominated by reads affiliated with Proteobacteria. The sludge after TAD treatment had considerably higher number of reads of thermotolerant/thermophilic taxa, such as the phyla Deinococcus-Thermus and Thermotogae or the genus Coprothermobacter. Only one operational taxonomic unit (OTU), which clustered with Rhodanobacter, was detected in all communities at a relative abundance >1 %. All of the communities were screened for the presence of 16S rRNA gene sequences of pathogenic bacteria using a database of 122 pathogenic species and ≥98 % identity threshold. The abundance of such sequences ranged between 0.23 and 1.57 % of the total community, with lower numbers present after the TAD treatment, indicating its higher hygienization efficiency. Sequences clustering with nontuberculous mycobacteria were present in all samples. Other detected sequences of pathogenic bacteria included Streptomyces somaliensis, Acinetobacter calcoaceticus, Alcaligenes faecalis, Gordonia spp., Legionella anisa, Bordetella bronchiseptica, Enterobacter aerogenes, Brucella melitensis, and Staphylococcus aureus. PMID:25921720

  4. Mathematical models and bacterial communities for ammonia toxicity in mesophilic anaerobes not acclimated to high concentrations of ammonia.

    PubMed

    Park, Seyong; Cui, Fenghao; Mo, Kyung; Kim, Moonil

    2016-01-01

    In this study, we evaluated ammonia toxicity in mesophilic anaerobic digestion at various pH values and total ammonia nitrogen (TAN) concentrations. We performed anaerobic toxicity assays (ATAs) to evaluate the toxicity effects of TAN and pH on mesophilic anaerobic digestion. Modeling based on the results of the ATAs indicated that the specific methanogenic activity (SMA) decreased by 30% at a TAN concentration higher than 3.0 g/L compared to a TAN concentration of 0 g/L. In addition, the highest SMA for a given TAN level (0.5-10.0 g/L) was observed at a pH of around 7.6. The results of bacterial community analyses showed that the diversity and richness of microorganisms with increasing TAN concentration were decreased. Chloroflexi and Synergistetes were the dominant phyla at TAN concentrations less than 3.0 g/L, and Firmicutes was the dominant phylum at TAN concentrations higher than 3.0 g/L, implying that the ammonia toxicity concentration may influence the kind of dominant species. In conclusion, to start a stable mesophilic anaerobic digestion concerning ammonia toxicity, a TAN concentration less than 3.0 g/L is preferable. PMID:27533868

  5. Trends of Antibiotic Resistance in Mesophilic and Psychrotrophic Bacterial Populations during Cold Storage of Raw Milk

    PubMed Central

    Munsch-Alatossava, Patricia; Gauchi, Jean-Pierre; Chamlagain, Bhawani; Alatossava, Tapani

    2012-01-01

    Psychrotrophic bacteria in raw milk are most well known for their spoilage potential and cause significant economic losses in the dairy industry. Despite their ability to produce several exoenzyme types at low temperatures, psychrotrophs that dominate the microflora at the time of spoilage are generally considered benign bacteria. It was recently reported that raw milk-spoiling Gram-negative-psychrotrophs frequently carried antibiotic resistance (AR) features. The present study evaluated AR to four antibiotics (ABs) (gentamicin, ceftazidime, levofloxacin, and trimethoprim-sulfamethoxazole) in mesophilic and psychrotrophic bacterial populations recovered from 18 raw milk samples, after four days storage at 4°C or 6°C. Robust analysis of variance and non parametric statistics (e.g., REGW and NPS) revealed that AR prevalence among psychrotrophs, for milk samples stored at 4°C, often equalled the initial levels and equalled or increased during the cold storage at 6°C, depending on the AB. The study performed at 4°C with an intermediate sampling point at day 2 suggested that (1) different psychrotrophic communities with varying AR levels dominate over time and (2) that AR (determined from relative amounts) was most prevalent, transiently, after 2-day storage in psychrotrophic or mesophilic populations, most importantly at a stage where total counts were below or around 105 CFU/mL, at levels at which the milk is acceptable for industrial dairy industrial processes. PMID:23724333

  6. Inactivation of selected bacterial pathogens in dairy cattle manure by mesophilic anaerobic digestion (balloon type digester).

    PubMed

    Manyi-Loh, Christy E; Mamphweli, Sampson N; Meyer, Edson L; Okoh, Anthony I; Makaka, Golden; Simon, Michael

    2014-07-14

    Anaerobic digestion of animal manure in biogas digesters has shown promise as a technology in reducing the microbial load to safe and recommended levels. We sought to treat dairy manure obtained from the Fort Hare Dairy Farm by investigating the survival rates of bacterial pathogens, through a total viable plate count method, before, during and after mesophilic anaerobic digestion. Different microbiological media were inoculated with different serial dilutions of manure samples that were withdrawn from the biogas digester at 3, 7 and 14 day intervals to determine the viable cells. Data obtained indicated that the pathogens of public health importance were 90%-99% reduced in the order: Campylobacter sp. (18 days) < Escherichia coli sp. (62 days) < Salmonella sp. (133 days) from a viable count of 10.1 × 103, 3.6 × 105, 7.4 × 103 to concentrations below the detection limit (DL = 102 cfu/g manure), respectively. This disparity in survival rates may be influenced by the inherent characteristics of these bacteria, available nutrients as well as the stages of the anaerobic digestion process. In addition, the highest p-value i.e., 0.957 for E. coli showed the statistical significance of its model and the strongest correlation between its reductions with days of digestion. In conclusion, the results demonstrated that the specific bacterial pathogens in manure can be considerably reduced through anaerobic digestion after 133 days.

  7. Reassessment of the Enteropathogenicity of Mesophilic Aeromonas Species

    PubMed Central

    Teunis, Peter; Figueras, Maria J.

    2016-01-01

    Cases of Aeromonas diarrhea have been described all over the world. The genus Aeromonas includes ca. 30 species, of which 10 have been isolated in association with gastroenteritis. The dominating species that account for ca. 96% of the identified strains are Aeromonas caviae, A. veronii, A. dhakensis, and A. hydrophila. However, the role of Aeromonas as a true enteropathogen has been questioned on the basis of the lack of outbreaks, the non-fulfillment of Koch’s postulates and the low numbers of acute illnesses in the only existing human challenge study. In the present study we reassess the enteropathogenicity of Aeromonas using dose response models for microbial infection and acute illness. The analysis uses the data from the human challenge study and additional data from selected outbreak investigations where the numbers exposed and the dose were reported, allowing their inclusion as “natural experiments”. In the challenge study several cases of asymptomatic shedding were found (26.3%, 15/57), however, only 3.5% (2/57) of those challenged with Aeromonas developed acute enteric symptoms (i.e., diarrhea). The “natural experiments” showed a much higher risk of illness associated with exposure to Aeromonas, even at moderate to low doses. The median dose required for 1% illness risk, was ~1.4 × 104 times higher in the challenge study (1.24 × 104 cfu) compared to natural exposure events (0.9 cfu). The dose response assessment presented in this study shows that the combined challenge and outbreak data are consistent with high infectivity of Aeromonas, and a wide range of susceptibility to acute enteric illness. To illustrate the outcomes, we simulate the risk associated with concentrations of Aeromonas found in different water and food matrices, indicating the disease burden potentially associated with these bacteria. In conclusion this study showed that Aeromonas is highly infectious, and that human susceptibility to illness may be high, similar to

  8. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

    NASA Technical Reports Server (NTRS)

    Haney, P. J.; Badger, J. H.; Buldak, G. L.; Reich, C. I.; Woese, C. R.; Olsen, G. J.

    1999-01-01

    The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

  9. Reactor performance and bacterial pathogen removal in response to sludge retention time in a mesophilic anaerobic digester treating sewage sludge.

    PubMed

    Chen, Yan; Fu, Bo; Wang, Yan; Jiang, Qian; Liu, He

    2012-02-01

    The effects of sludge retention time (SRT) on reactor performance and bacterial pathogen removal of sludge mesophilic anaerobic digestion (MAD) were investigated in a continuous stirred tank reactor. The average volatile solids removal remained around 20% and the biogas production rate varied from 100 to 132ml/ld. The MAD process was efficient to remove Salmonella sp. and Escherichia coli with removal efficiencies increased with SRT from 11d, 16d to 25d. However, the Shigella sp. removal was insignificant. The difference in the resistance of the three pathogens to sludge MAD process is helpful to the selection of pathogen indicators in the biosolids. Log reduction of pathogens determined by MPN was much higher than the data by quantitative PCR, suggesting the presence of viable but non-culturable pathogen cells. This study confirms that the control of appropriate SRT for sludge MAD should take both reactor performance and pathogen removal into account.

  10. Temperature Sensitivity Conferred by ligA Alleles from Psychrophilic Bacteria upon Substitution in Mesophilic Bacteria and a Yeast Species

    PubMed Central

    Pankowski, Jarosław A.; Puckett, Stephanie M.

    2016-01-01

    We have assembled a collection of 13 psychrophilic ligA alleles that can serve as genetic elements for engineering mesophiles to a temperature-sensitive (TS) phenotype. When these ligA alleles were substituted into Francisella novicida, they conferred a TS phenotype with restrictive temperatures between 33 and 39°C. When the F. novicida ligA hybrid strains were plated above their restrictive temperatures, eight of them generated temperature-resistant variants. For two alleles, the mutations that led to temperature resistance clustered near the 5′ end of the gene, and the mutations increased the predicted strength of the ribosome binding site at least 3-fold. Four F. novicida ligA hybrid strains generated no temperature-resistant variants at a detectable level. These results suggest that multiple mutations are needed to create temperature-resistant variants of these ligA gene products. One ligA allele was isolated from a Colwellia species that has a maximal growth temperature of 12°C, and this allele supported growth of F. novicida only as a hybrid between the psychrophilic and the F. novicida ligA genes. However, the full psychrophilic gene alone supported the growth of Salmonella enterica, imparting a restrictive temperature of 27°C. We also tested two ligA alleles from two Pseudoalteromonas strains for their ability to support the viability of a Saccharomyces cerevisiae strain that lacked its essential gene, CDC9, encoding an ATP-dependent DNA ligase. In both cases, the psychrophilic bacterial alleles supported yeast viability and their expression generated TS phenotypes. This collection of ligA alleles should be useful in engineering bacteria, and possibly eukaryotic microbes, to predictable TS phenotypes. PMID:26773080

  11. The formation of illite from nontronite by mesophilic and thermophilic bacterial reaction

    USGS Publications Warehouse

    Jaisi, D.P.; Eberl, D.D.; Dong, H.; Kim, J.

    2011-01-01

    The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic (Shewanella putrefaciens CN32) and thermophilic (Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65??C) were the most favorable conditions forthe formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

  12. From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples.

    PubMed

    Sun, Weimin; Yu, Guangwei; Louie, Tiffany; Liu, Tong; Zhu, Chengsheng; Xue, Gang; Gao, Pin

    2015-12-01

    The shift of microbial communities during a transition from mesophilic anaerobic digestion (MAD) to thermophilic anaerobic digestion (TAD) was characterized in two treatments. One treatment was inoculated with sludge and the other was inoculated with manure. In this study, methane was produced both in MAD and TAD, but TAD has slightly more methane produced than MAD. A broad phylogenetic spectrum of bacterial, archaeal, and fungal taxa at thermophilic conditions was detected. Coprothermobacter, Bacillus, Haloplasma, Clostridiisalibacter, Methanobacterium, Methanothermobacter, Saccharomycetales, Candida, Alternaria, Cladosporium, and Penicillium were found almost exclusively in TAD, suggesting their adaptation to thermophilic conditions and ecological roles in digesting the organic compounds. The characterization of the lesser-known fungal community revealed that fungi probably constituted an important portion of the overall community within TAD and contributed to this process by degrading complex organic compounds. The shift of the microbial communities between MAD and TAD implied that temperature drastically affected the microbial diversity in anaerobic digestion. In addition, the difference in microbial communities between sludge and manure indicated that different source of inoculum also affected the microbial diversity and community.

  13. Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure.

    PubMed

    Jang, Hyun Min; Ha, Jeong Hyub; Kim, Mi-Sun; Kim, Jong-Oh; Kim, Young Mo; Park, Jong Moon

    2016-08-01

    In recent years, anaerobic co-digestion (AcoD) has been widely used to improve reactor performance, especially methane production. In this study, we applied two different operating temperatures (thermophilic and mesophilic) and gradually increased the load of food wastewater (FWW) to investigate the bacterial communities during the AcoD of waste activated sludge (WAS) and FWW. As the load of FWW was increased, methane production rate (MPR; L CH4/L d) and methane content (%) in both Thermophilic AcoD (TAcoD) and Mesophilic AcoD (MAcoD) increased significantly; the highest MPR and methane content in TAcoD (1.423 L CH4/L d and 68.24%) and MAcoD (1.233 L CH4/L d and 65.21%) were observed when the FWW mixing ratio was 75%. However, MPR and methane yield in both reactors decreased markedly and methane production in TAcoD ceased completely when only FWW was fed into the reactor, resulting from acidification of the reactor caused by accumulation of organic acids. Pyrosequencing analysis revealed a decrease in bacterial diversity in TAcoD and a markedly different composition of bacterial communities between TAcoD and MAcoD with an increase in FWW load. For example, Bacterial members belonging to two genera Petrotoga (assigned to phylum Thermotogae) and Petrimonas (assigned to phylum Bacteroidetes) became dominant in TAcoD and MAcoD with an increase in FWW load, respectively. In addition, quantitative real-time PCR (qPCR) results showed higher bacterial and archaeal populations (expressed as 16S rRNA gene concentration) in TAcoD than MAcoD with an increase in FWW load and showed maximum population when the FWW mixing ratio was 75% in both reactors. Collectively, this study demonstrated the dynamics of key bacterial communities in TAcoD and MAcoD, which were highly affected by the load of FWW. PMID:27155112

  14. Recombinant thermoactive phosphoenolpyruvate carboxylase (PEPC) from Thermosynechococcus elongatus and its coupling with mesophilic/thermophilic bacterial carbonic anhydrases (CAs) for the conversion of CO2 to oxaloacetate.

    PubMed

    Del Prete, Sonia; De Luca, Viviana; Capasso, Clemente; Supuran, Claudiu T; Carginale, Vincenzo

    2016-01-15

    With the continuous increase of atmospheric CO2 in the last decades, efficient methods for carbon capture, sequestration, and utilization are urgently required. The possibility of converting CO2 into useful chemicals could be a good strategy to both decreasing the CO2 concentration and for achieving an efficient exploitation of this cheap carbon source. Recently, several single- and multi-enzyme systems for the catalytic conversion of CO2 mainly to bicarbonate have been implemented. In order to design and construct a catalytic system for the conversion of CO2 to organic molecules, we implemented an in vitro multienzyme system using mesophilic and thermophilic enzymes. The system, in fact, was constituted by a recombinant phosphoenolpyruvate carboxylase (PEPC) from the thermophilic cyanobacterium Thermosynechococcus elongatus, in combination with mesophilic/thermophilic bacterial carbonic anhydrases (CAs), for converting CO2 into oxaloacetate, a compound of potential utility in industrial processes. The catalytic procedure is in two steps: the conversion of CO2 into bicarbonate by CA, followed by the carboxylation of phosphoenolpyruvate with bicarbonate, catalyzed by PEPC, with formation of oxaloacetate (OAA). All tested CAs, belonging to α-, β-, and γ-CA classes, were able to increase OAA production compared to procedures when only PEPC was used. Interestingly, the efficiency of the CAs tested in OAA production was in good agreement with the kinetic parameters for the CO2 hydration reaction of these enzymes. This PEPC also revealed to be thermoactive and thermostable, and when coupled with the extremely thermostable CA from Sulphurhydrogenibium azorense (SazCA) the production of OAA was achieved even if the two enzymes were exposed to temperatures up to 60 °C, suggesting a possible role of the two coupled enzymes in biotechnological processes.

  15. Eradication of bacterial species via photosensitization

    NASA Astrophysics Data System (ADS)

    Golding, Paul S.; Maddocks, L.; King, Terence A.; Drucker, D. B.

    1999-02-01

    Photosensitization and inactivation efficacy of three bacterial species: Prevotella nigrescens, Staphylococcus aureus and Escherichia coli have been investigated. Samples of Staphylococcus aureus and Escherichia coli were treated with the triphenylmethane dye malachite green isothiocyanate and exposed to light from a variety of continuous and pulsed light sauces at a wavelength of approximately 630 nm. Inactivation of the Gram-positive species Staphylococcus aureus was found to increase with radiation dose, whilst Gram-negative Escherichia coli was resistant to such treatment. Samples of the pigmented species Prevotella nigrescens were found to be inactivated by exposure to light alone. The mechanism of photosensitization and inactivation of Staphylococcus aureus with malachite green isothiocyanate is addressed. The possible roles of the excited triplet state of the photosensitizer, the involvement of molecular oxygen, and the bacterial cell wall are discussed. Photosensitization may provide a way of eliminating naturally pigmented species responsible for a variety of infections, including oral diseases such as gingivitis and periodontitis.

  16. Bacterial responses to reactive chlorine species.

    PubMed

    Gray, Michael J; Wholey, Wei-Yun; Jakob, Ursula

    2013-01-01

    Hypochlorous acid (HOCl), the active ingredient of household bleach, is the most common disinfectant in medical, industrial, and domestic use and plays an important role in microbial killing in the innate immune system. Given the critical importance of the antimicrobial properties of chlorine to public health, it is surprising how little is known about the ways in which bacteria sense and respond to reactive chlorine species (RCS). Although the literature on bacterial responses to reactive oxygen species (ROS) is enormous, work addressing bacterial responses to RCS has begun only recently. Transcriptomic and proteomic studies now provide new insights into how bacteria mount defenses against this important class of antimicrobial compounds. In this review, we summarize the current knowledge, emphasizing the overlaps between RCS stress responses and other more well-characterized bacterial defense systems, and identify outstanding questions that represent productive avenues for future research. PMID:23768204

  17. Characterization and comparative analysis of psychrophilic and mesophilic alpha-amylases from Euplotes species: a contribution to the understanding of enzyme thermal adaptation.

    PubMed

    Yang, Guang; Yang, Guang; Aprile, Lino; Turturo, Vincenzo; Pucciarelli, Sandra; Pucciarelli, Stefania; Miceli, Cristina

    2013-09-01

    The eukaryotic α-amylase isolated from the psychrophilic ciliated protozoon Euplotes focardii (EfAmy) was expressed in Escherichia coli and biochemically characterized. Its enzymatic activity was compared to that of the homologous protein from the mesophilic congeneric species Euplotes crassus (EcAmy). The comparison of the amino acid composition and the surface residue composition of the two enzymes indicated a preference for tiny residues and the avoidance of charged, aromatic and hydrophobic residues in EfAmy. Our comparative homology modeling study reveals a lack of surface salt bridges, a decreased number of the surface charged residues, decreased hydrogen bonds and bound ions, and a reduction of aromatic-sulfur interactions, cationic-π interactions and disulfide interactions in EfAmy. In contrast, sequence alignment and homology modeling showed five unconserved prolines located on the surface loops of EcAmy. By analyzing amylolytic activity towards soluble starch as the substrate, we determined the temperature and pH dependence, thermostability and kinetic parameters of these two enzymes. We demonstrated that EfAmy shows the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at low temperatures and high thermolability. In contrast, the EcAmy showed mesophilic characteristics with the highest activity at moderate temperatures and a more than 2-fold increased half-life at 50°C compared to EfAmy. The kcat and KM values of EfAmy were higher than those of the mesophilic EcAmy at all tested temperatures. Furthermore, both EfAmy and EcAmy showed maximum activities at pH 9 and maintained high activities in the presence of surfactants. These results suggest the potential applications of EfAmy and EcAmy as ingredients in detergents for industrial applications.

  18. Bacterial Community Diversity Harboured by Interacting Species.

    PubMed

    Bili, Mikaël; Cortesero, Anne Marie; Mougel, Christophe; Gauthier, Jean Pierre; Ermel, Gwennola; Simon, Jean Christophe; Outreman, Yannick; Terrat, Sébastien; Mahéo, Frédérique; Poinsot, Denis

    2016-01-01

    All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts. PMID:27258532

  19. Bacterial Community Diversity Harboured by Interacting Species

    PubMed Central

    Bili, Mikaël; Cortesero, Anne Marie; Mougel, Christophe; Gauthier, Jean Pierre; Ermel, Gwennola; Simon, Jean Christophe; Outreman, Yannick; Terrat, Sébastien; Mahéo, Frédérique; Poinsot, Denis

    2016-01-01

    All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts. PMID:27258532

  20. Full-scale mesophilic biogas plants using manure as C-source: bacterial community shifts along the process cause changes in the abundance of resistance genes and mobile genetic elements.

    PubMed

    Wolters, Birgit; Ding, Guo-Chun; Kreuzig, Robert; Smalla, Kornelia

    2016-02-01

    The application of manure, typically harboring bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs), as co-substrate in biogas plants (BGPs) might be critical when digestates are used as fertilizers. In the present study, the relative abundance of RGs and MGEs in total community (TC-) DNA from manure, fermenters and digestate samples taken at eight full-scale BGPs co-fermenting manure were determined by real-time PCR. In addition, the bacterial community composition of all digestates as well as manure and fermenter material from one BGP (BGP3) was characterized by 454-pyrosequencing of 16S rRNA amplicons from TC-DNA. Compared to respective input manures, relative abundances determined for sul1, sul2, tet(M), tet(Q), intI1, qacEΔ1, korB and traN were significantly lower in fermenters, whereas relative abundances of tet(W) were often higher in fermenters. The bacterial communities in all digestates were dominated by Firmicutes and Bacteroidetes while Proteobacteria were low in abundance and no Enterobacteriaceae were detected. High-throughput sequencing revealed shifts in bacterial communities during treatment for BGP3. Although in comparison to manure, digestate bacteria had lower relative abundances of RGs and MGEs except for tet(W), mesophilic BGPs seem not to be effective for prevention of the spread of RGs and MGEs via digestates into arable soils.

  1. Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

    PubMed Central

    Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

    2015-01-01

    The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters. PMID:26648921

  2. Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

    PubMed

    Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

    2015-01-01

    The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

  3. Bacterial species dominance within a binary culture biofilm.

    PubMed Central

    Banks, M K; Bryers, J D

    1991-01-01

    Studies with two species of bacteria, Pseudomonas putida and Hyphomicrobium sp. strain ZV620, were carried out to evaluate the overall net rate of accumulation of biofilm, the biofilm species composition, and individual species shear-related removal rates. Bacterial cells of either or both species were deposited onto glass or biofilm surfaces to initiate multispecies biofilms. Subsequent biofilm development was carried out under known conditions of nutrient concentration and laminar flow. Establishment of a depositing organism in a biofilm composed of another species was found to be a function of the relative growth rates of the bacterial species. In the case of simultaneous species deposition and subsequent binary culture development, the faster-growing organisms rapidly became the dominant biofilm species, but the slower-growing organisms remained established within the biofilm and continued to increase in numbers over time. The results also indicated that the rate of cell removal by fluid shear for a species was a function of biofilm cell number only if the species concentration was uniform with depth; in essence, only the upper layers of the biofilm were sheared off. PMID:1892387

  4. Bladder surface mucin. Its antibacterial effect against various bacterial species.

    PubMed Central

    Parsons, C. L.; Mulholland, S. G.

    1978-01-01

    We previously reported the results of quantitative and histochemical studies implicating the surface mucin of the bladder mucosa as an important antibacterial defense mechanism, which functions by preventing bacteria from adhering to the bladder wall. We call the mucin "anti-adherence factor" and we feel this is a previously undocumented role for mucin as a type of host antibacterial defense. These experiments were conduced with Escherichia coli. In an effort to determine whether the anti-adherence ability of the vesical mucin was a generalized phenomenon, we repeated these studies using unrelated bacterial species, including E coli, Klebsiella pneumoniae, and Staphylococcus aureus. The ability of the vesical mucosa to resist bacterial adherence to its surface was found to be independent of the bacterial species that was investigated. PMID:362941

  5. Penicillin amidohydrolase productivity of locally isolated bacterial species.

    PubMed

    Mahmood, Z A; Shaikh, D; Zoha, S M

    1991-01-01

    Penicillin amidohydrolase productivity of four locally isolated bacterial species is described. Organisms were identified as Escherichia coli, Pseudomonas aeruginosa, Sarcina lutea and Bacillus megaterium. Highest enzyme productivity of 3.2 U/mL with a corresponding dry cell mass of 4.5 g/L was recorded from S. lutea. PMID:1821869

  6. Prevalent bacterial species and novel phylotypes in advanced noma lesions.

    PubMed

    Paster, B J; Falkler Jr, W A; Enwonwu, C O; Idigbe, E O; Savage, K O; Levanos, V A; Tamer, M A; Ericson, R L; Lau, C N; Dewhirst, F E

    2002-06-01

    The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.

  7. Influence of Multiple Bacterial Populations on Phenanthrene Degradation, Bacterial Cell Elution, and Species Distribution

    NASA Astrophysics Data System (ADS)

    Patterson, B. M.; Brusseau, M. L.; Maier, R. M.; Frye, R.

    2001-05-01

    A single set of degradation coefficients is typically used when representing biodegradation in contaminant transport models. Implicit to this approach is the assumption that only a single degrading isolate exists, or that the entire community of degraders more typically present in natural systems has a uniform, constant growth rate and affinity for the contaminant. This assumption was evaluated through a miscible displacement experiment conducted using a column packed with a soil containing an indigenous microbial community comprised of 24 identified phenanthrene-degrading isolates. Results produced oscillating phenanthrene concentrations in the column effluent, indicating potential competitive interactions among the isolates. A second series of experiments, conducted in a simplified system comprised of sand and 1,2, or 3 indigenous isolates, examined the effects of species interactions on phenanthrene degradation and bacterial cell elution. Bacterial growth rates, density of cells within the column, and bacterial distribution were also evaluated. Results show single bacterial species produced relatively stable cell elution and phenanthrene concentrations in the effluent. Conversely, the behavior in the multiple species systems indicated synergistic and antagonistic interactions occurred among the species. These results illustrate that the dynamics of heterogeneous microbial communities should be considered when evaluating contaminant biodegradation and transport in subsurface systems.

  8. Attached bacterial populations shared by four species of aquatic angiosperms.

    PubMed

    Crump, Byron C; Koch, Evamaria W

    2008-10-01

    Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.

  9. Panamanian frog species host unique skin bacterial communities

    PubMed Central

    Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

    2015-01-01

    Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont

  10. Panamanian frog species host unique skin bacterial communities.

    PubMed

    Belden, Lisa K; Hughey, Myra C; Rebollar, Eria A; Umile, Thomas P; Loftus, Stephen C; Burzynski, Elizabeth A; Minbiole, Kevin P C; House, Leanna L; Jensen, Roderick V; Becker, Matthew H; Walke, Jenifer B; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N

    2015-01-01

    Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont

  11. The bacterial species dilemma and the genomic–phylogenetic species concept

    PubMed Central

    Staley, James T

    2006-01-01

    The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels. PMID:17062409

  12. Cutaneous bacterial species from Lithobates catesbeianus can inhibit pathogenic dermatophytes.

    PubMed

    Lauer, Antje; Hernandez, Trang

    2015-04-01

    Antibiotics are being successfully used to fight many infectious diseases caused by pathogenic microorganisms. However, new infectious diseases are continuously being identified, and some known pathogens are becoming resistant against known antibiotics. Furthermore, many antifungals are causing serious side effects in long-term treatments of patients, and many skin infections caused by dermatophytes are difficult to cure. The beneficial roles of resident cutaneous microbiota to inhibit pathogenic microorganisms have been shown for many vertebrate species. Microbial symbionts on the amphibian skin for example can be a source of powerful antimicrobial metabolites that can protect amphibians against diseases, such as chytridiomycosis, caused by a fungal pathogen. In this research, we investigated whether cutaneous bacterial species isolated from Lithobates catesbeianus (North American bullfrog), an invasive amphibian species that is resistant to chytridiomycosis, produce secondary metabolites that can be used to inhibit the growth of three species of dermatophytes (Microsporum gypseum, Epidermophyton floccosum, and Trichophyton mentagrophytes) which are known to cause topical or subdermal skin infections in humans. Strongly anti-dermatophyte bacterial species that belonged to the Bacillaceae, Streptomycetaceae, Pseudomonadaceae, Xanthomonadaceae, Aeromonadaceae, and Enterobacteriaceae were identified. This research has provided evidence of the presence of cutaneous anti-dermatophyte bacteria from L. catesbeianus which might provide a basis for health care providers to experiment with new antifungals in the future. PMID:25431089

  13. New approaches to understanding double-stranded RNA processing by ribonuclease III purification and assays of homodimeric and heterodimeric forms of RNase III from bacterial extremophiles and mesophiles.

    PubMed

    Meng, Wenzhao; Nicholson, Rhonda H; Nathania, Lilian; Pertzev, Alexandre V; Nicholson, Allen W

    2008-01-01

    Ribonuclease III (RNase III) is a double-stranded (ds)-RNA-specific endonuclease that plays essential roles in the maturation and decay of coding and noncoding RNAs. Bacterial RNases III are structurally the simplest members of the RNase III family, which includes the eukaryotic orthologs Dicer and Drosha. High-resolution crystal structures of RNase III of the hyperthermophilic bacteria Aquifex aeolicus and Thermotoga maritima are available. A. aeolicus RNase III also has been cocrystallized with dsRNA or specific hairpin substrates. These structures have provided essential structural insight to the mechanism of dsRNA recognition and cleavage. However, comparatively little is known about the catalytic behaviors of A. aeolicus or T. maritima RNases III. This chapter provides protocols for the purification of A. aeolicus and T. maritima RNases III and also describes the preparation of artificial heterodimers of Escherichia coli RNase III, which are providing new insight on the subunit and domain interactions involved in dsRNA recognition and cleavage.

  14. Temporal changes in species interactions in simple aquatic bacterial communities

    PubMed Central

    2012-01-01

    Background Organisms modify their environment and in doing so change the quantity and possibly the quality of available resources. Due to the two-way relationship between organisms and their resource environment, and the complexity it brings to biological communities, measuring species interactions reliably in any biological system is a challenging task. As the resource environment changes, the intensity and even the sign of interactions may vary in time. We used Serratia marcescens and Novosphingobium capsulatum bacteria to study how the interaction between resource environment and organisms influence the growth of the bacterial species during circa 200 generations. We used a sterile-filtering method to measure how changes in resource environment are reflected in growth rates of the two species. Results Changes in the resource environment caused complex time and species composition-dependent effects on bacterial growth performance. Variation in the quality of the growth medium indicated existence of temporally fluctuating within-species facilitation and inhibition, and between-species asymmetric facilitation. Conclusions The interactions between the community members could not be fully predicted based only on the knowledge of the growth performance of each member in isolation. Growth dynamics in sterile-filtered samples of the conditioned growth medium can reveal both biologically meaningful changes in resource availability and temporally changing facilitative resource-mediated interactions between study species. This is the first study we are aware of where the filter-sterilization – growth assay method is applied to study the effect of long-term changes in the environment on species interactions. PMID:22984961

  15. The bacterial species definition in the genomic era

    PubMed Central

    Konstantinidis, Konstantinos T; Ramette, Alban; Tiedje, James M

    2006-01-01

    The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction. PMID:17062412

  16. Patterns of Gut Bacterial Colonization in Three Primate Species

    PubMed Central

    McKenney, Erin A.; Rodrigo, Allen; Yoder, Anne D.

    2015-01-01

    Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies. PMID:25970595

  17. Identification and ecology of bacterial communities associated with necroses of three cactus species.

    PubMed

    Foster, J L; Fogleman, J C

    1993-01-01

    To compare the bacterial communities residing in necrotic tissues of columnar cacti of the Sonoran Desert, isolates from 39 organ pipe, 19 saguaro, and 16 senita cacti were obtained. The isolates were clustered into 28 conspecific groups on the basis of their fatty acid profiles. The distributions of the individual bacterial isolates varied among cactus species. Seven of the 28 species groups were unique to a particular cactus species, whereas 8 species groups were found in all three cacti. The effective number of bacterial species for each cactus species was positively correlated with both the chemical complexity and glucose concentration of the plant tissues. The effective number of bacterial species and bacterial distribution patterns were compared with those known for communities of cactophilic yeasts. The observed bacterial distribution patterns are most likely due to differences in the chemical compositions of the three cactus species. PMID:8439142

  18. Bacterial Communities of Two Ubiquitous Great Barrier Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

    PubMed Central

    Kvennefors, E. Charlotte E.; Sampayo, Eugenia; Ridgway, Tyrone; Barnes, Andrew C.; Hoegh-Guldberg, Ove

    2010-01-01

    Background Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. Methodology/Principal Findings Denaturing Gradient Gel Electrophoresis (DGGE) of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by “White Syndrome” (WS) underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. Conclusions/Significance This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine invertebrate associates

  19. Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

    NASA Astrophysics Data System (ADS)

    Ghebremedhin, Meron; Yesupriya, Shubha; Luka, Janos; Crane, Nicole J.

    2015-03-01

    Recent studies have demonstrated the potential advantages of the use of Raman spectroscopy in the biomedical field due to its rapidity and noninvasive nature. In this study, Raman spectroscopy is applied as a method for differentiating between bacteria isolates for Gram status and Genus species. We created models for identifying 28 bacterial isolates using spectra collected with a 785 nm laser excitation Raman spectroscopic system. In order to investigate the groupings of these samples, partial least squares discriminant analysis (PLSDA) and hierarchical cluster analysis (HCA) was implemented. In addition, cluster analyses of the isolates were performed using various data types consisting of, biochemical tests, gene sequence alignment, high resolution melt (HRM) analysis and antimicrobial susceptibility tests of minimum inhibitory concentration (MIC) and degree of antimicrobial resistance (SIR). In order to evaluate the ability of these models to correctly classify bacterial isolates using solely Raman spectroscopic data, a set of 14 validation samples were tested using the PLSDA models and consequently the HCA models. External cluster evaluation criteria of purity and Rand index were calculated at different taxonomic levels to compare the performance of clustering using Raman spectra as well as the other datasets. Results showed that Raman spectra performed comparably, and in some cases better than, the other data types with Rand index and purity values up to 0.933 and 0.947, respectively. This study clearly demonstrates that the discrimination of bacterial species using Raman spectroscopic data and hierarchical cluster analysis is possible and has the potential to be a powerful point-of-care tool in clinical settings.

  20. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species

    PubMed Central

    Merino, Enrique; Bonomi, Hernán Ruy; Goldbaum, Fernando Alberto; García-Angulo, Víctor Antonio

    2015-01-01

    Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria. PMID:25938806

  1. Whole-genome sequence comparison as a method for improving bacterial species definition.

    PubMed

    Zhang, Wen; Du, Pengcheng; Zheng, Han; Yu, Weiwen; Wan, Li; Chen, Chen

    2014-01-01

    We compared pairs of 1,226 bacterial strains with whole genome sequences and calculated their average nucleotide identity (ANI) between genomes to determine whether whole genome comparison can be directly used for bacterial species definition. We found that genome comparisons of two bacterial strains from the same species (SGC) have a significantly higher ANI than those of two strains from different species (DGC), and that the ANI between the query and the reference genomes can be used to determine whether two genomes come from the same species. Bacterial species definition based on ANI with a cut-off value of 0.92 matched well (81.5%) with the current bacterial species definition. The ANI value was shown to be consistent with the standard for traditional bacterial species definition, and it could be used in bacterial taxonomy for species definition. A new bioinformatics program (ANItools) was also provided in this study for users to obtain the ANI value of any two bacterial genome pairs (http://genome.bioinfo-icdc.org/). This program can match a query strain to all bacterial genomes, and identify the highest ANI value of the strain at the species, genus and family levels respectively, providing valuable insights for species definition.

  2. Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability

    PubMed Central

    Moss, Anthony G.; Chadwick, Nanette E.; Liles, Mark R.

    2012-01-01

    Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude

  3. Bacterial communities and species-specific associations with the mucus of Brazilian coral species.

    PubMed

    Carlos, Camila; Torres, Tatiana T; Ottoboni, Laura M M

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  4. Bacterial communities and species-specific associations with the mucus of Brazilian coral species

    PubMed Central

    Carlos, Camila; Torres, Tatiana T.; Ottoboni, Laura M. M.

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  5. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    PubMed

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  6. Biomimetic/Optical Sensors for Detecting Bacterial Species

    NASA Technical Reports Server (NTRS)

    Homer, Margie; Ksendzov, Alexander; Yen, Shiao-Pin; Ryan, Margaret; Lazazzera, Beth

    2006-01-01

    Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites

  7. Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome.

    PubMed

    Palama, T L; Canard, I; Rautureau, G J P; Mirande, C; Chatellier, S; Elena-Herrmann, B

    2016-08-01

    Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis. PMID:27349704

  8. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

    PubMed Central

    McKenzie, Valerie J; Bowers, Robert M; Fierer, Noah; Knight, Rob; Lauber, Christian L

    2012-01-01

    Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens. PMID:21955991

  9. Catecholamines and in vitro growth of pathogenic bacteria: enhancement of growth varies greatly among bacterial species

    NASA Technical Reports Server (NTRS)

    Belay, Tesfaye; Aviles, Hernan; Vance, Monique; Fountain, Kimberly; Sonnenfeld, Gerald

    2003-01-01

    The purpose of this study was to examine the effects of catecholamines on in vitro growth of a range of bacterial species, including anaerobes. Bacteria tested included: Porphyromonas gingivalis, Bacteriodes fragilis, Shigella boydii, Shigella sonnie, Enterobacter Sp, and Salmonella choleraesuis. The results of the current study indicated that supplementation of bacterial cultures in minimal medium with norepinephrine or epinephrine did not result in increased growth of bacteria. Positive controls involving treatment of Escherichia coli with catecholamines did result in increased growth of that bacterial species. The results of the present study extend previous observations that showed differential capability of catecholamines to enhance bacterial growth in vitro.

  10. Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules

    PubMed Central

    Sekiguchi, Yuji; Kamagata, Yoichi; Nakamura, Kazunori; Ohashi, Akiyoshi; Harada, Hideki

    1999-01-01

    16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge, mesophilic (35°C) and thermophilic (55°C), in upflow anaerobic sludge blanket reactors fed with sucrose-, acetate-, and propionate-based artificial wastewater. The spatial organization of the microbes was visualized in thin sections of the granules by using fluorescent oligonucleotide probes specific to several phylogenetic groups of microbes. In situ hybridization with archaeal- and bacterial-domain probes within granule sections clearly showed that both mesophilic and thermophilic granules had layered structures and that the outer layer harbored mainly bacterial cells while the inner layer consisted mainly of archaeal cells. Methanosaeta-, Methanobacterium-, Methanospirillum-, and Methanosarcina-like cells were detected with oligonucleotide probes specific for the different groups of methanogens, and they were found to be localized inside the granules, in both types of which dominant methanogens were members of the genus Methanosaeta. For specific detection of bacteria which were previously detected by whole-microbial-community 16S ribosomal DNA (rDNA)-cloning analysis (Y. Sekiguchi, Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura, Microbiology 144:2655–2665, 1998) we designed probes specific for clonal 16S rDNAs related to unidentified green nonsulfur bacteria and clones related to Syntrophobacter species. The probe designed for the cluster closely related to Syntrophobacter species hybridized with coccoid cells in the inner layer of the mesophilic granule sections. The probe for the unidentified bacteria which were clustered with the green nonsulfur bacteria detected filamentous cells in the outermost layer of the thermophilic sludge granule sections. These results revealed the spatial organizations of methanogens and uncultivated bacteria and

  11. Column bioleaching of uranium embedded in granite porphyry by a mesophilic acidophilic consortium.

    PubMed

    Qiu, Guanzhou; Li, Qian; Yu, Runlan; Sun, Zhanxue; Liu, Yajie; Chen, Miao; Yin, Huaqun; Zhang, Yage; Liang, Yili; Xu, Lingling; Sun, Limin; Liu, Xueduan

    2011-04-01

    A mesophilic acidophilic consortium was enriched from acid mine drainage samples collected from several uranium mines in China. The performance of the consortium in column bioleaching of low-grade uranium embedded in granite porphyry was investigated. The influences of several chemical parameters on uranium extraction in column reactor were also investigated. A uranium recovery of 96.82% was achieved in 97 days column leaching process including 33 days acid pre-leaching stage and 64 days bioleaching stage. It was reflected that indirect leaching mechanism took precedence over direct. Furthermore, the bacterial community structure was analyzed by using Amplified Ribosomal DNA Restriction Analysis. The results showed that microorganisms on the residual surface were more diverse than that in the solution. Acidithiobacillus ferrooxidans was the dominant species in the solution and Leptospirillum ferriphilum on the residual surface.

  12. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

    PubMed Central

    Schmitt, Susanne; Tsai, Peter; Bell, James; Fromont, Jane; Ilan, Micha; Lindquist, Niels; Perez, Thierry; Rodrigo, Allen; Schupp, Peter J; Vacelet, Jean; Webster, Nicole; Hentschel, Ute; Taylor, Michael W

    2012-01-01

    Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations. PMID:21993395

  13. Resource-dependent attenuation of species interactions during bacterial succession

    PubMed Central

    Rivett, Damian W; Scheuerl, Thomas; Culbert, Christopher T; Mombrikotb, Shorok B; Johnstone, Emma; Barraclough, Timothy G; Bell, Thomas

    2016-01-01

    Bacterial communities are vital for many economically and ecologically important processes. The role of bacterial community composition in determining ecosystem functioning depends critically on interactions among bacterial taxa. Several studies have shown that, despite a predominance of negative interactions in communities, bacteria are able to display positive interactions given the appropriate evolutionary or ecological conditions. We were interested in how interspecific interactions develop over time in a naturalistic setting of low resource supply rates. We assembled aquatic bacterial communities in microcosms and assayed the productivity (respiration and growth) and substrate degradation while tracking community composition. The results demonstrated that while bacterial communities displayed strongly negative interactions during the early phase of colonisation and acclimatisation to novel biotic and abiotic factors, this antagonism declined over time towards a more neutral state. This was associated with a shift from use of labile substrates in early succession to use of recalcitrant substrates later in succession, confirming a crucial role of resource dynamics in linking interspecific interactions with ecosystem functioning. PMID:26894447

  14. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    PubMed

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes. PMID:25103911

  15. Crustose coralline algal species host distinct bacterial assemblages on their surfaces.

    PubMed

    Sneed, Jennifer M; Ritson-Williams, Raphael; Paul, Valerie J

    2015-11-01

    Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1-V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria. PMID:25918832

  16. A comparison of microbial characteristics between the thermophilic and mesophilic anaerobic digesters exposed to elevated food waste loadings.

    PubMed

    Guo, Xiaohui; Wang, Cheng; Sun, Faqian; Zhu, Weijing; Wu, Weixiang

    2014-01-01

    Thermophilic and mesophilic anaerobic digestion reactors (TR and MR) using food waste as substrate were compared with emphasis on microbial responses to increasing organic loading rate (OLR). At OLR ranging from 1.0 to 2.5 g VS L(-1) d(-1), MR exhibited more stable performance compared to TR in terms of methane yield. Amplicons pyrosequencing results revealed the distinct microbial dynamics in the two reactors. Primarily, MR had greater richness and evenness of bacteria species. With OLR elevated, larger shifts of bacterial phylogeny were observed in MR; Methanosaeta dominated in archaeal community in MR while Methanothermobacter and Methanoculleus were favored in TR. The high functional redundancy in bacterial community integrated with acetoclastic methanogenesis in MR resulted in its better performance; whereas delicate interactions between hydrogen-producer and hydrogenotrophic methanogens in TR were much more prone to disruption. These results are conductive to understanding the microbial mechanisms of low methane yield during food waste anaerobic digestion.

  17. "Lachnoclostridium bouchesdurhonense," a new bacterial species isolated from human gut microbiota.

    PubMed

    Amadou, T; Hosny, M; La Scola, B; Cassir, N

    2016-09-01

    We report the main characteristics of "Lachnoclostridium bouchesdurhonense" strain AT5(T) (=CSUR P2181), a new bacterial species isolated from the gut microbiota of an obese patient from Marseille. PMID:27493758

  18. 'Lachnoclostridium massiliosenegalense', a new bacterial species isolated from the human gut microbiota.

    PubMed

    Tidjani Alou, M; Lagier, J-C; La Scola, B; Cassir, N

    2016-11-01

    We report the main characteristics of 'Lachnoclostridium massiliosenegalense' strain mt23(T) (=CSUR P299 =DSM 102084), a new bacterial species isolated from the gut microbiota of a healthy young girl from Senegal. PMID:27595004

  19. 'Lachnoclostridium massiliosenegalense', a new bacterial species isolated from the human gut microbiota.

    PubMed

    Tidjani Alou, M; Lagier, J-C; La Scola, B; Cassir, N

    2016-11-01

    We report the main characteristics of 'Lachnoclostridium massiliosenegalense' strain mt23(T) (=CSUR P299 =DSM 102084), a new bacterial species isolated from the gut microbiota of a healthy young girl from Senegal.

  20. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species

    PubMed Central

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Background Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. Methodology and Results To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. Conclusions The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation. PMID:27008327

  1. Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.

    PubMed

    Shcherbakov, D; Dontsova, M; Tribus, M; Garber, M; Piendl, W

    2006-01-01

    The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called 'L12 stalk' on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the 'L12 stalk'. The 'L12 stalk' plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L12(4) complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent.

  2. Confocal Raman microscopy for identification of bacterial species in biofilms

    NASA Astrophysics Data System (ADS)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2011-03-01

    Implemented through a confocal microscope, Raman spectroscopy has been used to distinguish between biofilm samples of two common oral bacteria species, Streptococcus sanguinis and mutans, which are associated with healthy and cariogenic plaque, respectively. Biofilms of these species are studied as a model of dental plaque. A prediction model has been calibrated and validated using pure biofilms. This model has been used to identify the species of transferred and dehydrated samples (much like a plaque scraping) as well as hydrated biofilms in situ. Preliminary results of confocal Raman mapping of species in an intact two-species biofilm will be shown.

  3. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    PubMed Central

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  4. Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction

    PubMed Central

    Gaiarsa, Stefano; De Marco, Leone; Comandatore, Francesco; Marone, Piero; Bandi, Claudio; Sassera, Davide

    2015-01-01

    Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main bacterial pathogens. Here, we present a review of some of the most recent and groundbreaking studies in this field. PMID:26878934

  5. Emerging Bacterial Infection: Identification and Clinical Significance of Kocuria Species

    PubMed Central

    Palange, Padmavali; Vaish, Ritu; Bhatti, Adnan Bashir; Kale, Vinod; Kandi, Maheshwar Reddy; Bhoomagiri, Mohan Rao

    2016-01-01

    Recently there have been reports of gram-positive cocci which are morphologically similar to both Staphylococci and the Micrococci. These bacteria have been identified as Kocuria species with the help of automated identification system and other molecular methods including 16S rRNA (ribosomal ribonucleic acid) evaluation. Kocuria belongs to the family Micrococcaceae which also includes Staphylococcus species and Micrococcus species. Isolation and clinical significance of these bacteria from human specimens warrant great caution as it does not necessarily confirm infection due to their ubiquitous presence, and as a normal flora of skin and mucous membranes in human and animals. Most clinical microbiology laboratories ignore such bacteria as laboratory and specimen contaminants. With increasing reports of infections associated with these bacteria, it is now important for clinical microbiologists to identify and enumerate the virulence and antibiotic susceptibility patterns of such bacteria and assist clinicians in improving the patient care and management. We review the occurrence and clinical significance of Kocuria species. PMID:27630804

  6. Emerging Bacterial Infection: Identification and Clinical Significance of Kocuria Species.

    PubMed

    Kandi, Venkataramana; Palange, Padmavali; Vaish, Ritu; Bhatti, Adnan Bashir; Kale, Vinod; Kandi, Maheshwar Reddy; Bhoomagiri, Mohan Rao

    2016-01-01

    Recently there have been reports of gram-positive cocci which are morphologically similar to both Staphylococci and the Micrococci. These bacteria have been identified as Kocuria species with the help of automated identification system and other molecular methods including 16S rRNA (ribosomal ribonucleic acid) evaluation. Kocuria belongs to the family Micrococcaceae which also includes Staphylococcus species and Micrococcus species. Isolation and clinical significance of these bacteria from human specimens warrant great caution as it does not necessarily confirm infection due to their ubiquitous presence, and as a normal flora of skin and mucous membranes in human and animals. Most clinical microbiology laboratories ignore such bacteria as laboratory and specimen contaminants. With increasing reports of infections associated with these bacteria, it is now important for clinical microbiologists to identify and enumerate the virulence and antibiotic susceptibility patterns of such bacteria and assist clinicians in improving the patient care and management. We review the occurrence and clinical significance of Kocuria species. PMID:27630804

  7. Synthetic riboswitches that induce gene expression in diverse bacterial species.

    PubMed

    Topp, Shana; Reynoso, Colleen M K; Seeliger, Jessica C; Goldlust, Ian S; Desai, Shawn K; Murat, Dorothée; Shen, Aimee; Puri, Aaron W; Komeili, Arash; Bertozzi, Carolyn R; Scott, June R; Gallivan, Justin P

    2010-12-01

    We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria. PMID:20935124

  8. Emerging Bacterial Infection: Identification and Clinical Significance of Kocuria Species

    PubMed Central

    Palange, Padmavali; Vaish, Ritu; Bhatti, Adnan Bashir; Kale, Vinod; Kandi, Maheshwar Reddy; Bhoomagiri, Mohan Rao

    2016-01-01

    Recently there have been reports of gram-positive cocci which are morphologically similar to both Staphylococci and the Micrococci. These bacteria have been identified as Kocuria species with the help of automated identification system and other molecular methods including 16S rRNA (ribosomal ribonucleic acid) evaluation. Kocuria belongs to the family Micrococcaceae which also includes Staphylococcus species and Micrococcus species. Isolation and clinical significance of these bacteria from human specimens warrant great caution as it does not necessarily confirm infection due to their ubiquitous presence, and as a normal flora of skin and mucous membranes in human and animals. Most clinical microbiology laboratories ignore such bacteria as laboratory and specimen contaminants. With increasing reports of infections associated with these bacteria, it is now important for clinical microbiologists to identify and enumerate the virulence and antibiotic susceptibility patterns of such bacteria and assist clinicians in improving the patient care and management. We review the occurrence and clinical significance of Kocuria species.

  9. [Purification and characterization of thermostable amylases from two bacterial species].

    PubMed

    Dong, Yongcun; Liu, Yang; Chen, Yuanyuan; Niu, Dandan; Zhang, Liang; Shi, Guiyang; Wang, Zhengxiang

    2008-02-01

    Two thermophilic bacterial isolates, strain 173 and strain 174, with raw starch-digesting activities were selected from thermophilic bacteria growing in hot spring of Tengchong County, Yunnan Province, China. By amplification, sequencing and alignment analysis of 16S ribosomal DNAs, they were identified as members of genus Geobacillus. In shaker flask culture Geobacillus sp. 173 produced 14.5 U/mL amylase and for Geobacillus sp. 174 with 12.9 U/mL. Both amylases were purified by starch absorption-desorption and chromatograph. The amylases from strain 173 and strain 174 purified to about 50 and 29 folds were respectively achieved with an overall yield of 34% and 41%. The maximum gelatinized-starch-digesting activity of the purified amylases were at 70 degrees C and pH 5.0 - 5.5. The high raw-starch-digesting activity of these enzymes were observed at 50 degrees C - 60 degrees C (from strain 173) and 40 degrees C - 60 degrees C (from strain 174). Both enzymes were not sensitive to ions including mental ions (Na+, K+, Mg2+, Ca2+, Mn2+, Zn2+) and others (EDTA, Citrate), but were slightly inhibited by ions such as Co2+, Cu2+ for amylase from strain 173 and Cu2+ for amylase from strain 174. Both enzyme had specificity of starch substrates.

  10. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

    PubMed Central

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-01-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species. PMID:26884157

  11. Effect of species, breed, and age on bacterial load in bovine and bubaline semen

    PubMed Central

    Sannat, Chandrahas; Nair, Ajit; Sahu, S. B.; Sahasrabudhe, S. A.; Kumar, Ashish; Gupta, Amit Kumar; Shende, R. K.

    2015-01-01

    Aim: The present study was conducted to investigate the effect of species, breed and age on bacterial load in fresh and frozen semen of Cattle and Buffalo bull. Materials and Methods: Present study covered 56 cow and 10 buffalo bulls stationed at Central Semen Station Anjora, Durg (Chhattisgarh). Impact of breeds on bacterial load in semen was assessed using six breeds of cattle viz. Sahiwal, Gir, Red Sindhi, Tharparkar, Jersey and Holstein Friesian (HF) cross. Cow bulls were categorized into four different groups based on their age (<4 years, 4-5 years, 5-6 years and > 6 years) to study variation among age groups. Bacterial load was measured in fresh and frozen semen samples from these bulls using the standard plate count (SPC) method and count was expressed as colony forming unit (CFU) per ml of semen. Results: Higher bacterial load was reported in fresh (2.36 × 104 ± 1943 CFU/ml) and frozen (1.00 × 10 ± 90 CFU/ml) semen of cow bulls as compared to buffalo bulls (1.95 × 104 ± 2882 and 7.75 × 102 ± 160 CFU/ml in fresh and frozen semen, respectively). Jersey bull showed significantly higher bacterial count (p < 0.05) both in fresh (4.07 × 104 ± 13927 CFU/ml) and frozen (1.92 × 103 ± 178 CFU/ml) semen followed by HF cross, Sahiwal, Gir, Red Sindhi and Tharparkar bull. Bulls aged < 4 years and more than 6 years yielded increased bacterial load in their semen. Although a minor variation was reported between species and among age groups, no significant differences were measured. Conclusion: Bacterial load in semen did not differ significantly between species and age groups; however significant variation was reported among different breeds. Bulls of Jersey breed showed significantly higher bacterial load in semen as compared to the crossbred and indigenous bull. PMID:27047115

  12. Digester performance and microbial community changes in thermophilic and mesophilic sequencing batch reactors fed with the fine sieved fraction of municipal sewage.

    PubMed

    Ghasimi, Dara S M; Tao, Yu; de Kreuk, Merle; Abbas, Ben; Zandvoort, Marcel H; van Lier, Jules B

    2015-12-15

    This study investigates the start-up and operation of bench-scale mesophilic (35 °C) and thermophilic (55 °C) anaerobic sequencing batch reactor (SBR) digesters treating the fine sieved fraction (FSF) from raw municipal sewage. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter equipped with a 350 micron mesh. For the given wastewater, the major component of FSF was toilet paper, which is estimated to be 10-14 kg per year per average person in the western European countries. A seven months adaptation time was allowed for the thermophilic and mesophilic digesters in order to adapt to FSF as the sole substrate with varying dry solids content of 10-25%. Different SBR cycle durations (14, 9 and 2 days) were applied for both temperature conditions to study methane production rates, volatile fatty acids (VFAs) dynamics, lag phases, as well as changes in microbial communities. The prevailing sludge in the two digesters consisted of very different bacterial and archaeal communities, with OP9 lineage and Methanothermobacter being pre-dominant in the thermophilic digester and Bacteroides and Methanosaeta dominating the mesophilic one. Eventually, decreasing the SBR cycle period, thus increasing the FSF load, resulted in improved digester performances, particularly with regard to the thermophilic digester, i.e. shortened lag phases following the batch feedings, and reduced VFA peaks. Over time, the thermophilic digester outperformed the mesophilic one with 15% increased volatile solids (VS) destruction, irrespective to lower species diversity found at high temperature.

  13. Digester performance and microbial community changes in thermophilic and mesophilic sequencing batch reactors fed with the fine sieved fraction of municipal sewage.

    PubMed

    Ghasimi, Dara S M; Tao, Yu; de Kreuk, Merle; Abbas, Ben; Zandvoort, Marcel H; van Lier, Jules B

    2015-12-15

    This study investigates the start-up and operation of bench-scale mesophilic (35 °C) and thermophilic (55 °C) anaerobic sequencing batch reactor (SBR) digesters treating the fine sieved fraction (FSF) from raw municipal sewage. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter equipped with a 350 micron mesh. For the given wastewater, the major component of FSF was toilet paper, which is estimated to be 10-14 kg per year per average person in the western European countries. A seven months adaptation time was allowed for the thermophilic and mesophilic digesters in order to adapt to FSF as the sole substrate with varying dry solids content of 10-25%. Different SBR cycle durations (14, 9 and 2 days) were applied for both temperature conditions to study methane production rates, volatile fatty acids (VFAs) dynamics, lag phases, as well as changes in microbial communities. The prevailing sludge in the two digesters consisted of very different bacterial and archaeal communities, with OP9 lineage and Methanothermobacter being pre-dominant in the thermophilic digester and Bacteroides and Methanosaeta dominating the mesophilic one. Eventually, decreasing the SBR cycle period, thus increasing the FSF load, resulted in improved digester performances, particularly with regard to the thermophilic digester, i.e. shortened lag phases following the batch feedings, and reduced VFA peaks. Over time, the thermophilic digester outperformed the mesophilic one with 15% increased volatile solids (VS) destruction, irrespective to lower species diversity found at high temperature. PMID:25976021

  14. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    NASA Astrophysics Data System (ADS)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  15. Identification of different bacterial species in biofilms using confocal Raman microscopy

    NASA Astrophysics Data System (ADS)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  16. Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species.

    PubMed

    Koeppel, Alexander F; Wertheim, Joel O; Barone, Laura; Gentile, Nicole; Krizanc, Danny; Cohan, Frederick M

    2013-06-01

    Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species-that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population's lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity.

  17. Assessing variation in bacterial composition between the rhizospheres of two mangrove tree species

    NASA Astrophysics Data System (ADS)

    Gomes, Newton C. M.; Cleary, Daniel F. R.; Pires, Ana C. C.; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

    2014-02-01

    This study aimed to determine to what extent roots from the common mangrove tree species Avicennia schaueriana and Laguncularia racemosa are able to impose a selective force on the composition of sediment bacterial communities in mangrove intertidal sediments using barcoded pyrosequencing analysis of 16S rRNA gene fragments (V4 hyper-variable region). The novel results showed that root systems of A. schaueriana and L. racemosa are associated with increased bacterial dominance, lower richness and compositional shifts of sediment bacterial communities. The proportion of OTUs (operational taxonomc units) belonging to the orders Rhizobiales and Vibrionales were enriched in rhizosphere samples from both plant species and sulphur-reducing bacteria (SRB) belonging to the order Desulfobacterales and Desulfuromonadales were enriched in the rhizosphere of A. schaueriana. In addition, Clostridium and Vibrio populations were more abundant in different mangrove rhizospheres. A. schaueriana and L. racemosa roots appear to be able to impose a selective force on the composition of mangrove sediment bacterial communities and this phenomenon appears to be plant species specific. Our findings provide new insights into the potential ecological roles of bacterial guilds in plant-microbe interactions and may aid rhizoengineering approaches for replanting impacted mangrove areas.

  18. Blooms of Single Bacterial Species in a Coastal Lagoon of the Southwestern Atlantic Ocean

    PubMed Central

    Piccini, Claudia; Conde, Daniel; Alonso, Cecilia; Sommaruga, Ruben; Pernthaler, Jakob

    2006-01-01

    We investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern Atlantic Ocean. Alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. After an intrusion of marine water, members of the SAR11 lineage became abundant in the brackish-water zone. These bacteria were apparently distributed over the lagoon during the following months until they constituted almost 30% of all prokaryotic cells at both sampling sites. At the first sampling date (March 2003) a single alphaproteobacterial species unrelated to SAR11, Sphingomonas echinoides, dominated the microbial assemblages in both zones of the lagoon concomitantly with a bloom of filamentous cyanobacteria. Pronounced maxima of leucine incorporation were observed once in each zone of the lagoon. In the freshwater zone, this highly active microbial assemblage was a mix of the typical bacteria lineages expected in aquatic systems. By contrast, a single bacterial genotype with >99% similarity to the facultative pathogen gammaproteobacterial species Stenotrophomonas maltophilia formed >90% of the bacterial assemblage (>107 cell ml−1) in the brackish-water zone at the time point of highest bacterial leucine incorporation. Moreover, these bacteria were equally dominant, albeit less active, in the freshwater zone. Thus, the pelagic zone of the studied lagoon harbored repeated short-term blooms of single bacterial species. This finding may have consequences for environmental protection. PMID:17021206

  19. Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China

    PubMed Central

    Wu, Peng; Xiong, Xiaofei; Xu, Zhanzhou; Lu, Chuqian; Cheng, Hao; Lyu, Xiangli; Zhang, Jinghuai; He, Wei; Deng, Wei; Lyu, Yihua; Lou, Quansheng; Hong, Yiguo; Fang, Hongda

    2016-01-01

    The bacterial communities played important roles in the high productivity mangrove ecosystem. In this study, we investigated the vertical distributions of rhizosphere bacteria from three mangrove species (Bruguiera gymnorrhiza, Kandelia candel and Aegiceras corniculatum) in Beilun Estuary, China using high throughput DNA pyrosequencing of the 16S rRNA gene. Phylogenetic analysis showed that bacterial communities from mangrove rhizosphere sediments were dominated by Proteobacteria (mostly Deltaproteobacteria and Gammaproteobacteria), followed by Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. However, the ANOVA analysis on Shannon and Chao1 indices indicated that bacterial communities among sediments of the three mangrove species varied more strongly than the sampling depths. In addition, the PCA result demonstrated that the bacterial communities could be separated into three groups according to the mangrove species. Moreover, the dominated orders Rhodospirillales, GCA004 and envOPS12 were significantly different among sediments of the three mangrove species. The results of this study provided valuable information about the distribution feature of rhizosphere bacteria from Chinese mangrove plants and shed insights into biogeochemical transformations driven by bacteria in rhizosphere sediments. PMID:27695084

  20. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    PubMed

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  1. Ribosomes, Polyribosomes, and Deoxyribonucleic Acid from Thermophilic, Mesophilic, and Psychrophilic Clostridia

    PubMed Central

    Irwin, Carol C.; Akagi, James M.; Himes, Richard H.

    1973-01-01

    Analysis of deoxyribonucleic acid (DNA) from four species of Clostridium, including two thermophiles, a mesophile, and a psychrophile, revealed no obvious relationship between growth temperature and DNA base composition. The melting temperatures (Tm) of the DNA from the four species varied no more among the thermophilic, mesophilic, and psychrophilic species than among many related mesophilic species. Characterization of ribosomes from the clostridia by means of optical rotatory dispersion yielded similar spectra in common with other unrelated organisms. Only small differences were noted in the base composition of ribosomal ribonucleic acid (RNA) and in the amino acid composition of ribosomal proteins, including half-cystine content, as determined by cysteic acid analysis, and accessible sulfhydryl groups, as determined by titration with dithiobis (2-nitrobenzoic acid). Except for the two thermophiles, the ribosomal protein electrophoretic patterns were dissimilar. No unusual thermal stability was manifested in the Tm values of thermophile ribosomal RNA. However, thermophile ribosome Tm values (69 C) were higher than were mesophile and psychrophile Tm values (64 C). Ribosomes from the four clostridial species were also examined in regard to the effect of heat on their functional integrity, measured by their activity in poly U-directed 14C-phenylaline incorporation, and their gross physical integrity, measured by sucrose gradient analysis. The Td, 5 values (temperature which produces 50% inactivation after 5 min) was found to be 70 and 72 C for the two thermophiles C. tartarivorum and C. thermosaccharolyticum, respectively; 57 C for a mesophile, C. pasteurianum; and 53 C for a psychrophile, Clostridium sp. strain 69. At 55 C, little effect was seen on the thermophile ribosomes, but the mesophile ribosomes lost 90% of their activity in 1 hr, and psychrophile ribosomes lost 100% of their activity within 10 min. According to sucrose gradient profiles, heating at 55 C

  2. Phosphoenolpyruvate:glycose phosphotransferase system in species of Vibrio, a widely distributed marine bacterial genus.

    PubMed Central

    Meadow, N D; Revuelta, R; Chen, V N; Colwell, R R; Roseman, S

    1987-01-01

    The genus Vibrio is one of the most common and widely distributed groups of marine bacteria. Studies on the physiology of marine Vibrio species were initiated by examining 15 species for the bacterial phosphoenolpyruvate:glycose phosphotransferase system (PTS). All species tested contained a PTS analogous to the glucose-specific (IIGlc) system in enteric bacteria. Crude extracts of the cells showed immunological cross-reactivity with antibodies to enzyme I, HPr, and IIIGlc from Salmonella typhimurium when assayed by the rocket-line method. Toluene-permeabilized cells of 11 species were tested and were active in phosphorylating methyl alpha-D-glucoside with phosphoenolpyruvate but not ATP as the phosphoryl donor. Membranes from 10 species were assayed, and they phosphorylated methyl alpha-D-glucoside when supplemented with a phospho-IIIGlc-generating system composed of homogeneous proteins from enteric bacteria. Toluene-permeabilized cells and membranes of seven species were assayed, as were phosphorylated fructose and 2-deoxyglucose. IIIGlc was isolated from Vibrio fluvialis and was active in phosphorylating methyl alpha-D-glucoside when supplemented with a phospho-HPr-generating system composed of homogeneous proteins from Escherichia coli and membranes from either E. coli or V. fluvialis. These results show that the bacterial PTS is widely distributed in the marine environment and that it is likely to have a significant role in marine bacterial physiology and in the marine ecosystem. Images PMID:3667518

  3. Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

    PubMed Central

    Koeppel, Alexander F; Wertheim, Joel O; Barone, Laura; Gentile, Nicole; Krizanc, Danny; Cohan, Frederick M

    2013-01-01

    Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species—that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population's lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity. PMID:23364353

  4. Species sorting and neutral processes are both important during the initial assembly of bacterial communities

    PubMed Central

    Langenheder, Silke; Székely, Anna J

    2011-01-01

    Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community. PMID:21270841

  5. Massive Infection of Seabird Ticks with Bacterial Species Related to Coxiella burnetii

    PubMed Central

    Dietrich, Muriel; Lebarbenchon, Camille; Jaeger, Audrey; Le Rouzic, Céline; Bastien, Matthieu; Lagadec, Erwan; McCoy, Karen D.; Pascalis, Hervé; Le Corre, Matthieu; Dellagi, Koussay; Tortosa, Pablo

    2014-01-01

    Seabird ticks are known reservoirs of bacterial pathogens of medical importance; however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and subpolar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combined a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigated the patterns of prevalence and host specificity within the biogeographical context of the western Indian Ocean islands. The bacterial community of the two tick species was characterized by a strong dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both the high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of next generation sequencing with targeted detection/genotyping approaches proves to be efficient in poorly investigated fields where research can be considered to be starting from scratch. PMID:24657860

  6. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    PubMed

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. PMID:25314594

  7. Massive infection of seabird ticks with bacterial species related to Coxiella burnetii.

    PubMed

    Wilkinson, David A; Dietrich, Muriel; Lebarbenchon, Camille; Jaeger, Audrey; Le Rouzic, Céline; Bastien, Matthieu; Lagadec, Erwan; McCoy, Karen D; Pascalis, Hervé; Le Corre, Matthieu; Dellagi, Koussay; Tortosa, Pablo

    2014-06-01

    Seabird ticks are known reservoirs of bacterial pathogens of medical importance; however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and subpolar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combined a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigated the patterns of prevalence and host specificity within the biogeographical context of the western Indian Ocean islands. The bacterial community of the two tick species was characterized by a strong dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both the high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of next generation sequencing with targeted detection/genotyping approaches proves to be efficient in poorly investigated fields where research can be considered to be starting from scratch.

  8. Cuticles of European and American lobsters harbor diverse bacterial species and differ in disease susceptibility.

    PubMed

    Whitten, Miranda M A; Davies, Charlotte E; Kim, Anita; Tlusty, Michael; Wootton, Emma C; Chistoserdov, Andrei; Rowley, Andrew F

    2014-06-01

    Diseases of lobster shells have a significant impact on fishing industries but the risk of disease transmission between different lobster species has yet to be properly investigated. This study compared bacterial biofilm communities from American (Homarus americanus) and European lobsters (H. gammarus), to assess both healthy cuticle and diseased cuticle during lesion formation. Culture-independent molecular techniques revealed diversity in the bacterial communities of cuticle biofilms both within and between the two lobster species, and identified three bacterial genera associated with shell lesions plus two putative beneficial bacterial species (detected exclusively in healthy cuticle or healing damaged cuticle). In an experimental aquarium shared between American and European lobsters, heterospecific transmission of potentially pathogenic bacteria appeared to be very limited; however, the claws of European lobsters were more likely to develop lesions when reared in the presence of American lobsters. Aquarium biofilms were also examined but revealed no candidate pathogens for environmental transmission. Aquimarina sp. 'homaria' (a potential pathogen associated with a severe epizootic form of shell disease) was detected at a much higher prevalence among American than European lobsters, but its presence correlated more with exacerbation of existing lesions rather than with lesion initiation. PMID:24817518

  9. Cuticles of European and American lobsters harbor diverse bacterial species and differ in disease susceptibility

    PubMed Central

    Whitten, Miranda M A; Davies, Charlotte E; Kim, Anita; Tlusty, Michael; Wootton, Emma C; Chistoserdov, Andrei; Rowley, Andrew F

    2014-01-01

    Diseases of lobster shells have a significant impact on fishing industries but the risk of disease transmission between different lobster species has yet to be properly investigated. This study compared bacterial biofilm communities from American (Homarus americanus) and European lobsters (H. gammarus), to assess both healthy cuticle and diseased cuticle during lesion formation. Culture-independent molecular techniques revealed diversity in the bacterial communities of cuticle biofilms both within and between the two lobster species, and identified three bacterial genera associated with shell lesions plus two putative beneficial bacterial species (detected exclusively in healthy cuticle or healing damaged cuticle). In an experimental aquarium shared between American and European lobsters, heterospecific transmission of potentially pathogenic bacteria appeared to be very limited; however, the claws of European lobsters were more likely to develop lesions when reared in the presence of American lobsters. Aquarium biofilms were also examined but revealed no candidate pathogens for environmental transmission. Aquimarina sp. ‘homaria’ (a potential pathogen associated with a severe epizootic form of shell disease) was detected at a much higher prevalence among American than European lobsters, but its presence correlated more with exacerbation of existing lesions rather than with lesion initiation. PMID:24817518

  10. Intestinal Bacterial Flora and Transit Time of Three Neotropical Bat Species

    PubMed Central

    Klite, P. D.

    1965-01-01

    Klite, P. D. (Middle America Research Unit, Balboa Heights, Canal Zone). Intestinal bacterial flora and transit time of three neotropical bat species. J. Bacteriol. 90:375–379. 1965.—Quantitative studies on the intestinal bacterial flora of three neotropical bat species revealed the following average bacterial populations: Molossus major, 104.8 bacteria per intestinal contents; Carollia perspicillata, 103.3; Chilonycteris rubiginosa, 103.9. In comparison, laboratory mice had an average of 109.7 bacteria per intestinal contents. Of 236 bacterial isolates obtained from 60 bats, bacteria of the Klebsiella-Aerobacter-Serratia group were found most frequently, followed by enterococci and Proteus spp. Bacteria of eight other groups were less frequently recovered. A large intestine, cecum, or appendix was absent in all three bat species, and the intestinal length was one-third to one-fifth of that in a mouse of comparable weight. The transit time through the short bat intestine was 15 min. The possible relationship of these unusual anatomical and physiological phenomena to the ability of Histoplasma capsulatum to survive in bat feces is discussed. PMID:14329450

  11. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    PubMed

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.

  12. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  13. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    USGS Publications Warehouse

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  14. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

    PubMed Central

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  15. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  16. Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity.

    PubMed

    Kanokratana, Pattanop; Mhuanthong, Wuttichai; Laothanachareon, Thanaporn; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Kruetreepradit, Trongtham; Mayes, Shawn; Champreda, Verawat

    2016-08-01

    Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system. PMID:27287538

  17. Bacterial-biota dynamics of eight bryophyte species from different ecosystems.

    PubMed

    Koua, Faisal Hammad Mekky; Kimbara, Kazuhide; Tani, Akio

    2015-03-01

    Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan. Forty-two bacterial species belonging to γ-proteobacteria and Firmicutes with 71.4% and 28.6%, respectively, were identified among 90 DGGE gel band population. These DGGE-bands were assigned to 13 different genera with obvious predomination the genus Clostridium with 21.4% from the total bacterial community. These analyses provide new insights into bryophyte-associated bacteria and their relations to the ecosystems. PMID:25737654

  18. Routine phenotypic identification of bacterial species of the family Pasteurellaceae isolated from animals.

    PubMed

    Dousse, Florence; Thomann, Andreas; Brodard, Isabelle; Korczak, Bozena M; Schlatter, Yvonne; Kuhnert, Peter; Miserez, Raymond; Frey, Joachim

    2008-11-01

    Pasteurellaceae are bacteria with an important role as primary or opportunistic, mainly respiratory, pathogens in domestic and wild animals. Some species of Pasteurellaceae cause severe diseases with high economic losses in commercial animal husbandry and are of great diagnostic concern. Because of new data on the phylogeny of Pasteurellaceae, their taxonomy has recently been revised profoundly, thus requiring an improved phenotypic differentiation procedure to identify the individual species of this family. A new and simplified procedure to identify species of Actinobacillus, Avibacterium, Gallibacterium, Haemophilus, Mannheimia, Nicoletella, and Pasteurella, which are most commonly isolated from clinical samples of diseased animals in veterinary diagnostic laboratories, is presented in the current study. The identification procedure was evaluated with 40 type and reference strains and with 267 strains from routine diagnostic analysis of various animal species, including 28 different bacterial species. Type, reference, and field strains were analyzed by 16S ribosomal RNA (rrs) and rpoB gene sequencing for unambiguous species determination as a basis to evaluate the phenotypic differentiation schema. Primary phenotypic differentiation is based on beta-nicotinamide adenine dinucleotide (beta-NAD) dependence and hemolysis, which are readily determined on the isolation medium. The procedure divides the 28 species into 4 groups for which particular biochemical reactions were chosen to identify the bacterial species. The phenotypic identification procedure allowed researchers to determine the species of 240 out of 267 field strains. The procedure is an easy and cost-effective system for the rapid identification of species of the Pasteurellaceae family isolated from clinical specimens of animals. PMID:18987220

  19. Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.

    PubMed

    Robinson, Christopher J; Vincent, Helen A; Wu, Ming-Cheng; Lowe, Phillip T; Dunstan, Mark S; Leys, David; Micklefield, Jason

    2014-07-30

    Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes. PMID:24971878

  20. Assessing the viability of bacterial species in drinking water by combined cellular and molecular analyses.

    PubMed

    Kahlisch, Leila; Henne, Karsten; Gröbe, Lothar; Brettar, Ingrid; Höfle, Manfred G

    2012-02-01

    The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining ("live/dead staining" indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the DNA- and RNA-based overall community structure differed substantially, (2) the community retrieved from RNA and DNA reflected different bacterial species, classified as 53 phylotypes (with only two common phylotypes), (3) the percentage of phylotypes with intact membranes or damaged cells were comparable for RNA- and DNA-based analyses, and (4) the retrieved species were primarily of aquatic origin. The pronounced difference between phylotypes obtained from DNA extracts (dominated by Betaproteobacteria, Bacteroidetes, and Actinobacteria) and from RNA extracts (dominated by Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria) demonstrate the relevance of concomitant RNA and DNA analyses for drinking water studies. Unexpected was that a comparable fraction (about 21%) of phylotypes with membrane-injured cells was observed for DNA- and RNA-based analyses, contradicting the current understanding that RNA-based analyses represent the actively growing fraction of the bacterial community. Overall, we think that this combined approach provides an interesting tool for a concomitant phylogenetic and viability analysis of bacterial species of drinking water.

  1. Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women

    PubMed Central

    MITCHELL, Caroline M.; HAICK, Anoria; NKWOPARA, Evangelyn; GARCIA, Rochelle; RENDI, Mara; AGNEW, Kathy; FREDRICKS, David N.; ESCHENBACH, David

    2016-01-01

    Objective Evaluate upper genital tract (UGT) presence of vaginal bacterial species using sensitive molecular methods capable of detecting fastidious bacterial vaginosis (BV)-associated bacteria. Study Design Vaginal swabs were collected prior to hysterectomy. The excised uterus was sterilely opened and swabs collected from endometrium and upper endocervix. DNA was tested in 11 quantitative PCR (qPCR) assays for 12 bacterial species: Lactobacillus iners, L. crispatus, L. jensenii, Gardnerella vaginalis, Atopobium vaginae, Megasphaera spp., Prevotella spp., Leptotrichia/Sneathia, BVAB1, BVAB2, BVAB3 and a broad-range16S rRNA gene assay. Endometrial fluid was tested with Luminex and ELISA for cytokines and defensins, and tissue for gene expression of defensins and cathelicidin. Results We enrolled 58 women: mean age 43 + 7 years, mostly white (n = 46; 79%) and BV-negative (n = 43; 74%). By species-specific qPCR, 55 (95%) had UGT colonization with at least one species (n = 52), or were positive by 16S PCR (n = 3). The most common species were L. iners (45% UGT, 61% vagina), Prevotella spp. (33% UGT, 76% vagina) and L. crispatus (33% UGT, 56% vagina). Median quantities of bacteria in the UGT were lower than vaginal levels by 2–4 log10 rRNA gene copies/swab. There were no differences in endometrial inflammatory markers between women with no bacteria, Lactobacillus only or any BV-associated species in the UGT. Conclusion Our data suggest that the endometrial cavity is not sterile in most women undergoing hysterectomy, and that the presence of low levels of bacteria in the uterus is not associated with significant inflammation. PMID:25524398

  2. Loline alkaloid production by fungal endophytes of Fescue species select for particular epiphytic bacterial microflora

    PubMed Central

    Roberts, Elizabeth; Lindow, Steven

    2014-01-01

    The leaves of fescue grasses are protected from herbivores by the production of loline alkaloids by the mutualist fungal endophytes Neotyphodium sp. or Epichloë sp. Most bacteria that reside on the leaf surface of such grasses can consume these defensive chemicals. Loline-consuming bacteria are rare on the leaves of other plant species. Several bacterial species including Burkholderia ambifaria recovered from tall fescue could use N-formyl loline as a sole carbon and nitrogen source in culture and achieved population sizes that were about eightfold higher when inoculated onto plants harboring loline-producing fungal endophytes than on plants lacking such endophytes or which were colonized by fungal variants incapable of loline production. In contrast, mutants of B. ambifaria and other bacterial species incapable of loline catabolism achieved similarly low population sizes on tall fescue colonized by loline-producing Neotyphodium sp. and on plants lacking this endophytic fungus. Lolines that are released onto the surface of plants benefiting from a fungal mutualism thus appear to be a major resource that can be exploited by epiphytic bacteria, thereby driving the establishment of a characteristic bacterial community on such plants. PMID:24108329

  3. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters.

    PubMed

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J; He, Lei; Yin, Kedong

    2015-01-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters. PMID:26404394

  4. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters

    PubMed Central

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J.; He, Lei; Yin, Kedong

    2015-01-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters. PMID:26404394

  5. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J.; He, Lei; Yin, Kedong

    2015-09-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  6. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters.

    PubMed

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J; He, Lei; Yin, Kedong

    2015-01-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  7. [Finding of the bacterial species Edwardsiella tarda in the aquarium fish Betta splendens].

    PubMed

    Vladík, P; Prouza, A; Vítovec, J

    1983-01-01

    A case of the mass occurrence of a disease in the aquarium fish species Betta splendens is described; morphologically the disease was characterized by the finding of large dermal changes located mainly in the dorsal part and by miliary granulomata in liver, spleen and kidneys. The granulomata consisted of epitheloid light cells with centrally located necrosis. Gram-negative bacteria with morphological and biochemical characteristics corresponding to the bacterial species Edwardsiella tarda were isolated from the kidneys, liver and from the dermal lesion. The characteristics of the strains isolated by us were compared with the reference Edwardsiella strain (Bth 1/64) obtained from the Czechoslovak collection of type cultures, Prague.

  8. Concordance of bacterial communities of two tick species and blood of their shared rodent host.

    PubMed

    Rynkiewicz, Evelyn C; Hemmerich, Chris; Rusch, Douglas B; Fuqua, Clay; Clay, Keith

    2015-05-01

    High-throughput sequencing is revealing that most macro-organisms house diverse microbial communities. Of particular interest are disease vectors whose microbiome could potentially affect pathogen transmission and vector competence. We investigated bacterial community composition and diversity of the ticks Dermacentor variabilis (n = 68) and Ixodes scapularis (n = 15) and blood of their shared rodent host, Peromyscus leucopus (n = 45) to quantify bacterial diversity and concordance. The 16S rRNA gene was amplified from genomic DNA from field-collected tick and rodent blood samples, and 454 pyrosequencing was used to elucidate their bacterial communities. After quality control, over 300 000 sequences were obtained and classified into 118 operational taxonomic units (OTUs, clustered at 97% similarity). Analysis of rarefied communities revealed that the most abundant OTUs were tick species-specific endosymbionts, Francisella and Rickettsia, and the commonly flea-associated bacterium Bartonella in rodent blood. An Arsenophonus and additional Francisella endosymbiont were also present in D. variabilis samples. Rickettsia was found in both tick species but not in rodent blood, suggesting that it is not transmitted during feeding. Bartonella was present in larvae and nymphs of both tick species, even those scored as unengorged. Relatively, few OTUs (e.g. Bartonella, Lactobacillus) were found in all sample types. Overall, bacterial communities from each sample type were significantly different and highly structured, independent of their dominant OTUs. Our results point to complex microbial assemblages inhabiting ticks and host blood including infectious agents, tick-specific endosymbionts and environmental bacteria that could potentially affect arthropod-vectored disease dynamics. PMID:25847197

  9. Concordance of bacterial communities of two tick species and blood of their shared rodent host.

    PubMed

    Rynkiewicz, Evelyn C; Hemmerich, Chris; Rusch, Douglas B; Fuqua, Clay; Clay, Keith

    2015-05-01

    High-throughput sequencing is revealing that most macro-organisms house diverse microbial communities. Of particular interest are disease vectors whose microbiome could potentially affect pathogen transmission and vector competence. We investigated bacterial community composition and diversity of the ticks Dermacentor variabilis (n = 68) and Ixodes scapularis (n = 15) and blood of their shared rodent host, Peromyscus leucopus (n = 45) to quantify bacterial diversity and concordance. The 16S rRNA gene was amplified from genomic DNA from field-collected tick and rodent blood samples, and 454 pyrosequencing was used to elucidate their bacterial communities. After quality control, over 300 000 sequences were obtained and classified into 118 operational taxonomic units (OTUs, clustered at 97% similarity). Analysis of rarefied communities revealed that the most abundant OTUs were tick species-specific endosymbionts, Francisella and Rickettsia, and the commonly flea-associated bacterium Bartonella in rodent blood. An Arsenophonus and additional Francisella endosymbiont were also present in D. variabilis samples. Rickettsia was found in both tick species but not in rodent blood, suggesting that it is not transmitted during feeding. Bartonella was present in larvae and nymphs of both tick species, even those scored as unengorged. Relatively, few OTUs (e.g. Bartonella, Lactobacillus) were found in all sample types. Overall, bacterial communities from each sample type were significantly different and highly structured, independent of their dominant OTUs. Our results point to complex microbial assemblages inhabiting ticks and host blood including infectious agents, tick-specific endosymbionts and environmental bacteria that could potentially affect arthropod-vectored disease dynamics.

  10. Bacterial community structure in freshwater springs infested with the invasive plant species Hydrilla verticillata

    PubMed Central

    Gordon-Bradley, N.; Li, N.

    2015-01-01

    The phylogenetic composition and physiological profiles of bacterial communities in freshwater springs were evaluated during the blooming and non-blooming stages of the invasive plant species, Hydrilla verticillata. Community-level physiological profiles (CLPPs) and pyrosequencing of 16S rRNA gene amplicons were used to study potential Hydrilla mediated shifts in the physiological potential and phylogenetic composition of the bacterial community in infested systems. The results of CLPP revealed that the microbes in the Hydrilla invaded sites utilized less substrates during blooming periods than during nonblooming periods of the plant. Spearman’s rank correlation analysis showed some relationships between the relative abundances of bacterial taxa and the Biolog substrate utilization pattern. The relative abundance of the identified taxa showed some striking differences based on the blooming status of Hydrilla and to a lesser extent on site variation. The relative abundance of Actinobacteria, Bacteriodetes, and Verrucomicrobia was generally higher during Hydrilla blooms, while Deltaproteobacteria was generally higher during non-blooming stages of Hydrilla. The detected genera also varied based on the blooming stages of the plant. Based on the findings, it appears that Hydrilla alters the phylogenetic composition and structure of the bacterial community during the blooming stage. PMID:26207069

  11. Potential core species and satellite species in the bacterial community within the rabbit caecum

    PubMed Central

    Monteils, Valérie; Cauquil, Laurent; Combes, Sylvie; Godon, Jean-Jacques; Gidenne, Thierry

    2008-01-01

    A bacteria library was constructed from the caecum of a rabbit maintained under standard conditions. The complete gene 16S rRNA gene was sequenced. The 228 clones obtained were distributed in 70 operational taxonomic units (OTUs). The large majority of the OTUs were composed of one or two clones and seven OTUs contained half of the sequences. Fourteen sequences had high similarity to the sequence already registered in databases (threshold of 97%). Only one of these sequences has been identified as Variovorax sp. (99% identity). Units were distributed mainly (94%) in the Firmicutes phylum. Three sequences were related to Bacteroidetes. Nine clusters were defined in the phylogenic tree. A great diversity of caecal bacteria of the rabbit was shown. Half of the sequences generated in this library were distributed in the phylogenetic tree near the sequences characterized previously in rabbit caecum (potential core species), and the other half of the sequences were well separated (satellite species). PMID:19049656

  12. Isolation and Characterization of Methanomicrobium paynteri sp. nov., a Mesophilic Methanogen Isolated from Marine Sediments †

    PubMed Central

    Rivard, Christopher J.; Henson, J. Michael; Thomas, Michael V.; Smith, Paul H.

    1983-01-01

    A new mesophilic methanogenic bacterial species isolated from marine sediments collected in the Cayman Islands is described. Cells are small rods occuring singly without filaments, are not motile, and do not possess flagella. Colonies are semitransparent and off-white in color. After 2 weeks of incubation at 37°C colonies are 1 to 2 mm in size, circular, and have entire edges. Only hydrogen-carbon dioxide is a substrate for growth and methane formation. Cells can tolerate a variety of organic secondary buffers (bicarbonate-CO2 being the primary buffer). Cells do not require yeast extract or Trypticase, but do require acetate, for growth. The optimum growth temperature is 40°C. The optimum sodium concentration is 0.15 M. The optimum pH for growth is 7.0. The minimum generation time is 4.8 h. The DNA base composition is 44.9 mol% guanine plus cytosine. The name Methanomicrobium paynteri is proposed in honor of M. J. B. Paynter. The type strain is G-2000 (=ATCC 33997, =DSM 2545). Images PMID:16346371

  13. A New Species of Pristionchus (Rhabditida: Diplogastridae) and Its Bacterial Symbiont from Yixing, China

    PubMed Central

    Li, Pengpeng; Dai, Chensheng; Bao, Haoran; Chen, Long; Gao, Di; Wang, Guoxiang; Wang, Jin; Wang, Hui; Yedid, Gabriel; Zhang, Keyun

    2015-01-01

    A new nematode species, Pristionchus entomophilus n. sp., was collected during a soil sample survey in Yixing of Jiangsu province, eastern China. P. entomophilus n. sp. is distinguished by its unique characteristics. This new species is mainly hermaphroditic, with males seldom found. The new nematode has a similar body length but has much narrower body width compared with P. pacificus. Its body is covered with longitudinal ridges: 12 ridges on head, 13 or 14 ridges in the middle, 11 and 7 ridges in front and rear of the anus, respectively. The eurystomatous form mouth includes a triangular dorsal tooth, a large claw-like right subventral tooth, and a row of five ventral denticles placed opposite the dorsal tooth. Only eight pairs of genital papillae and a pair of phasmids are present in the tail of the male as the sixth pair of papillae having seemingly been degenerated and lost. Molecular phylogenetic trees based on 18S rDNA confirmed that the new species belongs to the genus Pristionchus and is most closely related to P. pacificus. Moreover, the new species was found to be occasionally associated with the entomopathogenic bacterial strain 09FLYB1 of Serratia nematodophila and be able to stably transfer the bacterial strain for several generations. PMID:26527840

  14. Cold temperature decreases bacterial species richness in nitrogen-removing bioreactors treating inorganic mine waters.

    PubMed

    Karkman, A; Mattila, K; Tamminen, M; Virta, M

    2011-12-01

    Explosives used in mining, such as ammonium nitrate fuel oil (ANFO), can cause eutrophication of the surrounding environment by leakage of ammonium and nitrate from undetonated material that is not properly treated. Cold temperatures in mines affect nitrogen removal from water when such nutrients are treated with bioreactors in situ. In this study we identified bacteria in the bioreactors and studied the effect of temperature on the bacterial community. The bioreactors consisted of sequential nitrification and denitrification units running at either 5 or 10°C. One nitrification bioreactor running at 5°C was fed with salt spiked water. From the nitrification bioreactors, sequences from both ammonia- and nitrite-oxidizing bacteria were identified, but the species were distinct at different temperatures. The main nitrifiers in the lower temperature were closely related to the genera Nitrosospira and Candidatus Nitrotoga. 16S rRNA gene sequences closely related to halotolerant Nitrosomonas eutropha were found only from the salt spiked nitrification bioreactor. At 10°C the genera Nitrosomonas and Nitrospira were the abundant nitrifiers. The results showed that bacterial species richness estimates were low, <150 operational taxonomic units (OTUs), in all bioreactor clone libraries, when sequences were assigned to operational taxonomic units at an evolutionary distance of 0.03. The only exception was the nitrification bioreactor running at 10°C where species richness was higher, >300 OTUs. Species richness was lower in bioreactors running at 5°C compared to those operating at 10°C.

  15. Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance

    PubMed Central

    Kramer, Andrew M; Lyons, M Maille; Dobbs, Fred C; Drake, John M

    2013-01-01

    Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while colonization increases linearly with background density and aggregate size, extinction rates are expected to be nonlinear on small aggregates in a low background density of the pathogen. Under these conditions, we predict lower probabilities of pathogen presence and reduced abundance on aggregates compared with predictions based solely on colonization. These results suggest that the importance of aggregates to the dynamics of aquatic bacterial pathogens may be dependent on the interaction between aggregate size and background pathogen density, and that these interactions are strongly influenced by ecological interactions and pathogen traits. The model provides testable predictions and can be a useful tool for exploring how species-specific differences in pathogen traits may alter the effect of aggregates on disease transmission. PMID:24340173

  16. Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens

    PubMed Central

    Giaouris, Efstathios; Heir, Even; Desvaux, Mickaël; Hébraud, Michel; Møretrø, Trond; Langsrud, Solveig; Doulgeraki, Agapi; Nychas, George-John; Kačániová, Miroslava; Czaczyk, Katarzyna; Ölmez, Hülya; Simões, Manuel

    2015-01-01

    A community-based sessile life style is the normal mode of growth and survival for many bacterial species. Under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. Remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and form biofilms. Salmonella enterica, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus are important bacterial pathogens commonly implicated in outbreaks of foodborne diseases, while all are known to be able to create biofilms on both abiotic and biotic surfaces. Particularly challenging is the attempt to understand the complexity of inter-bacterial interactions that can be encountered in such unwanted consortia, such as competitive and cooperative ones, together with their impact on the final outcome of these communities (e.g., maturation, physiology, antimicrobial resistance, virulence, dispersal). In this review, up-to-date data on both the intra- and inter-species interactions encountered in biofilms of these pathogens are presented. A better understanding of these interactions, both at molecular and biophysical levels, could lead to novel intervention strategies for controlling pathogenic biofilm formation in food processing environments and thus improve food safety. PMID:26347727

  17. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

    PubMed

    Fouts, Derrick E; Matthias, Michael A; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L; Haake, David A; Haft, Daniel H; Hartskeerl, Rudy; Ko, Albert I; Levett, Paul N; Matsunaga, James; Mechaly, Ariel E; Monk, Jonathan M; Nascimento, Ana L T; Nelson, Karen E; Palsson, Bernhard; Peacock, Sharon J; Picardeau, Mathieu; Ricaldi, Jessica N; Thaipandungpanit, Janjira; Wunder, Elsio A; Yang, X Frank; Zhang, Jun-Jie; Vinetz, Joseph M

    2016-02-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

  18. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

    PubMed

    Fouts, Derrick E; Matthias, Michael A; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L; Haake, David A; Haft, Daniel H; Hartskeerl, Rudy; Ko, Albert I; Levett, Paul N; Matsunaga, James; Mechaly, Ariel E; Monk, Jonathan M; Nascimento, Ana L T; Nelson, Karen E; Palsson, Bernhard; Peacock, Sharon J; Picardeau, Mathieu; Ricaldi, Jessica N; Thaipandungpanit, Janjira; Wunder, Elsio A; Yang, X Frank; Zhang, Jun-Jie; Vinetz, Joseph M

    2016-02-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

  19. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

    PubMed Central

    Fouts, Derrick E.; Matthias, Michael A.; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E.; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L.; Haake, David A.; Haft, Daniel H.; Hartskeerl, Rudy; Ko, Albert I.; Levett, Paul N.; Matsunaga, James; Mechaly, Ariel E.; Monk, Jonathan M.; Nascimento, Ana L. T.; Nelson, Karen E.; Palsson, Bernhard; Peacock, Sharon J.; Picardeau, Mathieu; Ricaldi, Jessica N.; Thaipandungpanit, Janjira; Wunder, Elsio A.; Yang, X. Frank; Zhang, Jun-Jie; Vinetz, Joseph M.

    2016-01-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade’s refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

  20. Reverse Transcriptase-PCR Analysis of Bacterial rRNA for Detection and Characterization of Bacterial Species in Arthritis Synovial Tissue

    PubMed Central

    Kempsell, Karen E.; Cox, Charles J.; Hurle, Michael; Wong, Anthony; Wilkie, Scott; Zanders, Edward D.; Gaston, J. S. Hill; Crowe, J. Scott

    2000-01-01

    Onset of rheumatoid arthritis (RA) is widely believed to be preceded by exposure to some environmental trigger such as bacterial infectious agents. The influence of bacteria on RA disease onset or pathology has to date been controversial, due to inconsistencies between groups in the report of bacterial species isolated from RA disease tissue. Using a modified technique of reverse transcriptase-PCR amplification, we have detected bacterial rRNA in the synovial tissue of late-stage RA and non-RA arthritis controls. This may be suggestive of the presence of live bacteria. Sequencing of cloned complementary rDNA (crDNA) products revealed a number of bacterial sequences in joint tissue from each patient, and from these analyses a comprehensive profile of the organisms present was compiled. This revealed a number of different organisms in each patient, some of which are common to both RA and non-RA controls and are probably opportunistic colonizers of previously diseased tissue and others which are unique species. These latter organisms may be candidates for a specific role in disease pathology and require further investigation to exclude them as causative agents in the complex bacterial millieu. In addition, many of the detected bacterial species have not been identified previously from synovial tissue or fluid from arthritis patients. These may not be easily cultivable, since they were not revealed in previous studies using conventional in vitro bacterial culture methods. In situ hybridization analyses have revealed the joint-associated bacterial rRNA to be both intra- and extracellular. The role of viable bacteria or their nucleic acids as triggers in disease onset or pathology in either RA or non-RA arthritis controls is unclear and requires further investigation. PMID:10992514

  1. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    PubMed

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

  2. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    PubMed

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  3. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

    PubMed Central

    Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  4. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    PubMed

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  5. Bacterial growth rates are influenced by cellular characteristics of individual species when immersed in electromagnetic fields.

    PubMed

    Tessaro, Lucas W E; Murugan, Nirosha J; Persinger, Michael A

    2015-03-01

    Previous studies have shown that exposure to extremely low-frequency electromagnetic fields (ELF-EMFs) have negative effects on the rate of growth of bacteria. In the present study, two Gram-positive and two Gram-negative species were exposed to six magnetic field conditions in broth cultures. Three variations of the 'Thomas' pulsed frequency-modulated pattern; a strong-static "puck" magnet upwards of 5000G in intensity; a pair of these magnets rotating opposite one another at ∼30rpm; and finally a strong dynamic magnetic field generator termed the 'Resonator' with an average intensity of 250μT were used. Growth rate was discerned by optical density (OD) measurements every hour at 600nm. ELF-EMF conditions significantly affected the rates of growth of the bacterial cultures, while the two static magnetic field conditions were not statistically significant. Most interestingly, the 'Resonator' dynamic magnetic field increased the rates of growth of three species (Staphylococcus epidermidis, Staphylococcus aureus, and Escherichia coli), while slowing the growth of one (Serratia marcescens). We suggest that these effects are due to individual biophysical characteristics of the bacterial species.

  6. Surface-Selective Preferential Production of Reactive Oxygen Species on Piezoelectric Ceramics for Bacterial Killing.

    PubMed

    Tan, Guoxin; Wang, Shuangying; Zhu, Ye; Zhou, Lei; Yu, Peng; Wang, Xiaolan; He, Tianrui; Chen, Junqi; Mao, Chuanbin; Ning, Chengyun

    2016-09-21

    Reactive oxygen species (ROS) can be used to kill bacterial cells, and thus the selective generation of ROS from material surfaces is an emerging direction in antibacterial material discovery. We found the polarization of piezoelectric ceramic causes the two sides of the disk to become positively and negatively charged, which translate into cathode and anode surfaces in an aqueous solution. Because of the microelectrolysis of water, ROS are preferentially formed on the cathode surface. Consequently, the bacteria are selectively killed on the cathode surface. However, the cell experiment suggested that the level of ROS is safe for normal mammalian cells. PMID:27599911

  7. Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.

    PubMed

    Li, Tongtong; Long, Meng; Gatesoupe, François-Joël; Zhang, Qianqian; Li, Aihua; Gong, Xiaoning

    2015-01-01

    Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29 ± 0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune

  8. Photoinactivation of Eight Health-Relevant Bacterial Species: Determining the Importance of the Exogenous Indirect Mechanism.

    PubMed

    Maraccini, Peter A; Wenk, Jannis; Boehm, Alexandria B

    2016-05-17

    It is presently unknown to what extent the endogenous direct, endogenous indirect, and exogenous indirect mechanisms contribute to bacterial photoinactivation in natural surface waters. In this study, we investigated the importance of the exogenous indirect mechanism by conducting photoinactivation experiments with eight health-relevant bacterial species (Bacteroides thetaiotaomicron, Campylobacter jejuni, Enterococcus faecalis, Escherichia coli K12, E. coli O157:H7, Salmonella enterica serovar Typhimurium LT2, Staphylococcus aureus, and Streptococcus bovis). We used three synthetic photosensitizers (methylene blue, rose bengal, and nitrite) and two model natural photosensitizers (Suwannee River natural organic matter and dissolved organic matter isolated from a wastewater treatment wetland) that generated singlet oxygen and hydroxyl radical. B. thetaiotaomicron had larger first order rate constants than all other organisms under all conditions tested. The presence of the synthetic photosensitizers generally enhanced photoinactivation of Gram-positive facultative anaerobes (Ent. faecalis, Staph. aureus, and Strep. bovis). Among Gram-negative bacteria, only methylene blue with E. coli K12 and rose bengal with C. jejuni showed an enhancing effect. The presence of model natural photosensitizers either reduced or did not affect photoinactivation rate constants. Our findings highlight the importance of the cellular membrane and photosensitizer properties in modulating the contribution of the exogenous indirect mechanism to the overall bacterial photoinactivation.

  9. Bacterial species and their associations with acute and chronic mastitis in suckler ewes.

    PubMed

    Smith, E M; Willis, Z N; Blakeley, M; Lovatt, F; Purdy, K J; Green, L E

    2015-10-01

    Acute mastitis in suckler ewes is often detected because of systemic signs such as anorexia or lameness, whereas chronic mastitis, characterized by intramammary abscesses with no systemic disease, is typically detected when ewes are inspected before mating. The aims of the current study were to identify the species and strains of culturable bacteria associated with acutely diseased, chronically diseased, and unaffected mammary glands to investigate whether species and strains vary by state. To investigate acute mastitis, 28 milk samples were obtained from both glands of 14 ewes with acute mastitis in one gland only. To investigate chronic mastitis, 16 ovine udders were obtained from 2 abattoirs; milk was aspirated from the 32 glands where possible, and the udders were sectioned to expose intramammary abscesses, which were swab sampled. All milk and swab samples were cultured aerobically. In total, 37 bacterial species were identified, 4 from acute mastitis, 26 from chronic mastitis, and 8 from apparently healthy glands. In chronic mastitis, the overall coincidence index of overlap of species detected in intramammary abscesses and milk was 0.60, reducing to 0.36 within individual glands, indicating a high degree of species overlap in milk and abscesses overall, but less overlap within specific glands. Staphylococcus aureus was detected frequently in all sample types; it was isolated from 10/14 glands with acute mastitis. In 5 ewes, closely related strains were present in both affected and unaffected glands. In chronic mastitis, closely related Staphylococcus aureus strains were detected in milk and abscesses from the same gland.

  10. Individual growth detection of bacterial species in an in vitro oral polymicrobial biofilm model.

    PubMed

    Tabenski, L; Maisch, T; Santarelli, F; Hiller, K-A; Schmalz, G

    2014-11-01

    Most in vitro studies on the antibacterial effects of antiseptics have used planktonic bacteria in monocultures. However, this study design does not reflect the in vivo situation in oral cavities harboring different bacterial species that live in symbiotic relationships in biofilms. The aim of this study was to establish a simple in vitro polymicrobial model consisting of only three bacterial strains of different phases of oral biofilm formation to simulate in vivo oral conditions. Therefore, we studied the biofilm formation of Actinomyces naeslundii (An), Fusobacterium nucleatum (Fn), and Enterococcus faecalis (Ef) on 96-well tissue culture plates under static anaerobic conditions using artificial saliva according to the method established by Pratten et al. that was supplemented with 1 g l(-1) sucrose. Growth was separately determined for each bacterial strain after incubation periods of up to 72 h by means of quantitative real-time polymerase chain reaction and live/dead staining. Presence of an extracellular polymeric substance (EPS) was visualized by Concanavalin A staining. Increasing incubation times of up to 72 h showed adhesion and propagation of the bacterial strains with artificial saliva formulation. An and Ef had significantly higher growth rates than Fn. Live/dead staining showed a median of 49.9 % (range 46.0-53.0 %) of living bacteria after 72 h of incubation, and 3D fluorescence microscopy showed a three-dimensional structure containing EPS. An in vitro oral polymicrobial biofilm model was established to better simulate oral conditions and had the advantage of providing the well-controlled experimental conditions of in vitro testing.

  11. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience.

    PubMed

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo; Li, Yu-You

    2015-09-01

    While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000mg/L with free ammonia (FA) 2000mg/L compared to 16,000mg/L (FA1500mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gVSin in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages. PMID:26054964

  12. Natural Transformation Facilitates Transfer of Transposons, Integrons and Gene Cassettes between Bacterial Species

    PubMed Central

    Domingues, Sara; Harms, Klaus; Fricke, W. Florian; Johnsen, Pål J.; da Silva, Gabriela J.; Nielsen, Kaare Magne

    2012-01-01

    We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much

  13. Contribution of reactive oxygen species to (+)-catechin-mediated bacterial lethality.

    PubMed

    Ajiboye, T O; Aliyu, M; Isiaka, I; Haliru, F Z; Ibitoye, O B; Uwazie, J N; Muritala, H F; Bello, S A; Yusuf, I I; Mohammed, A O

    2016-10-25

    The contribution of reactive oxygen species to (+)-catechin-mediated bacterial lethality was investigated. Minimum inhibitory concentrations (MIC) and minimum bactericidal concentration (MBC) of (+)-catechin against E. coli, P. aeruginosa and S. aureus were investigated using 96-well microtitre plate. MIC and MBC of (+)-catechin against E. coli, P. aeruginosa and S. aureus are 600 and 700; 600 and 800; 600 and 800 μg/mL respectively. The optical densities and colony forming units of (+)-catechin-treated bacteria decreased. (+)-Catechin (4× MIC) significantly increased the superoxide anion content of E. coli, P. aeruginosa and S. aureus compared to DMSO. Superoxide dismutase and catalase in (+)-catechin treated E. coli, P. aeruginosa and S. aureus increased significantly. Conversely, level of reduced glutathione in (+)-catechin-treated E. coli, P. aeruginosa and S. aureus decreased significantly while glutathione disulfide increased significantly. Furthermore, malondialdehyde and fragmented DNA increased significantly following exposure to (+)-catechin. From the above findings, (+)-catechin enhanced the generation of reactive oxygen species (superoxide anion radical and hydroxyl radical) in E. coli, P. aeruginosa and S. aureus, possibly by autoxidation, Fenton chemistry and inhibiting electron transport chain resulting into lipid peroxidation and DNA fragmentation and consequentially bacterial cell death. PMID:27634360

  14. Differential bioavailability of soil-sorbed naphthalene to two bacterial species.

    PubMed Central

    Guerin, W F; Boyd, S A

    1992-01-01

    Prediction of the fate of hydrophobic organic contaminants in soils is complicated by the competing processes of sorption and biodegradation. To test the hypothesis that sorbed naphthalene is unavailable to degradative microorganisms, we developed a simple kinetic method to examine the rates and extents of naphthalene degradation in soil-free and soil-containing systems in a comparison of two bacterial species. The method is predicated on the first-order dependence of the initial mineralization rate on the naphthalene concentration when the latter is below the Michaelis-Menten half-saturation constant (Km) for naphthalene for the organism under study. Rates and extents of mineralization were estimated by nonlinear regression analysis of data by using both a simple first-order model and a three-parameter, coupled degradation-desorption model described for the first time here. Bioavailability assays with two bacterial species (Pseudomonas putida ATCC 17484 and a gram-negative soil isolate, designated NP-Alk) gave dramatically different results. For NP-Alk, sorption limited both the rate and extent of naphthalene mineralization, in accordance with values predicted on the basis of the equilibrium aqueous-phase naphthalene concentrations. For strain 17484, both the rates and extents of naphthalene mineralization exceeded the predicted values and resulted in enhanced rates of naphthalene desorption from the soils. We conclude that there are important organism-specific properties which make generalizations regarding the bioavailability of sorbed substrates inappropriate. PMID:1599237

  15. Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut

    PubMed Central

    Jemielita, Matthew; Taormina, Michael J.; Burns, Adam R.; Hampton, Jennifer S.; Rolig, Annah S.; Guillemin, Karen

    2014-01-01

    ABSTRACT The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. PMID:25516613

  16. Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

    PubMed Central

    Ormerod, Kate L.; George, Narelle M.; Fraser, James A.; Wainwright, Claire

    2015-01-01

    The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis. PMID:26401445

  17. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography

    PubMed Central

    Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

    2016-01-01

    The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach

  18. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

    PubMed

    Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

    2016-01-01

    The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach

  19. Waste Workers’ Exposure to Airborne Fungal and Bacterial Species in the Truck Cab and During Waste Collection

    PubMed Central

    Madsen, Anne Mette; Alwan, Taif; Ørberg, Anders; Uhrbrand, Katrine; Jørgensen, Marie Birk

    2016-01-01

    A large number of people work with garbage collection, and exposure to microorganisms is considered an occupational health problem. However, knowledge on microbial exposure at species level is limited. The aim of the study was to achieve knowledge on waste collectors’ exposure to airborne inhalable fungal and bacterial species during waste collection with focus on the transport of airborne microorganisms into the truck cab. Airborne microorganisms were collected with samplers mounted in the truck cab, on the workers’ clothes, and outdoors. Fungal and bacterial species were quantified and identified. The study showed that the workers were exposed to between 112 and 4.8×104 bacteria m−3 air and 326 and 4.6×104 fungi m−3 air. The personal exposures to bacteria and fungi were significantly higher than the concentrations measured in the truck cabs and in the outdoor references. On average, the fungal and bacterial concentrations in truck cabs were 111 and 7.7 times higher than outdoor reference measurements. In total, 23 fungal and 38 bacterial species were found and identified. Most fungal species belonged to the genus Penicillium and in total 11 Penicillium species were found. Identical fungal species were often found both in a personal sample and in the same person’s truck cab, but concentrations were on average 27 times higher in personal samples. Concentrations of fungal and bacterial species found only in the personal samples were lower than concentrations of species also found in truck cabs. Skin-related bacteria constituted a large fraction of bacterial isolates found in personal and truck cab samples. In total, six Staphylococcus species were found. In outdoor samples, no skin-related bacteria were found. On average, concentrations of bacterial species found both in the truck cab and personal samples were 77 times higher in personal samples than in truck cab samples. In conclusion, high concentrations of fungi were found in truck cabs, but the

  20. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    PubMed

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.

  1. Dancing for food in the deep sea: bacterial farming by a new species of Yeti crab.

    PubMed

    Thurber, Andrew R; Jones, William J; Schnabel, Kareen

    2011-01-01

    Vent and seep animals harness chemosynthetic energy to thrive far from the sun's energy. While symbiont-derived energy fuels many taxa, vent crustaceans have remained an enigma; these shrimps, crabs, and barnacles possess a phylogenetically distinct group of chemosynthetic bacterial epibionts, yet the role of these bacteria has remained unclear. We test whether a new species of Yeti crab, which we describe as Kiwa puravida n. sp, farms the epibiotic bacteria that it grows on its chelipeds (claws), chelipeds that the crab waves in fluid escaping from a deep-sea methane seep. Lipid and isotope analyses provide evidence that epibiotic bacteria are the crab's main food source and K. puravida n. sp. has highly-modified setae (hairs) on its 3(rd) maxilliped (a mouth appendage) which it uses to harvest these bacteria. The ε- and γ- proteobacteria that this methane-seep species farms are closely related to hydrothermal-vent decapod epibionts. We hypothesize that this species waves its arm in reducing fluid to increase the productivity of its epibionts by removing boundary layers which may otherwise limit carbon fixation. The discovery of this new species, only the second within a family described in 2005, stresses how much remains undiscovered on our continental margins. PMID:22140426

  2. Dancing for food in the deep sea: bacterial farming by a new species of Yeti crab.

    PubMed

    Thurber, Andrew R; Jones, William J; Schnabel, Kareen

    2011-01-01

    Vent and seep animals harness chemosynthetic energy to thrive far from the sun's energy. While symbiont-derived energy fuels many taxa, vent crustaceans have remained an enigma; these shrimps, crabs, and barnacles possess a phylogenetically distinct group of chemosynthetic bacterial epibionts, yet the role of these bacteria has remained unclear. We test whether a new species of Yeti crab, which we describe as Kiwa puravida n. sp, farms the epibiotic bacteria that it grows on its chelipeds (claws), chelipeds that the crab waves in fluid escaping from a deep-sea methane seep. Lipid and isotope analyses provide evidence that epibiotic bacteria are the crab's main food source and K. puravida n. sp. has highly-modified setae (hairs) on its 3(rd) maxilliped (a mouth appendage) which it uses to harvest these bacteria. The ε- and γ- proteobacteria that this methane-seep species farms are closely related to hydrothermal-vent decapod epibionts. We hypothesize that this species waves its arm in reducing fluid to increase the productivity of its epibionts by removing boundary layers which may otherwise limit carbon fixation. The discovery of this new species, only the second within a family described in 2005, stresses how much remains undiscovered on our continental margins.

  3. Dancing for Food in the Deep Sea: Bacterial Farming by a New Species of Yeti Crab

    PubMed Central

    Thurber, Andrew R.; Jones, William J.; Schnabel, Kareen

    2011-01-01

    Vent and seep animals harness chemosynthetic energy to thrive far from the sun's energy. While symbiont-derived energy fuels many taxa, vent crustaceans have remained an enigma; these shrimps, crabs, and barnacles possess a phylogenetically distinct group of chemosynthetic bacterial epibionts, yet the role of these bacteria has remained unclear. We test whether a new species of Yeti crab, which we describe as Kiwa puravida n. sp, farms the epibiotic bacteria that it grows on its chelipeds (claws), chelipeds that the crab waves in fluid escaping from a deep-sea methane seep. Lipid and isotope analyses provide evidence that epibiotic bacteria are the crab's main food source and K. puravida n. sp. has highly-modified setae (hairs) on its 3rd maxilliped (a mouth appendage) which it uses to harvest these bacteria. The ε- and γ- proteobacteria that this methane-seep species farms are closely related to hydrothermal-vent decapod epibionts. We hypothesize that this species waves its arm in reducing fluid to increase the productivity of its epibionts by removing boundary layers which may otherwise limit carbon fixation. The discovery of this new species, only the second within a family described in 2005, stresses how much remains undiscovered on our continental margins. PMID:22140426

  4. Epidemiology of urinary tract infections, bacterial species and resistances in primary care in France.

    PubMed

    Malmartel, A; Ghasarossian, C

    2016-03-01

    General practitioners often have to manage urinary tract infections (UTI) with probabilistic treatments, although bacterial resistances are increasing. Therefore, the French Society of Infectious Diseases published new guidelines in 2014. The aim of this study was to investigate the bacterial epidemiology of UTI in the general population in primary care and analyse risk factors for Escherichia coli resistance to antibiotics. A cross-sectional study was conducted in 12 ambulatory laboratories. Patients over 18 years of age coming for urinalysis were included. Risk factors for UTI were collected using a questionnaire and the laboratory records. Bacteria meeting criteria for UTI were analysed. A positive urinalysis was found in 1119 patients, corresponding to 1125 bacterial isolates. The bacterial species were: E. coli (73 %), Enterococcus spp. (7 %), Klebsiella spp. (6 %), Proteus spp. (4 %), Staphylococcus spp. (3 %) and Pseudomonas spp. (2 %). Regardless of the bacteria, the most common resistance was that to co-trimoxazole: 27 % (95 % confidence interval [CI] = [0.24; 0.30]), followed by ofloxacin resistance: 16 % [0.14; 0.18]. Escherichia coli resistances to co-trimoxazole, ofloxacin, cefixime, nitrofurantoin and fosfomycin were, respectively, 25.5 % [0.23; 0.28], 17 % [0.14; 0.20], 5.6 % [0.04; 0.07], 2.2 % [0.01; 0.03] and 1.2 % [0.005; 0.02]. Independent risk factors for E. coli resistance to ofloxacin were age over 85 years (odds ratio [OR] = 3.08; [1.61; 5.87]) and a history of UTI in the last 6 months (OR = 2.34; [1.54; 3.52]). Our findings support the guidelines recommending fluoroquinolone sparing. The scarcity of E. coli resistance to fosfomycin justifies its use as a first-line treatment in acute cystitis. These results should be reassessed in a few years to identify changes in the bacterial epidemiology of UTI. PMID:26740324

  5. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

    SciTech Connect

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo; Li, Yu-You

    2015-09-15

    Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S{sub in} in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.

  6. In situ identification of bacterial species in marine microfouling films by using an immunofluorescence technique.

    PubMed Central

    Zambon, J J; Huber, P S; Meyer, A E; Slots, J; Fornalik, M S; Baier, R E

    1984-01-01

    An immunofluorescence technique was developed for the in situ identification of specific bacteria in marine microfouling films. Microorganisms adherent to glass plates after 30 days of immersion in a synthetic seawater system were cultured and classified by biochemical tests, flagellar arrangement, and the API 20E system. All isolates were gram-negative aerobic or facultative motile rods, predominantly Pseudomonas spp. Rabbit antisera to the five dominant organisms including Achromobacter spp., Comamonas terrigena, P. putrefaciens, a yellow-pigmented Pseudomonas sp., and Vibrio alginolyticus were prepared. These antisera were shown to be species specific in indirect immunofluorescence assays against a battery of 26 marine isolates from 14 bacterial species, with the exception of antisera to the Pseudomonas spp, which cross-reacted with each other but not with test bacteria of other genera. These immunofluorescent reagents enabled the in situ identification of all five bacterial species in microfouling films. Low-surface-energy test plates had smaller numbers of adherent bacteria in microfouling films than medium-surface-energy test plates, suggesting that the degree of microfouling may be influenced by the surface energy. In addition, the reagents could identify up to 39% of the attached bacteria in microfouling films spontaneously formed on steel plates in flow cells deployed in different areas of the Atlantic Ocean. The microbial composition of the ocean-formed films varied with the geographical area of their formation. The present results indicate that immunofluorescence techniques may provide a rapid and reliable means to identify, in situ, specific bacteria in marine microfouling films. PMID:6393875

  7. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    PubMed Central

    Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz

    2012-01-01

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals. PMID:22865078

  8. Relationship between the Presence of Bartonella Species and Bacterial Loads in Cats and Cat Fleas (Ctenocephalides felis) under Natural Conditions.

    PubMed

    Gutiérrez, Ricardo; Nachum-Biala, Yaarit; Harrus, Shimon

    2015-08-15

    Cats are considered the main reservoir of three zoonotic Bartonella species: Bartonella henselae, Bartonella clarridgeiae, and Bartonella koehlerae. Cat fleas (Ctenocephalides felis) have been experimentally demonstrated to be a competent vector of B. henselae and have been proposed as the potential vector of the two other Bartonella species. Previous studies have reported a lack of association between the Bartonella species infection status (infected or uninfected) and/or bacteremia levels of cats and the infection status of the fleas they host. Nevertheless, to date, no study has compared the quantitative distributions of these bacteria in both cats and their fleas under natural conditions. Thus, the present study explored these relationships by identifying and quantifying the different Bartonella species in both cats and their fleas. Therefore, EDTA-blood samples and fleas collected from stray cats were screened for Bartonella bacteria. Bacterial loads were quantified by high-resolution melt real-time quantitative PCR assays. The results indicated a moderate correlation between the Bartonella bacterial loads in the cats and their fleas when both were infected with the same Bartonella species. Moreover, a positive effect of the host infection status on the Bartonella bacterial loads of the fleas was observed. Conversely, the cat bacterial loads were not affected by the infection status of their fleas. Our results suggest that the Bartonella bacterial loads of fleas are positively affected by the presence of the bacteria in their feline host, probably by multiple acquisitions/accumulation and/or multiplication events.

  9. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    USGS Publications Warehouse

    Pearson, T.; Giffard, P.; Beckstrom-Sternberg, S.; Auerbach, R.; Hornstra, H.; Tuanyok, A.; Price, E.P.; Glass, M.B.; Leadem, B.; Beckstrom-Sternberg, J. S.; Allan, G.J.; Foster, J.T.; Wagner, D.M.; Okinaka, R.T.; Sim, S.H.; Pearson, O.; Wu, Z.; Chang, J.; Kaul, R.; Hoffmaster, A.R.; Brettin, T.S.; Robison, R.A.; Mayo, M.; Gee, J.E.; Tan, P.; Currie, B.J.; Keim, P.

    2009-01-01

    Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an

  10. Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily.

    PubMed

    Matsunaga, James; Barocchi, Michele A; Croda, Julio; Young, Tracy A; Sanchez, Yolanda; Siqueira, Isadora; Bolin, Carole A; Reis, Mitermayer G; Riley, Lee W; Haake, David A; Ko, Albert I

    2003-08-01

    Proteins with bacterial immunoglobulin-like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface-expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig-like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudogene, ligC, were identified. The ligA and ligB genes encode amino-terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy-terminal non-repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High-pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis. PMID:12890019

  11. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

    PubMed Central

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-01-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  12. Biomarkers for Tuberculosis Based on Secreted, Species-Specific, Bacterial Small Molecules.

    PubMed

    Pan, Shih-Jung; Tapley, Asa; Adamson, John; Little, Tessa; Urbanowski, Michael; Cohen, Keira; Pym, Alexander; Almeida, Deepak; Dorasamy, Afton; Layre, Emilie; Young, David C; Singh, Ravesh; Patel, Vinod B; Wallengren, Kristina; Ndung'u, Thumbi; Wilson, Douglas; Moody, D Branch; Bishai, William

    2015-12-01

    Improved biomarkers are needed for tuberculosis. To develop tests based on products secreted by tubercle bacilli that are strictly associated with viability, we evaluated 3 bacterial-derived, species-specific, small molecules as biomarkers: 2 mycobactin siderophores and tuberculosinyladenosine. Using liquid chromatography-tandem mass spectrometry, we demonstrated the presence of 1 or both mycobactins and/or tuberculosinyladenosine in serum and whole lung tissues from infected mice and sputum, cerebrospinal fluid (CSF), or lymph nodes from infected patients but not uninfected controls. Detection of the target molecules distinguished host infection status in 100% of mice with both serum and lung as the target sample. In human subjects, we evaluated detection of the bacterial small molecules (BSMs) in multiple body compartments in 3 patient cohorts corresponding to different forms of tuberculosis. We detected at least 1 of the 3 molecules in 90%, 71%, and 40% of tuberculosis patients' sputum, CSF, and lymph node samples, respectively. In paucibacillary forms of human tuberculosis, which are difficult to diagnose even with culture, detection of 1 or more BSM was rapid and compared favorably to polymerase chain reaction-based detection. Secreted BSMs, detectable in serum, warrant further investigation as a means for diagnosis and therapeutic monitoring in patients with tuberculosis.

  13. Efficacy of two sperm preparation techniques in reducing non-specific bacterial species from human semen

    PubMed Central

    Abeysundara, Prabath K; Dissanayake, DMAB; Wijesinghe, Prasantha S; Perera, RRDP; Nishad, AAN

    2013-01-01

    CONTEXT: Artificial reproductive techniques using seminal preparations with bacteria may cause pelvic inflammatory disease and its sequalae. AIMS: To assess efficacy of two sperm preparation techniques to clear bacteria and the effect of bacteriospermia on sperm recovery rates. SETTINGS AND DESIGN: A descriptive cross-sectional study was carried out among males of subfertile couples. SUBJECTS AND METHODS: Semen samples were randomly allocated into swim-up method (group S, n = 68) and density gradient method (group D, n = 50) for sperm preparation. Seminal fluid analysis and bacterial cultures were performed in each sample before and after sperm preparation. STATISTICAL ANALYSIS: McNemar's chi-squared test and independent samples t-test in SPSS version 16.0 were used. RESULTS: Organisms were found in 86 (72.88%) out of 118 samples, before sperm preparation; Streptococcus species (n = 40, 46.51% of which 14 were Group D Streptococcus species), Coagulase negative Staphylococcus species (n = 17, 19.76%), Staphylococcus aureus (n = 13, 15.11%), Coliform species (n = 11, 12.79% of which 09 were Escherichia coli) and Corynebacterium species (n = 5, 5.81%). There was a statistically significant reduction of culture positive samples in raw vs. processed samples; in group S, 49 (72.05%) vs. 16 (23.52%) and in group D, 37 (74%) vs. 18 (36%). In group S and D, mean (SD) recovery rates of culture positive vs. culture negative samples were 39.44% (SD-14.02) vs. 44.22% (SD-22.38), P = 0.39 and 52.50% (SD-37.16) vs. 49.58% (SD-40.32), P = 0.82 respectively. CONCLUSIONS: Both sperm preparation methods significantly reduced bacteria in semen, but total clearance was not achieved. Sperm recovery rate was not affected by bacteriospermia. PMID:24082658

  14. Species Specific Bacterial Spore Detection Using Lateral-Flow Immunoassay with DPA-Triggered Tb Luminescence

    NASA Technical Reports Server (NTRS)

    Ponce, Adrian

    2003-01-01

    A method of detecting bacterial spores incorporates (1) A method of lateral-flow immunoassay in combination with (2) A method based on the luminescence of Tb3+ ions to which molecules of dipicolinic acid (DPA) released from the spores have become bound. The present combination of lateral-flow immunoassay and DPA-triggered Tb luminescence was developed as a superior alternative to a prior lateral-flow immunoassay method in which detection involves the visual observation and/or measurement of red light scattered from colloidal gold nanoparticles. The advantage of the present combination method is that it affords both (1) High selectivity for spores of the species of bacteria that one seeks to detect (a characteristic of lateral-flow immunoassay in general) and (2) Detection sensitivity much greater (by virtue of the use of DPA-triggered Tb luminescence instead of gold nanoparticles) than that of the prior lateral-flow immunoassay method

  15. Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization

    PubMed Central

    Manching, Heather C.; Balint-Kurti, Peter J.; Stapleton, Ann E.

    2014-01-01

    Plant leaves are inhabited by a diverse group of microorganisms that are important contributors to optimal growth. Biotic and abiotic effects on plant growth are usually studied in controlled settings examining response to variation in single factors and in field settings with large numbers of variables. Multi-factor experiments with combinations of stresses bridge this gap, increasing our understanding of the genotype-environment-phenotype functional map for the host plant and the affiliated epiphytic community. The maize inbred B73 was exposed to single and combination abiotic and the biotic stress treatments: low nitrogen fertilizer and high levels of infection with southern leaf blight (causal agent Cochliobolus heterostrophus). Microbial epiphyte samples were collected at the vegetative early-season phase and species composition was determined using 16S ribosomal intergenic spacer analysis. Plant traits and level of southern leaf blight disease were measured late-season. Bacterial diversity was different among stress treatment groups (P < 0.001). Lower species richness—alpha diversity—was correlated with increased severity of southern leaf blight disease when disease pressure was high. Nitrogen fertilization intensified the decline in bacterial alpha diversity. While no single bacterial ribotype was consistently associated with disease severity, small sets of ribotypes were good predictors of disease levels. Difference in leaf bacterial-epiphyte diversity early in the season were correlated with plant disease severity, supporting further tests of microbial epiphyte-disease correlations for use in predicting disease progression. PMID:25177328

  16. Surviving chytridiomycosis: differential anti-Batrachochytrium dendrobatidis activity in bacterial isolates from three lowland species of Atelopus.

    PubMed

    Flechas, Sandra V; Sarmiento, Carolina; Cárdenas, Martha E; Medina, Edgar M; Restrepo, Silvia; Amézquita, Adolfo

    2012-01-01

    In the Neotropics, almost every species of the stream-dwelling harlequin toads (genus Atelopus) have experienced catastrophic declines. The persistence of lowland species of Atelopus could be explained by the lower growth rate of Batrachochytrium dendrobatidis (Bd) at temperatures above 25 °C. We tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis. We isolated 148 cultivable bacterial strains from three lowland Atelopus species and quantified the anti-Bd activity through antagonism assays. Twenty-six percent (38 strains representing 12 species) of the bacteria inhibited Bd growth and just two of them were shared among the toad species sampled in different localities. Interestingly, the strongest anti-Bd activity was measured in bacteria isolated from A. elegans, the only species that tested positive for the pathogen. The cutaneous bacterial microbiota is thus likely a fitness-enhancing trait that may (adaptation) or not (exaptation) have appeared because of natural selection mediated by chytridiomycosis. Our findings reveal bacterial strains for development of local probiotic treatments against chytridiomycosis and also shed light on the mechanisms behind the frog-bacteria-pathogen interaction. PMID:22970314

  17. Surviving Chytridiomycosis: Differential Anti-Batrachochytrium dendrobatidis Activity in Bacterial Isolates from Three Lowland Species of Atelopus

    PubMed Central

    Flechas, Sandra V.; Sarmiento, Carolina; Cárdenas, Martha E.; Medina, Edgar M.; Restrepo, Silvia; Amézquita, Adolfo

    2012-01-01

    In the Neotropics, almost every species of the stream-dwelling harlequin toads (genus Atelopus) have experienced catastrophic declines. The persistence of lowland species of Atelopus could be explained by the lower growth rate of Batrachochytrium dendrobatidis (Bd) at temperatures above 25°C. We tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis. We isolated 148 cultivable bacterial strains from three lowland Atelopus species and quantified the anti-Bd activity through antagonism assays. Twenty-six percent (38 strains representing 12 species) of the bacteria inhibited Bd growth and just two of them were shared among the toad species sampled in different localities. Interestingly, the strongest anti-Bd activity was measured in bacteria isolated from A. elegans, the only species that tested positive for the pathogen. The cutaneous bacterial microbiota is thus likely a fitness-enhancing trait that may (adaptation) or not (exaptation) have appeared because of natural selection mediated by chytridiomycosis. Our findings reveal bacterial strains for development of local probiotic treatments against chytridiomycosis and also shed light on the mechanisms behind the frog-bacteria-pathogen interaction. PMID:22970314

  18. Psychrophilic and mesophilic fungi in frozen food products.

    PubMed

    KUEHN, H H; GUNDERSON, M F

    1963-07-01

    The mold flora of certain frozen pastries and chicken pies was investigated. Molds were determined qualitatively or quantitatively, or both, by preparing pour plates of the blended product and incubating the plates at various temperatures. The mesophilic fungal flora developed on plates incubated at 10 and 20 C, whereas psychrophilic fungi were obtained on plates incubated at 0 and 5 C. About 2,000 cultures of fungi, representing about 100 different species, were isolated from various products. Four different brands of blueberry, two brands of cherry pastries, two brands of apple, and one brand of raspberry pastries were examined. In addition, two brands of chicken pies were studied. Blueberry pastries had a much higher total fungal population than the other products, although different brands of blueberry pastries varied considerably. Blueberry pastries had from 347 to 1,586 psychrophilic fungi per g. Cherry pastries had about 70 to 110 psychrophiles per g, and apple pastries had 19 to 92 psychrophiles per g. Chicken pies contained very few psychrophilic fungi, about 15 per g. Aureobasidium pullulans was recovered most frequently. About 90% of the psychrophilic fungi found in blueberry products was A. pullulans. Depending upon the brand of cherry pastry, either Phoma spp. or A. pullulans was the most common fungus present. Apple pastries also displayed brand variation, but were unique in having many mesophilic aspergilli. This genus was generally absent from other products. The Penicillium content of apple pastries was also rather high; 50% of the psychrophilic flora was represented by this genus. The psychrophilic fungal flora of chicken pies was composed primarily of penicillia (50%) and Chrysosporium pannorum (46%). PMID:13927344

  19. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

    PubMed Central

    Wei, Yulong; Wang, Juan; Xia, Xuhua

    2016-01-01

    Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range. PMID:27297468

  20. Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere▿

    PubMed Central

    Hunter, Paul J.; Hand, Paul; Pink, David; Whipps, John M.; Bending, Gary D.

    2010-01-01

    Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community. PMID:20952648

  1. Mesophilic fermentation of renewable biomass: does hydraulic retention time regulate methanogen diversity?

    PubMed

    Krakat, Niclas; Schmidt, Stefan; Scherer, Paul

    2010-09-01

    The present long-term study (about 1,100 days) monitored the diversity of methanogens during the mesophilic, anaerobic digestion of beet silage. Six fermentor samples were analyzed by ribosomal RNA gene restriction analysis, fluorescence in situ hybridization, and fluorescence microscopy. Hydrogenotrophic methanogens dominated within the population in all samples analyzed. Multidimensional scaling revealed that a rapid decrease in hydraulic retention time resulted in increased species richness, which in turn led to slightly higher CH(4) yields. PMID:20675458

  2. Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

    PubMed

    McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

    2014-05-01

    Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior.

  3. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

    PubMed Central

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

  4. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    PubMed

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  5. Co-operative inhibitory effects of hydrogen peroxide and iodine against bacterial and yeast species

    PubMed Central

    2013-01-01

    Background Hydrogen peroxide and iodine are powerful antimicrobials widely used as antiseptics and disinfectants. Their antimicrobial properties are known to be enhanced by combining them with other compounds. We studied co-operative inhibitory activities (synergism, additive effects and modes of growth inhibition) of hydrogen peroxide and iodine used concurrently against 3 bacterial and 16 yeast species. Results Synergistic or additive inhibitory effects were shown for hydrogen peroxide and iodine mixtures against all 19 species used in the study. Both biocides were mostly cidal individually and in mixtures against Pseudomonas aeruginosa and Staphylococcus aureus. Both compounds manifested static inhibitory effects individually, but their mixtures were synergistically cidal for Saccharomyces cerevisiae and Escherihia coli. Cells of S. cerevisiae treated with hydrogen peroxide and iodine-hydrogen peroxide mixture produced increased numbers of respiratory deficient mutants indicating genotoxic effects. Conclusion Iodine and hydrogen peroxide used concurrently interact synergistically or additively against a range of prokaryotic and eukaryotic microorganisms. The study provides an insight as to how these traditional antimicrobials could be used more effectively for disinfection and antisepsis. In addition, a simple approach is proposed for scoring genotoxicity of different biocides by using the budding yeast system. PMID:23856115

  6. Diversity and variability of methanogens during the shift from mesophilic to thermohilic conditions while biogas production.

    PubMed

    Ziembińska-Buczyńska, A; Banach, A; Bacza, T; Pieczykolan, M

    2014-12-01

    Anaerobic digestion (AD) is the most popular path of organic waste disposal. It is often used in wastewater treatment plants for excessive sludge removal. Methanogenic fermentation had usually been performed under mesophilic conditions, but in the past few years the thermophilic processes have become more popular due to economics and sludge sanitation. Methanogens, the group of microorganisms responsible for methane production, are thought to be sensitive to temperature change and it has already been proven that the communities performing methanogenesis under mesophilic and thermophilic conditions differ. But in most cases the research performed on methanogen diversity and changeability was undertaken in two separate anaerobic chambers for meso- and thermophilic conditions. It is also known that there is a group of microorganisms performing AD which are insensitive to temperature. Also the linkage between digester performance and its microbial content and community changeability is still not fully understood. That is why in this experiment we analyzed the bacterial community performing methanogenesis in a pilot scale anaerobic chamber during the shift from mesophilic to thermophilic conditions to point at the group of temperature tolerant microorganisms and their performance. The research was performed with PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). It occurred that the community biodiversity decreased together with a temperature increase. The changes were coherent for both the total bacteria community and methanogens. These bacterial shifts were also convergent with biogas production-it decreased in the beginning of the thermophilic phase with the bacterial biodiversity decrease and increased when the community seemed to be restored. DGGE results suggest that among a wide variety of microorganisms involved in AD there is a GC-rich group relatively insensitive towards temperature change, able to adapt quickly to shifts in

  7. Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

    PubMed Central

    Caro-Quintero, Alejandro; Konstantinidis, Konstantinos T

    2015-01-01

    Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼16% of the total genes and ∼35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla. PMID:25314320

  8. Diversity and Localization of Bacterial Endosymbionts from Whitefly Species Collected in Brazil

    PubMed Central

    Marubayashi, Julio Massaharu; Kliot, Adi; Yuki, Valdir Atsushi; Rezende, Jorge Alberto Marques; Krause-Sakate, Renate; Pavan, Marcelo Agenor; Ghanim, Murad

    2014-01-01

    Whiteflies (Hemiptera: Aleyrodidae) are sap-sucking insect pests, and some cause serious damage in agricultural crops by direct feeding and by transmitting plant viruses. Whiteflies maintain close associations with bacterial endosymbionts that can significantly influence their biology. All whitefly species harbor a primary endosymbiont, and a diverse array of secondary endosymbionts. In this study, we surveyed 34 whitefly populations collected from the states of Sao Paulo, Bahia, Minas Gerais and Parana in Brazil, for species identification and for infection with secondary endosymbionts. Sequencing the mitochondrial Cytochrome Oxidase I gene revealed the existence of five whitefly species: The sweetpotato whitefly Bemisia tabaci B biotype (recently termed Middle East-Asia Minor 1 or MEAM1), the greenhouse whitefly Trialeurodes vaporariorum, B. tabaci A biotype (recently termed New World 2 or NW2) collected only from Euphorbia, the Acacia whitefly Tetraleurodes acaciae and Bemisia tuberculata both were detected only on cassava. Sequencing rRNA genes showed that Hamiltonella and Rickettsia were highly prevalent in all MEAM1 populations, while Cardinium was close to fixation in only three populations. Surprisingly, some MEAM1 individuals and one NW2 population were infected with Fritschea. Arsenopnohus was the only endosymbiont detected in T. vaporariorum. In T. acaciae and B. tuberculata populations collected from cassava, Wolbachia was fixed in B. tuberculata and was highly prevalent in T. acaciae. Interestingly, while B. tuberculata was additionally infected with Arsenophonus, T. acaciae was infected with Cardinium and Fritschea. Fluorescence in situ hybridization analysis on representative individuals showed that Hamiltonella, Arsenopnohus and Fritschea were localized inside the bacteriome, Cardinium and Wolbachia exhibited dual localization patterns inside and outside the bacteriome, and Rickettsia showed strict localization outside the bacteriome. This study is

  9. Diversity and localization of bacterial endosymbionts from whitefly species collected in Brazil.

    PubMed

    Marubayashi, Julio Massaharu; Kliot, Adi; Yuki, Valdir Atsushi; Rezende, Jorge Alberto Marques; Krause-Sakate, Renate; Pavan, Marcelo Agenor; Ghanim, Murad

    2014-01-01

    Whiteflies (Hemiptera: Aleyrodidae) are sap-sucking insect pests, and some cause serious damage in agricultural crops by direct feeding and by transmitting plant viruses. Whiteflies maintain close associations with bacterial endosymbionts that can significantly influence their biology. All whitefly species harbor a primary endosymbiont, and a diverse array of secondary endosymbionts. In this study, we surveyed 34 whitefly populations collected from the states of Sao Paulo, Bahia, Minas Gerais and Parana in Brazil, for species identification and for infection with secondary endosymbionts. Sequencing the mitochondrial Cytochrome Oxidase I gene revealed the existence of five whitefly species: The sweetpotato whitefly Bemisia tabaci B biotype (recently termed Middle East-Asia Minor 1 or MEAM1), the greenhouse whitefly Trialeurodes vaporariorum, B. tabaci A biotype (recently termed New World 2 or NW2) collected only from Euphorbia, the Acacia whitefly Tetraleurodes acaciae and Bemisia tuberculata both were detected only on cassava. Sequencing rRNA genes showed that Hamiltonella and Rickettsia were highly prevalent in all MEAM1 populations, while Cardinium was close to fixation in only three populations. Surprisingly, some MEAM1 individuals and one NW2 population were infected with Fritschea. Arsenopnohus was the only endosymbiont detected in T. vaporariorum. In T. acaciae and B. tuberculata populations collected from cassava, Wolbachia was fixed in B. tuberculata and was highly prevalent in T. acaciae. Interestingly, while B. tuberculata was additionally infected with Arsenophonus, T. acaciae was infected with Cardinium and Fritschea. Fluorescence in situ hybridization analysis on representative individuals showed that Hamiltonella, Arsenopnohus and Fritschea were localized inside the bacteriome, Cardinium and Wolbachia exhibited dual localization patterns inside and outside the bacteriome, and Rickettsia showed strict localization outside the bacteriome. This study is

  10. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species.

    PubMed

    Pawluk, April; Staals, Raymond H J; Taylor, Corinda; Watson, Bridget N J; Saha, Senjuti; Fineran, Peter C; Maxwell, Karen L; Davidson, Alan R

    2016-01-01

    CRISPR-Cas systems provide sequence-specific adaptive immunity against foreign nucleic acids(1,2). They are present in approximately half of all sequenced prokaryotes(3) and are expected to constitute a major barrier to horizontal gene transfer. We previously described nine distinct families of proteins encoded in Pseudomonas phage genomes that inhibit CRISPR-Cas function(4,5). We have developed a bioinformatic approach that enabled us to discover additional anti-CRISPR proteins encoded in phages and other mobile genetic elements of diverse bacterial species. We show that five previously undiscovered families of anti-CRISPRs inhibit the type I-F CRISPR-Cas systems of both Pseudomonas aeruginosa and Pectobacterium atrosepticum, and a dual specificity anti-CRISPR inactivates both type I-F and I-E CRISPR-Cas systems. Mirroring the distribution of the CRISPR-Cas systems they inactivate, these anti-CRISPRs were found in species distributed broadly across the phylum Proteobacteria. Importantly, anti-CRISPRs originating from species with divergent type I-F CRISPR-Cas systems were able to inhibit the two systems we tested, highlighting their broad specificity. These results suggest that all type I-F CRISPR-Cas systems are vulnerable to inhibition by anti-CRISPRs. Given the widespread occurrence and promiscuous activity of the anti-CRISPRs described here, we propose that anti-CRISPRs play an influential role in facilitating the movement of DNA between prokaryotes by breaching the barrier imposed by CRISPR-Cas systems. PMID:27573108

  11. Trophic complexity in aqueous systems: bacterial species richness and protistan predation regulate dissolved organic carbon and dissolved total nitrogen removal.

    PubMed

    Saleem, Muhammad; Fetzer, Ingo; Harms, Hauke; Chatzinotas, Antonis

    2016-02-24

    Loading of water bodies with dissolved organic carbon (DOC) and dissolved total nitrogen (DTN) affects their integrity and functioning. Microbial interactions mitigate the negative effects of high nutrient loads in these ecosystems. Despite numerous studies on how biodiversity mediates ecosystem functions, whether and how diversity and complexity of microbial food webs (horizontal, vertical) and the underlying ecological mechanisms influence nutrient removal has barely been investigated. Using microbial microcosms accommodating systematic combinations of prey (bacteria) and predator (protists) species, we showed that increasing bacterial richness improved the extent and reliability of DOC and DTN removal. Bacterial diversity drove nutrient removal either due to species foraging physiology or functional redundancy, whereas protistan diversity affected nutrient removal through bacterial prey resource partitioning and changing nutrient balance in the system. Our results demonstrate that prey-predator diversity and trophic interactions interactively determine nutrient contents, thus implying the vital role of microbial trophic complexity as a biological buffer against DOC and DTN.

  12. Trophic complexity in aqueous systems: bacterial species richness and protistan predation regulate dissolved organic carbon and dissolved total nitrogen removal.

    PubMed

    Saleem, Muhammad; Fetzer, Ingo; Harms, Hauke; Chatzinotas, Antonis

    2016-02-24

    Loading of water bodies with dissolved organic carbon (DOC) and dissolved total nitrogen (DTN) affects their integrity and functioning. Microbial interactions mitigate the negative effects of high nutrient loads in these ecosystems. Despite numerous studies on how biodiversity mediates ecosystem functions, whether and how diversity and complexity of microbial food webs (horizontal, vertical) and the underlying ecological mechanisms influence nutrient removal has barely been investigated. Using microbial microcosms accommodating systematic combinations of prey (bacteria) and predator (protists) species, we showed that increasing bacterial richness improved the extent and reliability of DOC and DTN removal. Bacterial diversity drove nutrient removal either due to species foraging physiology or functional redundancy, whereas protistan diversity affected nutrient removal through bacterial prey resource partitioning and changing nutrient balance in the system. Our results demonstrate that prey-predator diversity and trophic interactions interactively determine nutrient contents, thus implying the vital role of microbial trophic complexity as a biological buffer against DOC and DTN. PMID:26888033

  13. Comparative study on the selective chalcopyrite bioleaching of a molybdenite concentrate with mesophilic and thermophilic bacteria.

    PubMed

    Romano, P; Blázquez, M L; Alguacil, F J; Muñoz, J A; Ballester, A; González, F

    2001-03-01

    This study evaluates different bioleaching treatments of a molybdenite concentrate using mesophilic and thermophilic bacterial cultures. Further studies on the chemical leaching and the electrochemical behavior of the MoS(2) concentrate were carried out. Bioleaching tests showed a progressive removal of chalcopyrite from the molybdenite concentrate with an increase in temperature. Chemical leaching tests support the idea of an indirect attack of the concentrate. Electrochemical tests indicate that chalcopyrite dissolution is favored when molybdenite is present. Therefore, this type of bioleaching treatment could be applied to purify molybdenite flotation concentrates by selectively dissolving chalcopyrite. PMID:11257551

  14. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities

    PubMed Central

    Aleklett, Kristin; Leff, Jonathan W.; Fierer, Noah

    2015-01-01

    Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed–Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy–Leucanthemum vulgare and Alsike clover–Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition. PMID:25755932

  15. Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment

    PubMed Central

    Staubach, Fabian; Baines, John F.; Künzel, Sven; Bik, Elisabeth M.; Petrov, Dmitri A.

    2013-01-01

    The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates. PMID:23967097

  16. Diversity and localization of bacterial symbionts in three whitefly species (Hemiptera: Aleyrodidae) from the east coast of the Adriatic Sea.

    PubMed

    Skaljac, M; Zanić, K; Hrnčić, S; Radonjić, S; Perović, T; Ghanim, M

    2013-02-01

    Several whitefly species (Hemiptera: Aleyrodidae) are cosmopolitan phloem-feeders that cause serious damage in numerous agricultural crops. All whitefly species harbor a primary bacterial symbiont and a diverse array of secondary symbionts which may influence several aspects of the insect's biology. We surveyed infections by secondary symbionts in Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood) and Siphoninus phillyreae (Haliday) from areas in the east cost of the Adriatic Sea. Both the Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) B. tabaci genetic groups were detected in Montenegro, whereas only the MED was confirmed in Croatia. Trialeurodes vaporariorum and S. phillyreae were found in all areas surveyed. MEAM1 and MED exhibited similarity to previously reported infections, while populations of T. vaporariorum from Montenegro harbored Rickettsia, Wolbachia and Cardinium in addition to previously reported Hamiltonella and Arsenopnohus. Siphoninus phillyreae harbored Hamiltonella, Wolbachia, Cardinium and Arsenophonus, with the latter appearing in two alleles. Multiple infections of all symbionts were common in the three insect species tested, with some reaching near fixation. Florescent in situ hybridization showed new localization patterns for Hamiltonella in S. phillyreae, and the morphology of the bacteriosome differed from that observed in other whitefly species. Our results show new infections with bacterial symbionts in the whitefly species studied. Infections with the same symbionts in reproductively isolated whitefly species confirm complex relationships between whiteflies and bacterial symbionts, and suggest possible horizontal transfer of some of these bacteria.

  17. Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Chen, De-ju; Zhu, Yu-jing; Chen, Zheng; Che, Jian-mei

    2015-01-01

    Virgibacillus pantothenticus DSM 26T is a Gram-positive, spore-forming, aerobic, mesophilic, and halotolerant bacterium. Here, we report its 4.76-Mb draft genome sequence, which is the first genome information of V. pantothenticus and will promote biological research and biotechnological application for the species. PMID:26383648

  18. Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil.

    PubMed

    Wang, Jie-Ping; Liu, Bo; Liu, Guo-Hong; Chen, De-Ju; Zhu, Yu-Jing; Chen, Zheng; Che, Jian-Mei

    2015-01-01

    Virgibacillus pantothenticus DSM 26(T) is a Gram-positive, spore-forming, aerobic, mesophilic, and halotolerant bacterium. Here, we report its 4.76-Mb draft genome sequence, which is the first genome information of V. pantothenticus and will promote biological research and biotechnological application for the species. PMID:26383648

  19. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

    PubMed Central

    Messier, Christian; Kembel, Steven W.

    2016-01-01

    Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual

  20. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

    PubMed Central

    Messier, Christian; Kembel, Steven W.

    2016-01-01

    Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual

  1. Red and infrared laser therapy inhibits in vitro growth of major bacterial species that commonly colonize skin ulcers.

    PubMed

    de Sousa, Natanael Teixeira Alves; Gomes, Rosana Caetano; Santos, Marcos Ferracioli; Brandino, Hugo Evangelista; Martinez, Roberto; de Jesus Guirro, Rinaldo Roberto

    2016-04-01

    Low-level laser therapy (LLLT) is used in chronic wounds due to its healing effects. However, bacterial species may colonize these wounds and the optimal parameters for effective bacterial inhibition are not clear. The aim of this study was to analyze the effect of LLLT on bacterial growth in vitro. Bacterial strains including Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa were suspended in saline solution at a concentration of 10(3) cells/ml and exposed to laser irradiation at wavelengths of 660, 830, and 904 nm at fluences of 0 (control), 3, 6, 12, 18, and 24 J/cm(2). An aliquot of the irradiated suspension was spread on the surface of petri plates and incubated at 37 °C for quantification of colony-forming unit after 24, 48, and 72 h. Laser irradiation inhibited the growth of S. aureus at all wavelengths and fluences higher than 12 J/cm(2), showing a strong correlation between increase in fluence and bacterial inhibition. However, for P. aeruginosa, LLLT inhibited growth at all wavelengths only at a fluence of 24 J/cm(2). E. coli had similar growth inhibition at a wavelength of 830 nm at fluences of 3, 6, 12, and 24 J/cm(2). At wavelengths of 660 and 904 nm, growth inhibition was only observed at fluences of 12 and 18 J/cm(2), respectively. LLLT inhibited bacterial growth at all wavelengths, for a maximum of 72 h after irradiation, indicating a correlation between bacterial species, fluence, and wavelength.

  2. Bacterial Profiling Reveals Novel "Ca. Neoehrlichia", Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks.

    PubMed

    Gofton, Alexander W; Doggett, Stephen; Ratchford, Andrew; Oskam, Charlotte L; Paparini, Andrea; Ryan, Una; Irwin, Peter

    2015-01-01

    In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279), Amblyomma triguttatum (n = 167), Haemaphysalis bancrofti (n = 7), and H. longicornis (n = 7) ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel "Candidatus Neoehrlichia" spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2%) ticks and a single I. holocyclus (0.6%) tick. Further phylogenetic analysis of novel "Ca. Neoehrlichia", Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation. PMID:26709826

  3. Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum.

    PubMed

    Wu, Yu-Fan; Zheng, Hui; Wu, Qing-Long; Yang, Hong; Liu, Shuang-Jiang

    2014-11-01

    Two anaerobic bacterial strains, MB9-7(T) and MB9-9, were isolated from decomposing algal scum and were characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strains MB9-7(T) and MB9-9 are closely related to each other (99.7% similarity) and they are also closely related to Clostridium tyrobutyricum (96.5%). The two strains were Gram-stain positive and rod-shaped. Growth occurred at 20-45 °C, at pH 4.0-8.0 and at NaCl concentrations of up to 2% (w/v). Acid was produced from glucose, xylose and mannose. Products of fermentation in PYG medium were mainly butyrate, acetate, carbon dioxide and hydrogen. The predominant cellular fatty acids were C(14:0) and C(16:0). The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two glycolipids, one phospholipid, one aminophospholipid and two aminolipids. The DNA G+C contents of strain MB9-7(T) and MB9-9 were 27.9 and 28.7 mol%, respectively. These results support the assignment of the new isolates to the genus Clostridium and also distinguish them from other species of the genus Clostridium. Hence, it is proposed that strains MB9-7(T) and MB9-9 represent a novel species of the genus Clostridium, with the suggested name Clostridium algifaecis sp. nov. The type strain is MB9-7(T) ( =CGMCC 1.5188(T) =DSM 28783(T)).

  4. Prevalence of selected bacterial named species and uncultivated phylotypes in endodontic abscesses from two geographic locations.

    PubMed

    Rôças, Isabela N; Baumgartner, J Craig; Xia, Tian; Siqueira, José F

    2006-12-01

    Evidence is mounting that the prevalence of some putative endodontic pathogens can significantly vary according to the geographic location in which samples were taken. This study aimed to provide additional knowledge on this subject by comparing the frequencies of 10 selected candidate endodontic pathogens in samples of acute apical abscesses obtained from two distinct geographic locations; Portland, OR, and Rio de Janeiro, Brazil. DNA was extracted from aspirates and used as template in nested PCR assays using 16S rRNA gene taxon-specific oligonucleotide primers. Of the target species/phylotypes, Treponema denticola (73% of the cases), Porphyromonas endodontalis (70%), and Tannerella forsythia (57%) were the most prevalent taxa found in Brazilian samples. Dialister invisus (70% of the cases), P. endodontalis (63%) and Dialister pneumosintes (55%) were the most frequent taxa in the Portland, OR samples. Data analysis revealed that T. denticola and T. forsythia were significantly more detected in Brazilian samples than in the Portland, OR samples. Although D. invisus, Filifactor alocis, and Synergistes oral clone W090 were detected in many more samples from the Portland, OR patients, differences were not found to be statistically significant. These findings confirmed that some bacterial taxa can markedly differ in the frequencies they occur in samples from different locations. It remains to be clarified whether this observation translates into relevant therapeutic implications.

  5. Antibiofilm Activity, Compound Characterization, and Acute Toxicity of Extract from a Novel Bacterial Species of Paenibacillus

    PubMed Central

    Alasil, Saad Musbah; Omar, Rahmat; Yusof, Mohd Yasim

    2014-01-01

    The effectiveness of many antimicrobial agents is currently decreasing; therefore, it is important to search for alternative therapeutics. Our study was carried out to assess the in vitro antibiofilm activity using microtiter plate assay, to characterize the bioactive compounds using Ultra Performance Liquid Chromatography-Diode Array Detection and Liquid Chromatography-Mass Spectrometry and to test the oral acute toxicity on Sprague Dawley rats of extract derived from a novel bacterial species of Paenibacillus strain 139SI. Our results indicate that the crude extract and its three identified compounds exhibit strong antibiofilm activity against a broad range of clinically important pathogens. Three potential compounds were identified including an amino acid antibiotic C8H20N3O4P (MW 253.237), phospholipase A2 inhibitor C21H36O5 (MW 368.512), and an antibacterial agent C14H11N3O2 (MW 253.260). The acute toxicity test indicates that the mortality rate among all rats was low and that the biochemical parameters, hematological profile, and histopathology examination of liver and kidneys showed no significant differences between experimental groups (P > 0.05). Overall, our findings suggest that the extract and its purified compounds derived from novel Paenibacillus sp. are nontoxic exhibiting strong antibiofilm activity against Gram-positive and Gram-negative pathogens that can be useful towards new therapeutic management of biofilm-associated infections. PMID:24790603

  6. Influence of fluoride on the bacterial composition of a dual-species biofilm composed of Streptococcus mutans and Streptococcus oralis.

    PubMed

    Jung, Ji-Eun; Cai, Jian-Na; Cho, Sung-Dae; Song, Kwang-Yeob; Jeon, Jae-Gyu

    2016-10-01

    Despite the widespread use of fluoride for the prevention of dental caries, few studies have demonstrated the effects of fluoride on the bacterial composition of dental biofilms. This study investigated whether fluoride affects the proportion of Streptococcus mutans and S. oralis in mono- and dual-species biofilm models, via microbiological, biochemical, and confocal fluorescence microscope studies. Fluoride did not affect the bacterial count and bio-volume of S. mutans and S. oralis in mono-species biofilms, except for the 24-h-old S. mutans biofilms. However, fluoride reduced the proportion and bio-volume of S. mutans but did not decrease those of S. oralis during both S. oralis and S. mutans dual-species biofilm formation, which may be related to the decrease in extracellular polysaccharide formation by fluoride. These results suggest that fluoride may prevent the shift in the microbial proportion to cariogenic bacteria in dental biofilms, subsequently inhibiting the cariogenic bacteria dominant biofilm formation. PMID:27643392

  7. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    PubMed

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.

  8. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    PubMed

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors. PMID:27278778

  9. Performance of mesophilic biohydrogen-producing cultures at thermophilic conditions.

    PubMed

    Gupta, Medhavi; Gomez-Flores, Maritza; Nasr, Noha; Elbeshbishy, Elsayed; Hafez, Hisham; Hesham El Naggar, M; Nakhla, George

    2015-09-01

    In this study, batch tests were conducted to investigate the performance of mesophilic anaerobic digester sludge (ADS) at thermophilic conditions and estimate kinetic parameters for co-substrate fermentation. Starch and cellulose were used as mono-substrate and in combination as co-substrates (1:1 mass ratio) to conduct a comparative assessment between mesophilic (37 °C) and thermophilic (60 °C) biohydrogen production. Unacclimatized mesophilic ADS responded well to the temperature change. The highest hydrogen yield of 1.13 mol H2/mol hexose was observed in starch-only batches at thermophilic conditions. The thermophilic cellulose-only yield (0.42 mol H2/mol hexose) was three times the mesophilic yield (0.13 mol H2/mol hexose). Interestingly, co-fermentation of starch-cellulose at mesophilic conditions enhanced the hydrogen yield by 26% with respect to estimated mono-substrate yields, while under thermophilic conditions no enhancement in the overall yield was observed. Interestingly, the estimated overall Monod kinetic parameters showed higher rates at mesophilic than thermophilic conditions.

  10. The evolution of size of the uropygial gland: mutualistic feather mites and uropygial secretion reduce bacterial loads of eggshells and hatching failures of European birds.

    PubMed

    Soler, J J; Peralta-Sánchez, J M; Martín-Platero, A M; Martín-Vivaldi, M; Martínez-Bueno, M; Møller, A P

    2012-09-01

    Potentially, pathogenic bacteria are one of the main infective agents against which a battery of chemical and physical barriers has evolved in animals. Among these are the secretions by the exocrine uropygial gland in birds. The antimicrobial properties of uropygial secretions may prevent colonization and growth of microorganisms on feathers, skin and eggshells. However, uropygial gland secretions also favour the proliferation of feather mites that feed on secretions and microorganisms living on feathers that would otherwise reach eggshells during incubation if not consumed by feather mites. Therefore, at the interspecific level, uropygial gland size (as an index of volume of uropygial secretion) should be positively related to eggshell bacterial load (i.e. the risk of egg infection), whereas eggshell bacterial loads may be negatively related to abundance of feather mites eating bacteria. Here, we explore these previously untested predictions in a comparative framework using information on eggshell bacterial loads, uropygial gland size, diversity and abundance of feather mites and hatching success of 22 species of birds. The size of the uropygial gland was positively related to eggshell bacterial loads (mesophilic bacteria and Enterobacteriaceae), and bird species with higher diversity and abundance of feather mites harboured lower bacterial density on their eggshells (Enterococcus and Staphylococcus), in accordance with the hypothesis. Importantly, eggshell bacterial loads of mesophilic bacteria, Enterococcus and Enterobacteriaceae were negatively associated with hatching success, allowing us to interpret these interspecific relationships in a functional scenario, where both uropygial glands and mutualistic feather mites independently reduce the negative effects of pathogenic bacteria on avian fitness.

  11. Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico.

    PubMed

    Aguirre-Garrido, J Félix; Montiel-Lugo, Daniel; Hernández-Rodríguez, César; Torres-Cortes, Gloria; Millán, Vicenta; Toro, Nicolás; Martínez-Abarca, Francisco; Ramírez-Saad, Hugo C

    2012-05-01

    The nature reserve of Tehuacan-Cuicatlan in central Mexico is known for its diversity and endemism mainly in cactus plants. Although the xerophytic flora is reasonably documented, the bacterial communities associated with these species have been largely neglected. We assessed the diversity and composition of bacterial communities in bulk (non-rhizospheric) soil and the rhizosphere of three cactus plant species: Mammillaria carnea, Opuntia pilifera and Stenocereus stellatus, approached using cultivation and molecular techniques, considering the possible effect of dry and rainy seasons. Cultivation-dependent methods were focused on putative N(2)-fixers and heterotrophic aerobic bacteria, in the two media tested the values obtained for dry season samples grouped together regardless of the sample type (rhizospheric or non-rhizospheric), these groups also included the non-rhizospheric sample for rainy season, on each medium. These CFU values were smaller and significantly different from those obtained on rhizospheric samples from rainy season. Genera composition among isolates of the rhizospheric samples was very similar for each season, the most abundant taxa being α-Proteobacteria, Actinobacteria and Firmicutes. Interestingly, the genus Ochrobactrum was highly represented among rhizospheric samples, when cultured in N-free medium. The structure of the bacterial communities was approached with molecular techniques targeting partial 16S rRNA sequences such as denaturing gradient gel electrophoresis and serial analysis of ribosomal sequence tags. Under these approaches, the most represented bacterial phyla were Actinobacteria, Proteobacteria and Acidobacteria. The first two were also highly represented when using isolation techniques.

  12. The soil bacterial communities of South African fynbos riparian ecosystems invaded by Australian Acacia species.

    PubMed

    Slabbert, Etienne; Jacobs, Shayne Martin; Jacobs, Karin

    2014-01-01

    Riparian ecosystem along rivers and streams are characterised by lateral and longitudinal ecological gradients and, as a result, harbour unique biodiversity. Riparian ecosystems in the fynbos of the Western Cape, South Africa, are characterised by seasonal dynamics, with summer droughts followed by high flows during winter. The unique hydrology and geomorphology of riparian ecosystems play an important role in shaping these ecosystems. The riparian vegetation in the Western Cape has, however, largely been degraded due to the invasion of non-indigenous plants, in particular Acacia mearnsii, A. saligna and A. dealbata. This study investigated the effect of hydrology and invasion on the bacterial communities associated with fynbos riparian ecosystems. Bacterial communities were characterised with automated ribosomal intergenic spacer analysis (ARISA) and 454 16S rDNA pyrosequencing. Chemical and physical properties of soil within sites were also determined and correlated with community data. Sectioning across the lateral zones revealed significant differences in community composition, and the specific bacterial taxa influenced. Results also showed that the bacterial community structure could be linked to Acacia invasion. The presence of invasive Acacia was correlated with specific bacterial phyla. However, high similarity between cleared and pristine sites suggests that the effect of Acacia on the soil bacterial community structure may not be permanent. This study demonstrates how soil bacterial communities are influenced by hydrological gradients associated with riparian ecosystems and the impact of Acacia invasion on these communities. PMID:24475145

  13. The soil bacterial communities of South African fynbos riparian ecosystems invaded by Australian Acacia species.

    PubMed

    Slabbert, Etienne; Jacobs, Shayne Martin; Jacobs, Karin

    2014-01-01

    Riparian ecosystem along rivers and streams are characterised by lateral and longitudinal ecological gradients and, as a result, harbour unique biodiversity. Riparian ecosystems in the fynbos of the Western Cape, South Africa, are characterised by seasonal dynamics, with summer droughts followed by high flows during winter. The unique hydrology and geomorphology of riparian ecosystems play an important role in shaping these ecosystems. The riparian vegetation in the Western Cape has, however, largely been degraded due to the invasion of non-indigenous plants, in particular Acacia mearnsii, A. saligna and A. dealbata. This study investigated the effect of hydrology and invasion on the bacterial communities associated with fynbos riparian ecosystems. Bacterial communities were characterised with automated ribosomal intergenic spacer analysis (ARISA) and 454 16S rDNA pyrosequencing. Chemical and physical properties of soil within sites were also determined and correlated with community data. Sectioning across the lateral zones revealed significant differences in community composition, and the specific bacterial taxa influenced. Results also showed that the bacterial community structure could be linked to Acacia invasion. The presence of invasive Acacia was correlated with specific bacterial phyla. However, high similarity between cleared and pristine sites suggests that the effect of Acacia on the soil bacterial community structure may not be permanent. This study demonstrates how soil bacterial communities are influenced by hydrological gradients associated with riparian ecosystems and the impact of Acacia invasion on these communities.

  14. The Soil Bacterial Communities of South African Fynbos Riparian Ecosystems Invaded by Australian Acacia Species

    PubMed Central

    Slabbert, Etienne; Jacobs, Shayne Martin; Jacobs, Karin

    2014-01-01

    Riparian ecosystem along rivers and streams are characterised by lateral and longitudinal ecological gradients and, as a result, harbour unique biodiversity. Riparian ecosystems in the fynbos of the Western Cape, South Africa, are characterised by seasonal dynamics, with summer droughts followed by high flows during winter. The unique hydrology and geomorphology of riparian ecosystems play an important role in shaping these ecosystems. The riparian vegetation in the Western Cape has, however, largely been degraded due to the invasion of non-indigenous plants, in particular Acacia mearnsii, A. saligna and A. dealbata. This study investigated the effect of hydrology and invasion on the bacterial communities associated with fynbos riparian ecosystems. Bacterial communities were characterised with automated ribosomal intergenic spacer analysis (ARISA) and 454 16S rDNA pyrosequencing. Chemical and physical properties of soil within sites were also determined and correlated with community data. Sectioning across the lateral zones revealed significant differences in community composition, and the specific bacterial taxa influenced. Results also showed that the bacterial community structure could be linked to Acacia invasion. The presence of invasive Acacia was correlated with specific bacterial phyla. However, high similarity between cleared and pristine sites suggests that the effect of Acacia on the soil bacterial community structure may not be permanent. This study demonstrates how soil bacterial communities are influenced by hydrological gradients associated with riparian ecosystems and the impact of Acacia invasion on these communities. PMID:24475145

  15. A comparative study on the alternating mesophilic and thermophilic two-stage anaerobic digestion of food waste.

    PubMed

    Ventura, Jey-R Sabado; Lee, Jehoon; Jahng, Deokjin

    2014-06-01

    An alternating mesophilic and thermophilic two stage anaerobic digestion (AD) process was conducted. The temperature of the acidogenic (A) and methanogenic (M) reactors was controlled as follows: System 1 (S1) mesophilic A-mesophilic M; (S2) mesophilic A-thermophilic M; and (S3) thermophilic A-mesophilic M. Initially, the AD reactor was acclimatized and inoculated with digester sludge. Food waste was added with the soluble chemical oxygen demand (SCOD) concentrations of 41.4-47.0 g/L and volatile fatty acids of 2.0-3.2 g/L. Based on the results, the highest total chemical oxygen demand removal (86.6%) was recorded in S2 while S3 exhibited the highest SCOD removal (96.6%). Comparing S1 with S2, total solids removal increased by 0.5%; S3 on the other hand decreased by 0.1 % as compared to S1. However, volatile solids (VS) removal in S1, S2, and S3 was 78.5%, 81.7%, and 79.2%, respectively. S2 also exhibited the highest CH4 content, yield, and production rate of 70.7%, 0.44 L CH4/g VSadded, and 1.23 L CH4/(L·day), respectively. Bacterial community structure revealed that the richness, diversity, evenness, and dominance of S2 were high except for the archaeal community. The terminal restriction fragments dendrogram also revealed that the microbial community of the acidogenic and methanogenic reactors in S2 was distinct. Therefore, S2 was the best among the systems for the operation of two-stage AD of food waste in terms of CH4 production, nutrient removal, and microbial community structure. PMID:25079836

  16. Effect of Organic Matter Decomposition Level on Bacterial Species Diversity and Composition in Relationship to Pythium Damping-Off Severity

    PubMed Central

    Boehm, M. J.; Madden, L. V.; Hoitink, H. A. J.

    1993-01-01

    Rhizosphere bacteria were isolated from root tip segments of cucumber seedlings grown in a suppressive, slightly decomposed light-colored peat mix, a conducive, more decomposed dark-colored peat mix, and a suppressive dark peat mix amended with composted hardwood bark. The bacteria were identified by a gas chromatographic fatty acid methyl ester analysis. The total number of taxa recovered from a single root tip segment ranged from 9 to 18. No single taxon predominated on all root tip segments harvested from any of the mixes. The highest relative population density reached by a given taxon on any root tip segment was 45%. Hill's first and second diversity numbers, the modified Hill's ratio, and Hurlbert's rarefaction method, which were used as measures of species diversity, indicated that the organic matter decomposition level of the potting mixes did not affect bacterial species diversity. Bray-Curtis polar ordination and Dice resemblance functions, however, indicated that the organic matter decomposition level of a mix significantly influenced the composition of bacterial species in the rhizosphere. Pseudomonas spp. and other taxa capable of inducing suppression of pythium damping-off predominated in the suppressive mixes. These organisms were absent from the conducive mix, in which Arthrobacter and Bacillus spp. predominated. Although effective bacterial biocontrol agents were isolated from both the suppressive mixes and the conducive mix, the majority were isolated from the less decomposed suppressive mixes. Finally, the efficacy of strains was significantly greater in the slightly decomposed light peat mix than in the decomposed dark peat mix. Natural disease suppression within these mixes was associated with the organic matter decomposition level and the bacterial species compositions of the mixes. PMID:16349117

  17. Effect of organic matter decomposition level on bacterial species diversity and composition in relationship to pythium damping-off severity.

    PubMed

    Boehm, M J; Madden, L V; Hoitink, H A

    1993-12-01

    Rhizosphere bacteria were isolated from root tip segments of cucumber seedlings grown in a suppressive, slightly decomposed light-colored peat mix, a conducive, more decomposed dark-colored peat mix, and a suppressive dark peat mix amended with composted hardwood bark. The bacteria were identified by a gas chromatographic fatty acid methyl ester analysis. The total number of taxa recovered from a single root tip segment ranged from 9 to 18. No single taxon predominated on all root tip segments harvested from any of the mixes. The highest relative population density reached by a given taxon on any root tip segment was 45%. Hill's first and second diversity numbers, the modified Hill's ratio, and Hurlbert's rarefaction method, which were used as measures of species diversity, indicated that the organic matter decomposition level of the potting mixes did not affect bacterial species diversity. Bray-Curtis polar ordination and Dice resemblance functions, however, indicated that the organic matter decomposition level of a mix significantly influenced the composition of bacterial species in the rhizosphere. Pseudomonas spp. and other taxa capable of inducing suppression of pythium damping-off predominated in the suppressive mixes. These organisms were absent from the conducive mix, in which Arthrobacter and Bacillus spp. predominated. Although effective bacterial biocontrol agents were isolated from both the suppressive mixes and the conducive mix, the majority were isolated from the less decomposed suppressive mixes. Finally, the efficacy of strains was significantly greater in the slightly decomposed light peat mix than in the decomposed dark peat mix. Natural disease suppression within these mixes was associated with the organic matter decomposition level and the bacterial species compositions of the mixes. PMID:16349117

  18. Molecular and Ecological Evidence for Species Specificity and Coevolution in a Group of Marine Algal-Bacterial Symbioses

    PubMed Central

    Ashen, Jon B.; Goff, Lynda J.

    2000-01-01

    The phylogenetic relationships of bacterial symbionts from three gall-bearing species in the marine red algal genus Prionitis (Rhodophyta) were inferred from 16S rDNA sequence analysis and compared to host phylogeny also inferred from sequence comparisons (nuclear ribosomal internal-transcribed-spacer region). Gall formation has been described previously on two species of Prionitis, P. lanceolata (from central California) and P. decipiens (from Peru). This investigation reports gall formation on a third related host, Prionitis filiformis. Phylogenetic analyses based on sequence comparisons place the bacteria as a single lineage within the Roseobacter grouping of the α subclass of the division Proteobacteria (99.4 to 98.25% sequence identity among phylotypes). Comparison of symbiont and host molecular phylogenies confirms the presence of three gall-bearing algal lineages and is consistent with the hypothesis that these red seaweeds and their bacterial symbionts are coevolving. The species specificity of these associations was investigated in nature by whole-cell hybridization of gall bacteria and in the laboratory by using cross-inoculation trials. Whole-cell in situ hybridization confirmed that a single bacterial symbiont phylotype is present in galls on each host. In laboratory trials, bacterial symbionts were incapable of inducing galls on alternate hosts (including two non-gall-bearing species). Symbiont-host specificity in Prionitis gall formation indicates an effective ecological separation between these closely related symbiont phylotypes and provides an example of a biological context in which to consider the organismic significance of 16S rDNA sequence variation. PMID:10877801

  19. Reductive dechlorination of methoxychlor by bacterial species of environmental origin: evidence for primary biodegradation of methoxychlor in submerged environments.

    PubMed

    Satsuma, Koji; Masuda, Minoru

    2012-02-29

    Methoxychlor [1,1,1-trichloro-2,2-bis(4-methoxyphenyl)ethane] is an organochlorine insecticide that undergoes dechlorination in natural submerged environments. We investigated the ability to dechlorinate this compound in seven environmental bacterial species ( Aeromonas hydrophila , Enterobacter amnigenus , Klebsiella terrigena , Bacillus subtilis , Achromobacter xylosoxidans , Acinetobacter calcoaceticus , and Mycobacterium obuense ) and the enteric bacterium Escherichia coli as a positive control. In R2A broth at 25 °C under aerobic, static culture, all species except Ach. xylosoxidans were observed to convert methoxychlor to dechlorinated methoxychlor [1,1-dichloro-2,2-bis(4-methoxyphenyl)ethane]. The medium was aerobic at first, but bacterial growth resulted in the consumption of oxygen and generated microaerobic and weakly reductive conditions. Replacement of the headspace of the culture tubes with nitrogen gas was found to decrease the dechlorination rate. Our findings suggest that extensive bacterial species ubiquitously inhabiting the subsurface water environment play an important role in the primary dechlorination of methoxychlor.

  20. Sequencing mesophilic and thermophilic anaerobic digesters. Final report

    SciTech Connect

    Not Available

    1982-12-01

    This project employed two laboratory bench scale, complete-mix anaerobic sludge digesters arranged in a series configuration. The first digester was operated at 35/sup 0/C (mesophilic) and the second at 50/sup 0/C (thermophilic). A portion of the thermophilic sludge was recycled through an aeration basin. As a comparison to the mesophilic-thermophilic sequencing, a mesophilic-mesophilic digester sequence, without sludge recycle to the aeration basin, was operated in parallel to the test units and loaded at an equivalent rate. Conclusions of this study are as follows: in establishing a thermophilic anaerobic digester, a slow-start procedure, in which the temperature is increased at a rate of 0.6/sup 0/C per day with loading, appears to produce a more stable thermophilic digester in a shorter period of time than a quick-start procedure, in which the temperature is increased rapidly with no loading. Even after a year, the slow-start thermophilic digester proved to be unstable once sequencing began. A greater volatile solids, COD, BOD, and grease reduction with a higher gas production was achieved using a mesophilic-mesophilic sequence, probably, in part, due to the instability (volatile acids in the effluent) of the thermophilic digester in the mesophilic-thermophilic sequence. A greater total kjeldahl N (TKN) and total coliform destruction was achieved in the thermophilic digester, however, poor dewatering characteristics, as indicated by the capillary suction time (CST), and an obnoxious odor were also evident. Other than an increase in effluent suspended solids, the recycle of thermophilic sludge to an aeration basin produced no discernable effect. 9 figs., 3 tabs.

  1. Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling

    PubMed Central

    Benavides, Julio A; Cross, Paul C; Luikart, Gordon; Creel, Scott

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced. PMID:25469159

  2. The native bacterioplankton community in the central baltic sea is influenced by freshwater bacterial species.

    PubMed

    Riemann, L; Leitet, C; Pommier, T; Simu, K; Holmfeldt, K; Larsson, U; Hagström, A

    2008-01-01

    The Baltic Sea is one of the largest brackish environments on Earth. Despite extensive knowledge about food web interactions and pelagic ecosystem functioning, information about the bacterial community composition in the Baltic Sea is scarce. We hypothesized that due to the eutrophic low-salinity environment and the long water residence time (>5 years), the bacterioplankton community from the Baltic proper shows a native "brackish" composition influenced by both freshwater and marine phylotypes. The bacterial community composition in surface water (3-m depth) was examined at a single station throughout a full year. Denaturing gradient gel electrophoresis (DGGE) showed that the community composition changed over the year. Further, it indicated that at the four extensive samplings (16S rRNA gene clone libraries and bacterial isolates from low- and high-nutrient agar plates and seawater cultures), different bacterial assemblages associated with different environmental conditions were present. Overall, the sequencing of 26 DGGE bands, 160 clones, 209 plate isolates, and 9 dilution culture isolates showed that the bacterial assemblage in surface waters of the central Baltic Sea was dominated by Bacteroidetes but exhibited a pronounced influence of typical freshwater phylogenetic groups within Actinobacteria, Verrucomicrobia, and Betaproteobacteria and a lack of typical marine taxa. This first comprehensive analysis of bacterial community composition in the central Baltic Sea points to the existence of an autochthonous estuarine community uniquely adapted to the environmental conditions prevailing in this brackish environment.

  3. A RAPD based study revealing a previously unreported wide range of mesophilic and thermophilic spore formers associated with milk powders in China.

    PubMed

    Sadiq, Faizan A; Li, Yun; Liu, TongJie; Flint, Steve; Zhang, Guohua; He, GuoQing

    2016-01-18

    Aerobic spore forming bacteria are potential milk powder contaminants and are viewed as indicators of poor quality. A total of 738 bacteria, including both mesophilic and thermophilic, isolated from twenty-five powdered milk samples representative of three types of milk powders in China were analyzed based on the random amplified polymorphic DNA (RAPD) protocol to provide insight into species diversity. Bacillus licheniformis was found to be the most prevalent bacterium with greatest diversity (~43% of the total isolates) followed by Geobacillus stearothermophilus (~21% of the total isolates). Anoxybacillus flavithermus represented only 8.5% of the total profiles. Interestingly, actinomycetes represented a major group of the isolates with the predominance of Laceyella sacchari followed by Thermoactinomyces vulgaris, altogether comprising of 7.3% of the total isolates. Out of the nineteen separate bacterial species (except five unidentified groups) recovered and identified from milk powders, twelve proved to belong to novel or previously unreported species in milk powders. Assessment and characterization of the harmful effects caused by this particular micro-flora on the quality and safety of milk powders will be worth doing in the future. PMID:26555161

  4. Mesophilic and psychrotrophic bacteria from meat and their spoilage potential in vitro and in beef.

    PubMed

    Ercolini, Danilo; Russo, Federica; Nasi, Antonella; Ferranti, Pasquale; Villani, Francesco

    2009-04-01

    Mesophilic and psychrotrophic populations from refrigerated meat were identified in this study, and the spoilage potential of microbial isolates in packaged beef was evaluated by analyzing the release of volatile organic compounds (VOC) by gas chromatography-mass spectrometry (GC/MS). Fifty mesophilic and twenty-nine psychrotrophic isolates were analyzed by random amplified polymorphic DNA-PCR, and representative strains were identified by 16S rRNA gene sequencing. Carnobacterium maltaromaticum and C. divergens were the species most frequently found in both mesophilic and psychrotrophic populations. Acinetobacter baumannii, Buttiauxella spp. and Serratia spp. were identified among the mesophilic isolates, while Pseudomonas spp. were commonly identified among the psychrotrophs. The isolates were further characterized for their growth at different temperatures and their proteolytic activity in vitro on meat proteins extracts at 7 degrees C. Selected proteolytic strains of Serratia proteamaculans, Pseudomonas fragi, and C. maltaromaticum were used to examine their spoilage potential in situ. Single strains of these species and mixtures of these strains were used to contaminate beef chops that were packed and stored at 7 degrees C. At time intervals up to 1 month, viable counts were determined, and VOC were identified by GC/MS. Generally, the VOC concentrations went to increase during the storage of the contaminated meats, and the profiles of the analyzed meat changed dramatically depending on the contaminating microbial species. About 100 volatiles were identified in the different contaminated samples. Among the detected volatiles, some specific molecules were identified only when the meat was contaminated by a specific microbial species. Compounds such as 2-ethyl-1-hexanol, 2-buten-1-ol, 2-hexyl-1-octanol, 2-nonanone, and 2-ethylhexanal were detectable only for C. maltaromaticum, which also produced the highest number of aldehydes, lactones, and sulfur compounds. The

  5. Mesophilic and Psychrotrophic Bacteria from Meat and Their Spoilage Potential In Vitro and in Beef ▿

    PubMed Central

    Ercolini, Danilo; Russo, Federica; Nasi, Antonella; Ferranti, Pasquale; Villani, Francesco

    2009-01-01

    Mesophilic and psychrotrophic populations from refrigerated meat were identified in this study, and the spoilage potential of microbial isolates in packaged beef was evaluated by analyzing the release of volatile organic compounds (VOC) by gas chromatography-mass spectrometry (GC/MS). Fifty mesophilic and twenty-nine psychrotrophic isolates were analyzed by random amplified polymorphic DNA-PCR, and representative strains were identified by 16S rRNA gene sequencing. Carnobacterium maltaromaticum and C. divergens were the species most frequently found in both mesophilic and psychrotrophic populations. Acinetobacter baumannii, Buttiauxella spp. and Serratia spp. were identified among the mesophilic isolates, while Pseudomonas spp. were commonly identified among the psychrotrophs. The isolates were further characterized for their growth at different temperatures and their proteolytic activity in vitro on meat proteins extracts at 7°C. Selected proteolytic strains of Serratia proteamaculans, Pseudomonas fragi, and C. maltaromaticum were used to examine their spoilage potential in situ. Single strains of these species and mixtures of these strains were used to contaminate beef chops that were packed and stored at 7°C. At time intervals up to 1 month, viable counts were determined, and VOC were identified by GC/MS. Generally, the VOC concentrations went to increase during the storage of the contaminated meats, and the profiles of the analyzed meat changed dramatically depending on the contaminating microbial species. About 100 volatiles were identified in the different contaminated samples. Among the detected volatiles, some specific molecules were identified only when the meat was contaminated by a specific microbial species. Compounds such as 2-ethyl-1-hexanol, 2-buten-1-ol, 2-hexyl-1-octanol, 2-nonanone, and 2-ethylhexanal were detectable only for C. maltaromaticum, which also produced the highest number of aldehydes, lactones, and sulfur compounds. The highest

  6. Enterobacter morus sp. nov., a novel Enterobacter species associated with bacterial wilt on mulberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mulberry pathogenetic bacterial strain R18-2T isolated from the diseased mulberry root was analyzed by a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated the strain R18-2T to the genus Enterobacter. The strain was Gram nega...

  7. Reactive Oxygen Species Mediated Bacterial Biofilm Inhibition via Zinc Oxide Nanoparticles and Their Statistical Determination

    PubMed Central

    Dwivedi, Sourabh; Wahab, Rizwan; Khan, Farheen; Mishra, Yogendra K.; Musarrat, Javed; Al-Khedhairy, Abdulaziz A.

    2014-01-01

    The formation of bacterial biofilm is a major challenge in clinical applications. The main aim of this study is to describe the synthesis, characterization and biocidal potential of zinc oxide nanoparticles (NPs) against bacterial strain Pseudomonas aeruginosa. These nanoparticles were synthesized via soft chemical solution process in a very short time and their structural properties have been investigated in detail by using X-ray diffraction and transmission electron microscopy measurements. In this work, the potential of synthesized ZnO-NPs (∼10–15 nm) has been assessed in-vitro inhibition of bacteria and the formation of their biofilms was observed using the tissue culture plate assays. The crystal violet staining on biofilm formation and its optical density revealed the effect on biofilm inhibition. The NPs at a concentration of 100 µg/mL significantly inhibited the growth of bacteria and biofilm formation. The biofilm inhibition by ZnO-NPs was also confirmed via bio-transmission electron microscopy (Bio-TEM). The Bio-TEM analysis of ZnO-NPs treated bacteria confirmed the deformation and damage of cells. The bacterial growth in presence of NPs concluded the bactericidal ability of NPs in a concentration dependent manner. It has been speculated that the antibacterial activity of NPs as a surface coating material, could be a feasible approach for controlling the pathogens. Additionally, the obtained bacterial solution data is also in agreement with the results from statistical analytical methods. PMID:25402188

  8. 'Lascolabacter vaginalis' strain KHD1, a new bacterial species cultivated from human female genital tract.

    PubMed

    Diop, K; Mediannikov, O; Fournier, P-E; Raoult, D; Bretelle, F; Fenollar, F

    2016-09-01

    We present the major characteristics of 'Lascolabacter vaginalis' strain KHD1 (= CSUR P0109 = DSM 101752), a new member of the family Prevotellaceae that was cultivated from a vaginal sample of a 33-year-old woman with bacterial vaginosis. PMID:27358744

  9. Lactobacillus species isolated from vaginal secretions of healthy and bacterial vaginosis-intermediate Mexican women: a prospective study

    PubMed Central

    2013-01-01

    Background Lactobacillus jensenii, L. iners, L. crispatus and L. gasseri are the most frequently occurring lactobacilli in the vagina. However, the native species vary widely according to the studied population. The present study was performed to genetically determine the identity of Lactobacillus strains present in the vaginal discharge of healthy and bacterial vaginosis (BV) intermediate Mexican women. Methods In a prospective study, 31 strains preliminarily identified as Lactobacillus species were isolated from 21 samples collected from 105 non-pregnant Mexican women. The samples were classified into groups according to the Nugent score criteria proposed for detection of BV: normal (N), intermediate (I) and bacterial vaginosis (BV). We examined the isolates using culture-based methods as well as molecular analysis of the V1–V3 regions of the 16S rRNA gene. Enterobacterial repetitive intergenic consensus (ERIC) sequence analysis was performed to reject clones. Results Clinical isolates (25/31) were classified into four groups based on sequencing and analysis of the 16S rRNA gene: L. acidophilus (14/25), L. reuteri (6/25), L. casei (4/25) and L. buchneri (1/25). The remaining six isolates were presumptively identified as Enterococcus species. Within the L. acidophilus group, L. gasseri was the most frequently isolated species, followed by L. jensenii and L. crispatus. L. fermentum, L. rhamnosus and L. brevis were also isolated, and were placed in the L. reuteri, L. casei and L. buchneri groups, respectively. ERIC profile analysis showed intraspecific variability amongst the L. gasseri and L. fermentum species. Conclusions These findings agree with previous studies showing that L. crispatus, L. gasseri and L. jensenii are consistently present in the healthy vaginal ecosystem. Additional species or phylotypes were detected in the vaginal microbiota of the non-pregnant Mexican (Hispanic-mestizo) population, and thus, these results further our understanding of

  10. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.

    PubMed

    Luo, Chengwei; Walk, Seth T; Gordon, David M; Feldgarden, Michael; Tiedje, James M; Konstantinidis, Konstantinos T

    2011-04-26

    Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.

  11. Loofah sponges as reservoirs and vehicles in the transmission of potentially pathogenic bacterial species to human skin.

    PubMed

    Bottone, E J; Perez, A A; Oeser, J L

    1994-02-01

    Loofah sponges are natural products used as exfoliative beauty aids. As a consequence of tracing a case of Pseudomonas aeruginosa folliculitis to a contaminated loofah sponge, we assessed the role of loofah sponges in supporting the growth of a wide variety of bacterial species. Our data show growth enhancement of sterile loofah fragments for numerous gram-negative (Pseudomonas, Xanthomonas, and Klebsiella) and gram-positive (Enterococcus and group B Streptococcus) species of human and environmental origin. Furthermore, hydrated new, unused loofah sponges undergo a shift in bacterial flora from sparse colonies of Bacillus spp. and Staphylococcus epidermidis to a predominantly gram-negative flora. The growth-promoting potential of loofah sponges (and other exfoliatives) can be further augmented by desquamated epithelial cells entrapped in the loofah fibrous matrix. Therefore, as loofah sponges (and other exfoliatives) can serve as a reservoir and a vehicle for the transmission of potentially pathogenic species to the human skin, we recommend their decontamination with hypochlorite (10%) bleach at regular intervals. PMID:8150959

  12. A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria.

    PubMed

    Bennett, Julia S; Jolley, Keith A; Earle, Sarah G; Corton, Craig; Bentley, Stephen D; Parkhill, Julian; Maiden, Martin C J

    2012-06-01

    In common with other bacterial taxa, members of the genus Neisseria are classified using a range of phenotypic and biochemical approaches, which are not entirely satisfactory in assigning isolates to species groups. Recently, there has been increasing interest in using nucleotide sequences for bacterial typing and taxonomy, but to date, no broadly accepted alternative to conventional methods is available. Here, the taxonomic relationships of 55 representative members of the genus Neisseria have been analysed using whole-genome sequence data. As genetic material belonging to the accessory genome is widely shared among different taxa but not present in all isolates, this analysis indexed nucleotide sequence variation within sets of genes, specifically protein-coding genes that were present and directly comparable in all isolates. Variation in these genes identified seven species groups, which were robust to the choice of genes and phylogenetic clustering methods used. The groupings were largely, but not completely, congruent with current species designations, with some minor changes in nomenclature and the reassignment of a few isolates necessary. In particular, these data showed that isolates classified as Neisseria polysaccharea are polyphyletic and probably include more than one taxonomically distinct organism. The seven groups could be reliably and rapidly generated with sequence variation within the 53 ribosomal protein subunit (rps) genes, further demonstrating that ribosomal multilocus sequence typing (rMLST) is a practicable and powerful means of characterizing bacteria at all levels, from domain to strain.

  13. Aspergillus fumigatus and mesophilic moulds in air in the surrounding environment downwind of non-hazardous waste landfill sites.

    PubMed

    Schlosser, Olivier; Robert, Samuel; Debeaupuis, Catherine

    2016-05-01

    Non-hazardous waste landfilling has the potential to release biological agents into the air, notably mould spores. Some species, such as Aspergillus fumigatus, may be a cause of concern for at-risk nearby residents. However, air concentration in the surrounding environment of non-hazardous waste landfill sites is poorly documented. An extensive sampling programme was designed to investigate the relationship between culturable mesophilic moulds and A. fumigatus concentrations in air and distance downwind of non-hazardous waste landfill sites. On-site and off-site repeated measurements were performed at four landfill sites during cold and warm seasons. A high-flow air-sampler device was selected so as to allow peak concentration measurement. Linear mixed-effects models were used to explain variability in the concentrations in air over time and across sites, seasons, instantaneous meteorological conditions and discharged waste tonnage. Concentrations of mesophilic moulds and A. fumigatus at off-site upwind sampling locations were compared with concentrations at each of the downwind sampling locations. At the tipping face location, peak concentration reached 480,000CFUm(-3) for mesophilic moulds and 9300CFUm(-3) for A. fumigatus. Compared with upwind background levels, these concentrations were, on average, approximately 20 and 40 times higher respectively. A steep decline in the concentration of both mesophilic moulds and A. fumigatus was observed between the tipping face location and the downwind property boundary (reduction by 77% and 84% respectively), followed by a low decline leading to a 90% and 94% reduction in concentration at 200m from the property boundary and beyond. With the 200m and 500m downwind sampling point values added together, the 97.5th percentile of concentration was 6013CFUm(-3) and 87CFUm(-3) for mesophilic moulds and A. fumigatus, respectively. Other determining factors were the discharged waste tonnage, the season, instantaneous temperature

  14. Hemoglobin toxicity in experimental bacterial peritonitis is due to production of reactive oxygen species.

    PubMed

    Yoo, Y M; Kim, K M; Kim, S S; Han, J A; Lea, H Z; Kim, Y M

    1999-11-01

    Hemoglobin (Hb) is a toxic molecule responsible for the extreme lethality associated with experimental Escherichia coli peritonitis, but the mechanism has yet to be elucidated. Hb, but not globin, showed toxic effects in a live E. coli model but not in a model using killed E. coli. Methemoglobin, hematin, and the well-known Fenton reagents iron and iron-EDTA demonstrated the same lethal effect in E. coli peritonitis as Hb, while the addition of the Fenton inhibitors desferrioxamine (DF) and diethylenetriamine pentaacetate removed most of the cytotoxic activity of iron. Administration of a combined dose of superoxide dismutase and catalase minimized the action of Hb and iron-EDTA, suggesting that both O(2)(.-) and H(2)O(2) are involved in the toxic action of Hb in this rat model. The combination of the antioxidative enzymes and DF further suppressed iron-mediated lethality. An electron spin resonance technique with the spin-trapping reagent 5, 5-dimethyl-1-pyroline-N-oxide (DMPO) showed O(2)(.-) generation in the peritoneal fluid of rats injected with E. coli alone or E. coli plus iron-DF, and (.)OH generation was detected in the peritoneal fluid of the rats injected with iron-EDTA. Hb did not show any spin adduct of oxygen radicals, suggesting that Hb produces non-spin-trapping radical ferryl ion, which decayed the spin adduct of DMPO. In the presence of Hb or iron-EDTA, O(2)(-)-generating activity and viability of phagocytes decreased, whereas lipid peroxidation of peritoneal phagocytes increased. Generation of oxygen radicals and lipid peroxidation did not differ in the live and dead bacterial models. Bacterial numbers in the peritoneal cavity and blood were markedly increased in the live bacterial model with Hb and iron-EDTA. The Fenton inhibitor iron-DF prevented the loss of phagocyte function, lipid peroxidation, and bacterial proliferation. These results led us to conclude that the lethal toxicity of Hb in bacterial peritonitis is associated with a Fenton

  15. Discovery of Rickettsia species in Dermacentor niveus Neumann ticks by investigating the diversity of bacterial communities.

    PubMed

    Zhuang, Lu; Wang, Cheng-Yan; Tong, Yi-Gang; Tang, Fang; Yang, Hong; Liu, Wei; Cao, Wu-Chun

    2014-09-01

    Ticks (Dermacentor niveus Neumann) were collected from Tacheng, Xinjiang Uygur Autonomous Region, and their bacterial diversity was investigated using the 16S RNA gene library method from one pooled sample. A total of 452 clones was successfully sequenced and assigned to 4 phyla. The dominant phylum was the Proteobacteria, accounting for 62.8% of all the clones of the 16S rRNA gene at the confidence level 80%. The other sequences were assigned to the phyla Bacteroidetes, Firmicutes, Actinobacteria and accounted for 13.5%, 12.4%, and 11.3%, respectively. These results provide an insight into the bacterial diversity associated with D. niveus ticks in the natural environment of Tacheng. They indicate the occurrence of Rickettsia raoultii and Rickettsia slovaca in D. niveus ticks in this area, and as a consequence, cases of TIBOLA/DEBONEL may occur (tick-borne lymphadenopathy/Dermacentor-borne necrosis erythema and lymphadenopathy).

  16. Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

    PubMed Central

    Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

    2014-01-01

    Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

  17. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri.

    PubMed

    Timilsina, Sujan; Jibrin, Mustafa O; Potnis, Neha; Minsavage, Gerald V; Kebede, Misrak; Schwartz, Allison; Bart, Rebecca; Staskawicz, Brian; Boyer, Claudine; Vallad, Gary E; Pruvost, Olivier; Jones, Jeffrey B; Goss, Erica M

    2015-02-01

    Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations. PMID:25527544

  18. Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut.

    PubMed

    Good, Ashley P; Gauthier, Marie-Pierre L; Vannette, Rachel L; Fukami, Tadashi

    2014-01-01

    The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees' health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees' health. However, numerically minor taxa might also influence the bees' efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees' health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior.

  19. Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut.

    PubMed

    Good, Ashley P; Gauthier, Marie-Pierre L; Vannette, Rachel L; Fukami, Tadashi

    2014-01-01

    The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees' health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees' health. However, numerically minor taxa might also influence the bees' efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees' health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior. PMID:24466119

  20. Honey Bees Avoid Nectar Colonized by Three Bacterial Species, But Not by a Yeast Species, Isolated from the Bee Gut

    PubMed Central

    Good, Ashley P.; Gauthier, Marie-Pierre L.; Vannette, Rachel L.; Fukami, Tadashi

    2014-01-01

    The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees’ health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees’ health. However, numerically minor taxa might also influence the bees’ efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees’ health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior. PMID:24466119

  1. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

    PubMed Central

    Yahara, Koji; Furuta, Yoshikazu; Morimoto, Shinpei; Kikutake, Chie; Komukai, Sho; Matelska, Dorota; Dunin-Horkawicz, Stanisław; Bujnicki, Janusz M.; Uchiyama, Ikuo; Kobayashi, Ichizo

    2016-01-01

    Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS > 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication, recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures. Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination. We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes. PMID:26961370

  2. Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor.

    PubMed

    Hahnke, Sarah; Striesow, Jutta; Elvert, Marcus; Mollar, Xavier Prieto; Klocke, Michael

    2014-08-01

    A novel anaerobic, mesophilic, hydrogen-producing bacterium, designated strain M2/40(T), was isolated from a mesophilic, two-phase, laboratory-scale biogas reactor fed continuously with maize silage supplemented with 5% wheat straw. 16S rRNA gene sequence comparison revealed an affiliation to the genus Clostridium sensu stricto (cluster I of the clostridia), with Clostridium cellulovorans as the closest characterized species, showing 93.8% sequence similarity to the type strain. Cells of strain M2/40(T) were rods to elongated filamentous rods that showed variable Gram staining. Optimal growth occurred at 35 °C and at pH 7. Grown on glucose, the main fermentation products were H2, CO2, formate, lactate and propionate. The DNA G+C content was 29.6 mol%. The major fatty acids (>10 %) were C(16 : 0), summed feature 10 (C(18 : 1)ω11c/ω9t/ω6t and/or unknown ECL 17.834) and C(18 : 1)ω11c dimethylacetal. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain M2/40(T) represents a novel species within the genus Clostridium, for which we propose the name Clostridium bornimense sp. nov. The type strain is M2/40(T) ( = DSM 25664(T) = CECT 8097(T)).

  3. Bacterial colonization of the phyllosphere of mediterranean perennial species as influenced by leaf structural and chemical features.

    PubMed

    Yadav, R K P; Karamanoli, K; Vokou, D

    2005-08-01

    In this study, we assessed various leaf structural and chemical features as possible predictors of the size of the phyllosphere bacterial population in the Mediterranean environment. We examined eight perennial species, naturally occurring and coexisting in the same area, in Halkidiki (northern Greece). They are Arbutus unedo, Quercus coccifera, Pistacia lentiscus, and Myrtus communis (evergreen sclerophyllous species), Lavandula stoechas and Cistus incanus (drought semi-deciduous species), and Calamintha nepeta and Melissa officinalis (non-woody perennial species). M. communis, L. stoechas, C. nepeta, and M. officinalis produce essential oil in substantial quantities. We sampled summer leaves from these species and (1) estimated the size of the bacterial population of their phyllosphere, (2) estimated the concentration of different leaf constituents, and (3) studied leaf morphological and anatomical features and expressed them in a quantitative way. The aromatic plants are on average more highly colonized than the other species, whereas the non-woody perennials are more highly colonized than the woody species. The population size of epiphytic bacteria is positively correlated with glandular and non-glandular trichome densities, and with water and phosphorus contents; it is negatively correlated with total phenolics content and the thickness of the leaf, of the mesophyll, and of the abaxial epidermis. No correlation was found with the density of stomata, the nitrogen, and the soluble sugar contents. By regression tree analysis, we found that the leaf-microbe system can be effectively described by three leaf attributes with leaf water content being the primary explanatory attribute. Leaves with water content >73% are the most highly colonized. For leaves with water content <73%, the phosphorus content, with a critical value of 1.34 mg g(-1) d.w., is the next explanatory leaf attribute, followed by the thickness of the adaxial epidermis. Leaves higher in phosphorus

  4. Intrinsic contributions of polar amino acid residues toward thermal stability of an ABC–ATPase of mesophilic origin

    PubMed Central

    Sarin, Jyoti; Raghava, Gajendra P.S.; Chakraborti, Pradip K.

    2003-01-01

    The nucleotide-binding subunit of phosphate-specific transporter (PstB) from mesophilic bacterium, Mycobacterium tuberculosis, is a unique ATP-binding cassette (ABC) ATPase because of its unusual ability to hydrolyze ATP at high temperature. In an attempt to define the basis of thermostability, we took a theoretical approach and compared amino acid composition of this protein to that of other PstBs from available bacterial genomes. Interestingly, based on the content of polar amino acids, this protein clustered with the thermophiles. PMID:12931011

  5. Rapid Identification of Biothreat and Other Clinically Relevant Bacterial Species by Use of Universal PCR Coupled with High-Resolution Melting Analysis▿

    PubMed Central

    Yang, Samuel; Ramachandran, Padmini; Rothman, Richard; Hsieh, Yu-Hsiang; Hardick, Andrew; Won, Helen; Kecojevic, Aleksandar; Jackman, Joany; Gaydos, Charlotte

    2009-01-01

    A rapid assay for eubacterial species identification is described using high-resolution melt analysis to characterize PCR products. Unique melt profiles generated from multiple hypervariable regions of the 16S rRNA gene for 100 clinically relevant bacterial pathogens, including category A and B biothreat agents and their surrogates, allowed highly specific species identification. PMID:19458181

  6. RT-PCR-DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations.

    PubMed

    Benítez-Cabello, Antonio; Bautista-Gallego, Joaquín; Garrido-Fernández, Antonio; Rantsiou, Kalliopi; Cocolin, Luca; Jiménez-Díaz, Rufino; Arroyo-López, Francisco N

    2016-01-01

    This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues. PMID:27582739

  7. Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

    PubMed Central

    Cárdenas, Anny; Rodriguez-R, Luis M; Pizarro, Valeria; Cadavid, Luis F; Arévalo-Ferro, Catalina

    2012-01-01

    Coral reefs are deteriorating at an alarming rate mainly as a consequence of the emergence of coral diseases. The white plague disease (WPD) is the most prevalent coral disease in the southwestern Caribbean, affecting dozens of coral species. However, the identification of a single causal agent has proved problematic. This suggests more complex etiological scenarios involving alterations in the dynamic interaction between environmental factors, the coral immune system and the symbiotic microbial communities. Here we compare the microbiome of healthy and WPD-affected corals from the two reef-building species Diploria strigosa and Siderastrea siderea collected at the Tayrona National Park in the Caribbean of Colombia. Microbiomes were analyzed by combining culture-dependent methods and pyrosequencing of 16S ribosomal DNA (rDNA) V5-V6 hypervariable regions. A total of 20 410 classifiable 16S rDNA sequences reads were obtained including all samples. No significant differences in operational taxonomic unit diversity were found between healthy and affected tissues; however, a significant increase of Alphaproteobacteria and a concomitant decrease in the Beta- and Gammaproteobacteria was observed in WPD-affected corals of both species. Significant shifts were also observed in the orders Rhizobiales, Caulobacteriales, Burkholderiales, Rhodobacterales, Aleteromonadales and Xanthomonadales, although they were not consistent between the two coral species. These shifts in the microbiome structure of WPD-affected corals suggest a loss of community-mediated growth control mechanisms on bacterial populations specific for each holobiont system. PMID:21955993

  8. RT-PCR–DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations

    PubMed Central

    Benítez-Cabello, Antonio; Bautista-Gallego, Joaquín; Garrido-Fernández, Antonio; Rantsiou, Kalliopi; Cocolin, Luca; Jiménez-Díaz, Rufino; Arroyo-López, Francisco N.

    2016-01-01

    This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues. PMID:27582739

  9. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species.

    PubMed

    Benomar, Saida; Ranava, David; Cárdenas, María Luz; Trably, Eric; Rafrafi, Yan; Ducret, Adrien; Hamelin, Jérôme; Lojou, Elisabeth; Steyer, Jean-Philippe; Giudici-Orticoni, Marie-Thérèse

    2015-02-23

    Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.

  10. Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River.

    PubMed

    Staley, Christopher; Gould, Trevor J; Wang, Ping; Phillips, Jane; Cotner, James B; Sadowsky, Michael J

    2015-02-01

    Bacterial community structure (BCS) in freshwater ecosystems varies seasonally and due to physicochemical gradients, but metacommunity structure of a major river remains understudied. Here we characterize the BCS along the Mississippi River and contributing rivers in Minnesota over three years using Illumina next-generation sequencing, to determine how changes in environmental conditions as well as inputs from surrounding land and confluences impacted community structure. Contributions of sediment to water microbial diversity were also evaluated. Long-term variation in community membership was observed, and significant shifts in relative abundances of major freshwater taxa, including α-Proteobacteria, Burkholderiales, and Actinomycetales, were observed due to temporal and spatial variations. Environmental parameters (e.g. temperature, rainfall, and nutrient concentrations) primarily contributed to differences in phyla abundances (88% of variance), with minimal influence from spatial distance alone (<1% of variance). Furthermore, an annually-recurrent BCS was observed in late summer, further suggesting that seasonal dynamics strongly influence community composition. Sediment communities differed from those in the water, but contributed up to 50% to community composition in the water column. Among water sampling sites, 34% showed significant variability in BCS of replicate samples indicating variability among riverine communities due to heterogeneity in the water column. Results of this study highlight the need for a better understanding of spatial and temporal variations in riverine bacterial diversity associated with physicochemical gradients and reveal how communities in sediments, and potentially other environmental reservoirs, impact waterborne BCS. Techniques used in this study may prove useful to determine sources of microbes from sediments and soils to waterways, which will facilitate best management practices and total maximum daily load determinations.

  11. Time-kill behavior against eight bacterial species and cytotoxicity of antibacterial monomers

    PubMed Central

    Li, Fang; Weir, Michael D.; Fouad, Ashraf F.; Xu, Hockin H. K.

    2013-01-01

    Objectives The objectives of this study were to investigate: (1) the antibacterial activity of two antibacterial monomers, dimethylaminododecyl methacrylate (DMADDM) and dimethylammoniumethyl dimethacrylate (DMAEDM), against eight different species of oral pathogens for the first time; (2) the cytotoxicity of DMAEDM and DMADDM. Methods DMAEDM and DMADDM were synthesized by reacting a tertiary amine group with an organo-halide. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against eight species of bacteria were tested. Time-kill determinations were performed to examine the bactericidal kinetics. Cytotoxicity of monomers on human gingival fibroblasts (HGF) was assessed using a methyl thiazolyltetrazolium assay and live/dead viability assay. Results DMADDM showed strong bactericidal activity against all bacteria, with MIC of 1.2 to 9.8μg/mL. DMAEDM had MIC of 20 to 80mg/mL. Time-kill determinations indicated that DMADDM and DMAEDM had rapid killing effects against eight species of bacteria, and eliminated all bacteria in 30min at the concentration of 4-fold MBC. Median lethal concentration for DMADDM and DMAEDM was between 20 to 40μg/mL, which was 20-fold higher than 1 to 2μg/mL for BisGMA control. Conclusions DMAEDM and DMADDM were tested in time-kill assay against eight species of oral bacteria for the first time. Both were effective in bacteria-inhibition, but DMADDM had a higher potency than DMAEDM. Different killing efficacy was found against different bacteria species. DMAEDM and DMADDM had much lower cytotoxicity than BisGMA. Therefore, DMADDM and DMAEDM are promising for use in bonding agents and other restorative/preventive materials to combat a variety of oral pathogens. PMID:23876930

  12. Cytotoxic responses to 405nm light exposure in mammalian and bacterial cells: Involvement of reactive oxygen species.

    PubMed

    Ramakrishnan, Praveen; Maclean, Michelle; MacGregor, Scott J; Anderson, John G; Grant, M Helen

    2016-06-01

    Light at wavelength 405 nm is an effective bactericide. Previous studies showed that exposing mammalian cells to 405 nm light at 36 J/cm(2) (a bactericidal dose) had no significant effect on normal cell function, although at higher doses (54 J/cm(2)), mammalian cell death became evident. This research demonstrates that mammalian and bacterial cell toxicity induced by 405 nm light exposure is accompanied by reactive oxygen species production, as detected by generation of fluorescence from 6-carboxy-2',7'-dichlorodihydrofluorescein diacetate. As indicators of the resulting oxidative stress in mammalian cells, a decrease in intracellular reduced glutathione content and a corresponding increase in the efflux of oxidised glutathione were observed from 405 nm light treated cells. The mammalian cells were significantly protected from dying at 54 J/cm(2) in the presence of catalase, which detoxifies H2O2. Bacterial cells were significantly protected by sodium pyruvate (H2O2 scavenger) and by a combination of free radical scavengers (sodium pyruvate, dimethyl thiourea (OH scavenger) and catalase) at 162 and 324 J/cm(2). Results therefore suggested that the cytotoxic mechanism of 405 nm light in mammalian cells and bacteria could be oxidative stress involving predominantly H2O2 generation, with other ROS contributing to the damage.

  13. Bacterial wilt resistance in tomato, pepper, and eggplant: genetic resources respond to diverse strains in the Ralstonia solanacearum species complex.

    PubMed

    Lebeau, A; Daunay, M-C; Frary, A; Palloix, A; Wang, J-F; Dintinger, J; Chiroleu, F; Wicker, E; Prior, P

    2011-01-01

    Bacterial wilt, caused by strains belonging to the Ralstonia solanacearum species complex, inflicts severe economic losses in many crops worldwide. Host resistance remains the most effective control strategy against this disease. However, wilt resistance is often overcome due to the considerable variation among pathogen strains. To help breeders circumvent this problem, we assembled a worldwide collection of 30 accessions of tomato, eggplant and pepper (Core-TEP), most of which are commonly used as sources of resistance to R. solanacearum or for mapping quantitative trait loci. The Core-TEP lines were challenged with a core collection of 12 pathogen strains (Core-Rs2) representing the phylogenetic diversity of R. solanacearum. We observed six interaction phenotypes, from highly susceptible to highly resistant. Intermediate phenotypes resulted from the plants' ability to tolerate latent infections (i.e., bacterial colonization of vascular elements with limited or no wilting). The Core-Rs2 strains partitioned into three pathotypes on pepper accessions, five on tomato, and six on eggplant. A "pathoprofile" concept was developed to characterize the strain clusters, which displayed six virulence patterns on the whole set of Core-TEP host accessions. Neither pathotypes nor pathoprofiles were phylotype specific. Pathoprofiles with high aggressiveness were mainly found in strains from phylotypes I, IIB, and III. One pathoprofile included a strain that overcame almost all resistance sources. PMID:20795852

  14. Exploration of methods used to describe bacterial communities in silage of maize (Zea mays) cultivars.

    PubMed

    Brusetti, Lorenzo; Borin, Sara; Rizzi, Aurora; Mora, Diego; Sorlini, Claudia; Daffonchio, Daniele

    2008-01-01

    Different techniques to assess bacterial community structure and diversity were evaluated in silages prepared with four different maize cultivars, three conventional and one transgenic (cv. Tundra, event Bt-176). Plants were cultivated in the greenhouse and harvested after 30 days of growth. Silage samples were collected at successive times during fermentation and analyzed for bacterial counts and by various DNA-based fingerprinting techniques. Bacterial counts were similar between cultivars for the total culturable bacteria, sporeforming, and mesophilic and thermophilic lactic acid bacteria (LAB). Further analysis of the species composition of 388 LAB strains by intergenic transcribed spacer (ITS) PCR followed by sequencing of 16S rRNA gene did not reveal differences between cultivars. In contrast, molecular fingerprinting methods targeting whole bacterial communities, such as automated ribosomal intergenic spacers analysis (ARISA) and 16S rRNA gene length heterogeneity-PCR (LH-PCR), indicated that different maize silage batches or cultivars hosted different bacterial communities. Thus, ARISA and LH-PCR fingerprinting techniques offer a fast and sensitive method to compare bacterial communities, and to detect differences in silage bacterial communities.

  15. Thermal stability of cytochrome c' from mesophilic Shewanella amazonensis.

    PubMed

    Kato, Yuki; Fujii, Sotaro; Kuribayashi, Taka-aki; Masanari, Misa; Sambongi, Yoshihiro

    2015-01-01

    Cytochrome c' (SACP) from mesophilic Shewanella amazonensis, growing optimally at 37 °C, was thermally more stable than cytochrome c' (AVCP) from mesophilic Allochromatium vinosum, growing optimally at 25 °C. In contrast, SACP was less stable than cytochrome c' (PHCP) from thermophilic Hydrogenophilus thermoluteolus, growing optimally at 52 °C. Although only 28% of the SACP amino acid sequence was identical to those of AVCP and PHCP, the latter two being 55% identical, the overall main chain structures of the three cytochromes c' were similar, and SACP exhibited thermal stability intermediate between those of AVCP and PHCP. For these three proteins, the higher the stability is, the lesser the number of Gly residues in the putative α-helical regions is. Cytochromes c' including the present three are suitable for examining the protein stabilization mechanisms, because they are structurally similar and available from environments with a wide range of temperatures.

  16. Characteristics of aerobic granulation at mesophilic temperatures in wastewater treatment.

    PubMed

    Cui, Fenghao; Park, Seyong; Kim, Moonil

    2014-01-01

    Compact and structurally stable aerobic granules were developed in a sequencing batch reactor (SBR) at mesophilic temperatures (35°C). The morphological, biological and chemical characteristics of the aerobic granulation were investigated and a theoretical granulation mechanism was proposed according to the results of the investigation. The mature aerobic granules had compact structure, small size (mean diameter of 0.24 mm), excellent settleability and diverse microbial structures, and were effective for the removal of organics and nitrification. The growth kinetics demonstrated that the biomass growth depended on coexistence and interactions between heterotrophs and autotrophs in the granules. The functions of heterotrophs and autotrophs created a compact and secure layer on the outside of the granules, protecting the inside sludge containing environmentally sensitive and slow growing microorganisms. The mechanism and the reactor performance may promise feasibility and efficiency for treating industry effluents at mesophilic temperatures using aerobic granulation. PMID:24211486

  17. The animal food supplement sepiolite promotes a direct horizontal transfer of antibiotic resistance plasmids between bacterial species.

    PubMed

    Rodríguez-Beltrán, Jerónimo; Rodríguez-Rojas, Alexandro; Yubero, Elva; Blázquez, Jesús

    2013-06-01

    Animal fodder is routinely complemented with antibiotics together with other food supplements to improve growth. For instance, sepiolite is currently used as a dietary coadjuvant in animal feed, as it increases animal growth parameters and improves meat and derived final product quality. This type of food additive has so far been considered innocuous for the development and spread of antibiotic resistance. In this study, we demonstrate that sepiolite promotes the direct horizontal transfer of antibiotic resistance plasmids between bacterial species. The conditions needed for plasmid transfer (sepiolite and friction forces) occur in the digestive tracts of farm animals, which routinely receive sepiolite as a food additive. Furthermore, this effect may be aggravated by the use of antibiotics supplied as growth promoters.

  18. An Empirical Strategy for Characterizing Bacterial Proteomes across Species in the Absence of Genomic Sequences

    PubMed Central

    Turse, Joshua E.; Marshall, Matthew J.; Fredrickson, James K.; Lipton, Mary S.; Callister, Stephen J.

    2010-01-01

    Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300–500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella. PMID:21103051

  19. [Bactericial activity of chlorhexidine gluconate against recent clinical isolates of various bacterial species in Japan].

    PubMed

    Kanazawa, Katsunori; Ueda, Yutaka

    2004-10-01

    The minimum inhibitory concentration (MIC) and bactericidal activity of chlorhexidine gluconate (CHG) were determined for methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), Escherichia coli, Serratia marcescens, Eterobacter cloacae, Pseudomonas aeruginosa and Burkholderia cepacia, isolated from patients in medical institutions all over Japan between 2000 and 2002. The following findings were obtained. 1. The MICs of CHG against MSSA, MRSA, E. coli and B. cepacia were 0.002% or less, and those against S. marcescens, E. cloacae and P. aeruginosa were 0.008% or less. 2. Rapid and strong bactericidal effects of CHG were observed against all clinical isolates of E. coli, E. cloacae and P. aeruginosa tested even at relatively low concentrations (0.02 to 0.05%). 3. Relatively high concentration or prolonged treatment time was required to achieve sufficient bactericidal effect of CHG against some isolates of S. aureus, S. marcescens and B. cepacia. These results suggest that CHG is useful antiseptic agent or disinfectant for recent clinical isolates of various bacterial pathogens. In addition, the selection of treatment concentration and treatment time for each organism and purpose was important to obtain sufficient bactericidal effect.

  20. Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments.

    PubMed

    Mench, Michel; Renella, Giancarlo; Gelsomino, Antonio; Landi, Loretta; Nannipieri, Paolo

    2006-11-01

    The effectiveness of two amendments for the in situ remediation of a Cd- and Ni-contaminated soil in the Louis Fargue long-term field experiment was assessed. In April 1995, one replicate plot (S1) was amended with 5% w/w of beringite (B), a coal fly ash (treatment S1+B), and a second plot with 1% w/w zerovalent-Fe iron grit (SS) (treatment S1+SS), with the aim of increasing metal sorption and attenuating metal impacts. Long-term responses of daily respiration rates, microbial biomass, bacterial species richness and the activities of key soil enzymes (acid and alkaline phosphatase, arylsulfatase, beta-glucosidase, urease and protease activities) were studied in relation to soil metal extractability. Seven years after initial amendments, the labile fractions of Cd and Ni in both the S1+B and S1+SS soils were reduced to various extents depending on the metal and fractions considered. The soil microbial biomass and respiration rate were not affected by metal contamination and amendments in the S1+B and S1+SS soils, whereas the activity of different soil enzymes was restored. The SS treatment was more effective in reducing labile pools of Cd and Ni and led to a greater recovery of soil enzyme activities than the B treatment. Bacterial species richness in the S1 soil did not alter with either treatment. It was concluded that monitoring of the composition and activity of the soil microbial community is important in evaluating the effectiveness of soil remediation practices.

  1. Biodegradation of free cyanide by bacterial species isolated from cyanide-contaminated artisanal gold mining catchment area in Burkina Faso.

    PubMed

    Razanamahandry, Lovasoa Christine; Andrianisa, Harinaivo Anderson; Karoui, Hela; Kouakou, Koffi Marcelin; Yacouba, Hamma

    2016-08-01

    Soil and water samples were collected from a watershed in Burkina Faso where illegal artisanal gold extraction using cyanidation occurs. The samples were used to evaluate cyanide contamination and the presence of cyanide degrading bacteria (CDB). Free cyanide (F-CN) was detected in all samples, with concentrations varying from 0.023 to 0.9 mg kg(-1), and 0.7-23 μg L(-1) in the soil and water samples, respectively. Potential CDB also were present in the samples. To test the effective F-CN degradation capacity of the isolated CDB species, the species were cultivated in growth media containing 40, 60 or 80 mg F-CN L(-1), with or without nutrients, at pH 9.5 and at room temperature. More than 95% of F-CN was degraded within 25 h, and F-CN degradation was associated with bacterial growth and ammonium production. However, initial concentrations of F-CN higher than 100 mg L(-1) inhibited bacterial growth and cyanide degradation. Abiotic tests showed that less than 3% of F-CN was removed by volatilization. Thus, the degradation of F-CN occurred predominately by biological mechanisms, and such mechanisms are recommended for remediation of contaminated soil and water. The bacteria consortium used in the experiment described above exist in a Sahelian climate, which is characterized by a long hot and dry season. Because the bacteria are already adapted to the local climate conditions and show the potential for cyanide biodegradation, further applicability to other contaminated areas in West Africa, where illegal gold cyanidation is widespread, should be explored. PMID:27209555

  2. Multifactorial Competition and Resistance in a Two-Species Bacterial System

    PubMed Central

    Khare, Anupama; Tavazoie, Saeed

    2015-01-01

    Microorganisms exist almost exclusively in interactive multispecies communities, but genetic determinants of the fitness of interacting bacteria, and accessible adaptive pathways, remain uncharacterized. Here, using a two-species system, we studied the antagonism of Pseudomonas aeruginosa against Escherichia coli. Our unbiased genome-scale approach enabled us to identify multiple factors that explained the entire antagonism observed. We discovered both forms of ecological competition–sequestration of iron led to exploitative competition, while phenazine exposure engendered interference competition. We used laboratory evolution to discover adaptive evolutionary trajectories in our system. In the presence of P. aeruginosa toxins, E. coli populations showed parallel molecular evolution and adaptive convergence at the gene-level. The multiple resistance pathways discovered provide novel insights into mechanisms of toxin entry and activity. Our study reveals the molecular complexity of a simple two-species interaction, an important first-step in the application of systems biology to detailed molecular dissection of interactions within native microbiomes. PMID:26647077

  3. Characterization of a Single Magnetotactic Bacterial Species from Devil's Bathtub, Mendon Ponds Park, Honeoye Falls, NY

    NASA Astrophysics Data System (ADS)

    Wagner, C.; Tarduno, J. A.; Stein, A.; Sia, E.

    2015-12-01

    Magnetotactic bacteria (MTB) belong to a lineage of prokaryotic bacteria that synthesize magnetosomes, single domain magnetic particles (typically magnetite or greigite) with an average size of 50 nanometers. MTB utilize magnetosomes through magnetotaxis, the alignment and movement along magnetic field lines to navigate towards preferred environmental conditions. MTB are sensitive to different environments and are thought to exhibit varying magnetosome morphologies, compositions, sizes, and quantities in regards to the environments which they inhabit. These characteristics allow MTB and magnetofossils (preserved magnetosomes) to be used as modern/paleoenvironmental recorders and biomarkers for environmental change(s). Devil's Bathtub (Mendon Ponds Park, Honeoye Falls, NY) is a meromictic glacial kettle pond surrounded by deciduous tree cover. Here we examine one species of MTB based on prominence of this particular morphology at this locale. Magnetotaxis and morphology of this species have been observed using light microscopy. Micrographs have also been taken using Transmission Electron Microscopy (TEM) to verify cell morphology and to determine magnetosome morphology. TEM and magnetic hysteresis measurements were done to find and test the composition of magnetosomes. In this study we also focus on DNA sequencing and characterization of this MTB, as there are few MTB species which have been DNA sequenced successfully. Data from these experiments are directly applicable to this up-and-coming area of research as it will aid in the understanding and correlation of magnetosome and magnetofossils with environmental characteristics.

  4. Accuracy of species identity of commercial bacterial cultures intended for probiotic or nutritional use.

    PubMed

    Huys, Geert; Vancanneyt, Marc; D'Haene, Klaas; Vankerckhoven, Vanessa; Goossens, Herman; Swings, Jean

    2006-11-01

    Independent studies have indicated that the microbiological composition of several commercial probiotic products does not correspond to the product label information. The present study set out to investigate to what extent these problems may be due to the use of misidentified cultures at the onset of production. For this purpose, 213 cultures of lactic acid bacteria (LAB) and propionibacteria intended for probiotic or nutritional use were collected from 26 manufacturers of probiotic products, three international culture collections and one research institute. The accuracy of the taxonomic identity provided by the strain depositor was assessed through a polyphasic approach based on validated and standardized identification methods including fluorescent amplified fragment length polymorphism (FAFLP) and repetitive DNA element (rep)-PCR fingerprinting, protein profiling and partial 16S rDNA sequencing. The majority of the cultures were received as members of the genera Lactobacillus (57%) and Bifidobacterium (22%); however, propionibacteria, enterococci, Lactococcus lactis (subsp. lactis), Streptococcus thermophilus and pediococci were also obtained. Upon reidentification, 46 cases of misidentification at the genus level (n=19) or species level (n=27) were recorded, including 34 commercial probiotic cultures deposited by 10 different companies. The finding that more than 28% of the commercial cultures intended for human and/or animal probiotic use were misidentified at the genus or species level suggests that many cases of probiotic product mislabeling originate from the incorporation of incorrectly identified strains. A large number of these discrepancies could be related to the use of methods with limited taxonomic resolution (e.g., API strips) or that are unsuitable for reliable identification up to species level (e.g., pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis). The current study has again highlighted that reliable

  5. Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species.

    PubMed

    Gutiérrez-Preciado, Ana; Yanofsky, Charles; Merino, Enrique

    2007-09-01

    The tryptophan biosynthetic operon has been widely used as a model system for studying transcription regulation. In Bacillus subtilis, the trp operon is primarily regulated by a tryptophan-activated RNA-binding protein, TRAP. Here we show that in many other Gram-positive species the trp operon is regulated differently, by tRNA(Trp) sensing by the RNA-based T-box mechanism, with T-boxes arranged in tandem. Our analyses reveal an apparent relationship between trp operon organization and the specific regulatory mechanism(s) used. PMID:17555843

  6. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms.

    PubMed

    Terefework, Zewdu; Pham, Chi L; Prosperi, Anja C; Entius, Mark M; Errami, Abdellatif; van Spanning, Rob J M; Zaura, Egija; Ten Cate, Jacob M; Crielaard, Wim

    2008-12-01

    A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.

  7. Effect of temperature on bacterial species diversity in thermophilic solid-waste composting.

    PubMed

    Strom, P F

    1985-10-01

    Continuously thermophilic composting was examined with a 4.5-liter reactor placed in an incubator maintained at representative temperatures. Feed was a mixture of dried table scraps and shredded newspaper wetted to 55% moisture. One run at 49 degrees C (run A) employed a 1:4 feed-to-compost ratio, while the other runs used a 10:1 ratio and were incubated at 50, 55, 60, or 65 degrees C. Due to self-heating, internal temperatures of the composting mass were 0 to 7 degrees C hotter than the incubator. Two full-scale composting plants (at Altoona, Pa., and Leicester, England) were also examined. Plate counts per gram (dry weight) on Trypticase soy broth (BBL Microbiology Systems) with 2% agar ranged from 0.7 X 10(9) to 5.3 X 10(9) for laboratory composting and 0.02 X 10(9) to 7.4 X 10(9) for field composting. Fifteen taxa were isolated, including 10 of genus Bacillus, which dominated all samples except that from run A. Species diversity decreased markedly in laboratory composting at 60 degrees C and above, but was similar for the three runs incubated at 49, 50, and 55 degrees C. The maximum desirable composting temperature based on species diversity is thus 60 degrees C, the same as that previously recommended based on measures of the rate of decomposition. PMID:4083885

  8. Translational control of small heat shock genes in mesophilic and thermophilic cyanobacteria by RNA thermometers.

    PubMed

    Cimdins, Annika; Klinkert, Birgit; Aschke-Sonnenborn, Ursula; Kaiser, Friederike M; Kortmann, Jens; Narberhaus, Franz

    2014-01-01

    Cyanobacteria constitute a heterogeneous phylum of oxygen-producing, photosynthetic prokaryotes. They are susceptible to various stress conditions like heat, salt, or light stress, all inducing the cyanobacterial heat shock response (HSR). Cyanobacterial small heat shock proteins (sHsps) are known to preserve thylakoid membrane integrity under stress conditions, thereby protecting the photosynthesis machinery. In Synechocystis sp PCC 6803, synthesis of the sHsp Hsp17 is regulated by an RNA thermometer (RNAT) in the 5'-untranslated region (5'-UTR) of the hsp17 mRNA. RNATs are direct temperature sensors that control expression of many bacterial heat shock and virulence genes. They hinder translation at low temperatures by base pairing, thus blocking ribosome access to the mRNA.   To explore the temperature range in which RNATs act, we studied various RNAT candidates upstream of sHsp genes from mesophilic and thermophilic cyanobacteria. The mesophilic cyanobacteria Anabaena variabilis and Nostoc sp chromosomally encode two sHsps each. Reporter gene studies suggested RNAT-mediated post-transcriptional regulation of shsp expression in both organisms. Detailed structural analysis of the two A. variabilis candidates revealed two novel RNAT types. The first, avashort, regulates translation primarily by masking of the AUG translational start codon. The second, featuring an extended initial hairpin, thus named avalong, presumably makes use of complex tertiary interaction. The 5'-UTR of the small heat shock gene hspA in the thermophile Thermosynechococcus elongatus is predicted to adopt an extended secondary structure. Structure probing revealed that the ribosome binding site was blocked at temperatures below 55 °C. The results of this study demonstrate that cyanobacteria commonly use RNATs to control expression of their small heat shock genes.

  9. Gene cloning and protein expression of γ-glutamyltranspeptidases from Thermus thermophilus and Deinococcus radiodurans: comparison of molecular and structural properties with mesophilic counterparts.

    PubMed

    Castellano, Immacolata; Di Salle, Anna; Merlino, Antonello; Rossi, Mosè; La Cara, Francesco

    2011-03-01

    γ-Glutamyltranspeptidase (γ-GT) is an ubiquitous enzyme that catalyzes the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. γ-GTs from extremophiles, bacteria adapted to live in hostile environments, were selected as model systems to study the molecular underpinnings of their adaptation to extreme conditions and to find out special properties of potential biotechnological interest. Here, we report the cloning, expression and purification of two members of γ-GT family from two different extremophilic species, Thermus thermophilus (TtGT) and Deinococcus radiodurans (DrGT); the first is an aerobic eubacterium, growing at high temperatures (50-82°C), the second is a polyextremophile, as it tolerates radiations, cold, dehydration, vacuum, and acid. TtGT and DrGT were both synthesized as precursor proteins of 59-60 kDa, undergoing an intramolecular auto-cleavage to yield two subunits of 40 and 19-20 kDa, respectively. However, like the γ-GT from Geobacillus thermodenitrificans, but differently from the other characterized bacterial and eukaryotic γ-GTs, the two new extremophilic enzymes displayed γ-glutamyl hydrolase, but not transpeptidase activity in the 37-50°C temperature range, pH 8.0. The comparison of sequences and structural models of these two proteins with experimental-determined structures of other known mesophilic γ-GTs suggests that the extremophilic members of this protein family have found a common strategy to adapt to different hostile environments. Moreover, a phylogenetic analysis suggests that γ-GTs displaying only γ-glutamyl hydrolase activity could represent the progenitors of the bacterial and eukaryotic counterparts.

  10. Impacts of silver nanoparticles on bacterial species B. subtilis and E. coli and the major crop plant Z. mays

    NASA Astrophysics Data System (ADS)

    Doody, Michael A.

    This thesis examines the impacts of citrate-coated silver nanoparticles (c-AgNPs) on two species of bacteria (Bacillus subtilis and Escherichia coli), the major crop plant Zea mays, and the beneficial plant-microbe relationship between Z. mays and B. subtilis. AgNPs are an increasing component of antimicrobial consumer, industrial, and military products. This has led to widespread scientific concern for the ecological safety outside their intended use. An overview of their history, use, and toxicity was used to inform the design of experiments and resulting data. Growth inhibition and sub-lethal toxic effects were used to assess the effects of c-AgNP exposure to bacteria. Similar analytical methods were used to quantify the response of Z. mays to c-AgNP exposure. Results showed that exposure to c-AgNP significantly reduced the growth of bacterial populations and alters their growth kinetics. Z. mays experienced significant sub-lethal effects due to exposure, including reduced root length and biomass, and hyper-accumulated Ag in root tissues. Beneficial interactions between B. subtilis and Z. mays were reduced as both species suffered sub-lethal effects of exposure to c-AgNPs.

  11. Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium.

    PubMed

    Douglas, Sarah M; Chubiz, Lon M; Harcombe, William R; Ytreberg, F Marty; Marx, Christopher J

    2016-01-01

    Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator and were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in terms of individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior. PMID:27617746

  12. Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium

    PubMed Central

    Douglas, Sarah M.; Chubiz, Lon M.; Harcombe, William R.; Ytreberg, F. Marty; Marx, Christopher J.

    2016-01-01

    Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator and were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in terms of individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior. PMID:27617746

  13. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species

    PubMed Central

    Moor, Kathrin; Wotzka, Sandra Y.; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

    2016-01-01

    Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 1010 peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency. PMID:26904024

  14. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species.

    PubMed

    Moor, Kathrin; Wotzka, Sandra Y; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

    2016-01-01

    Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 10(10) peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency.

  15. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species.

    PubMed

    Moor, Kathrin; Wotzka, Sandra Y; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

    2016-01-01

    Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 10(10) peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency. PMID:26904024

  16. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies

    PubMed Central

    Lhermie, Guillaume; El Garch, Farid; Toutain, Pierre-Louis; Ferran, Aude A.; Bousquet-Mélou, Alain

    2015-01-01

    We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting. PMID:26506096

  17. Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions.

    PubMed

    Azizi, Aqil; Kim, Wonduck; Lee, Jung Hyun

    2016-10-01

    Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities. PMID:27562592

  18. Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions.

    PubMed

    Azizi, Aqil; Kim, Wonduck; Lee, Jung Hyun

    2016-10-01

    Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

  19. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    NASA Astrophysics Data System (ADS)

    Song, Zhen; Kenney, Janice P. L.; Fein, Jeremy B.; Bunker, Bruce A.

    2012-06-01

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  20. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    SciTech Connect

    Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.; Bunker, Bruce A.

    2015-02-09

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  1. Increasing the dynamic control space of mammalian transcription devices by combinatorial assembly of homologous regulatory elements from different bacterial species.

    PubMed

    Bacchus, William; Weber, Wilfried; Fussenegger, Martin

    2013-01-01

    Prokaryotic transcriptional regulatory elements are widely utilized building blocks for constructing regulatory genetic circuits adapted for mammalian cells and have found their way into a broad range of biotechnological applications. Prokaryotic transcriptional repressors, fused to eukaryotic transactivation or repression domains, compose the transcription factor, which binds and adjusts transcription from chimeric promoters containing the repressor-specific operator sequence. Escherichia coli and Chlamydia trachomatis share common features in the regulatory mechanism of the biosynthesis of l-tryptophan. The repressor protein TrpR of C. trachomatis regulates the trpRBA operon and the TrpR of E. coli regulates the trpEDCBA operon, both requiring l-tryptophan as a co-repressor. Fusion of these bacterial repressors to the VP16 transactivation domain of Herpes simplex virus creates synthetic transactivators that could bind and activate chimeric promoters, assembled by placing repressor-specific operator modules adjacent to a minimal promoter, in an l-tryptophan-adjustable manner. Combinations of different transactivator and promoter variants from the same or different bacterial species resulted in a multitude of regulatory systems where l-tryptophan regulation properties, background noise, and maximal gene expression levels were significantly diverse. Different l-tryptophan analogues showed diverse regulatory capacity depending on the promoter/transactivator combination. We believe the systems approach to rationally choose promoters, transactivators and inducer molecules, to obtain desired and predefined genetic expression dynamics and control profiles, will significantly advance the design of new regulatory circuits as well as improving already existing ones. PMID:23178502

  2. Survival of added bacterial species and metabolism of toxic compounds in natural environments

    SciTech Connect

    King, V.M.

    1987-01-01

    Bacteria able to degrade either 2,4-dichlorophenol (DCP) or phenanthrene (PHEN) were isolated from polluted freshwater environments. Two isolates able to degrade each compound were tested for mineralization with a sensitive /sup 14/C assay and for survival in lake water and sewage using a selective medium. One DCP isolate was identified as Alcaligenes paradoxus and the other as Alcaligenes sp. One PHEN isolate was identified as Pseudomonas fluorescens and the other as Pseudomonas sp. All four isolates survived and grew in sterile environments which indicated that starvation would not be a factor in survival of these strains. The number of organisms declined immediately in number in nonsterile lake water. However, they did survive or even grow in nonsterile sewage for a short period before declining in number. Biotic factors appeared to be influential for survival and mineralization of target compounds in many environments. The removal of protozoa, which prey on bacteria, improved survival of the added cells, but had no influence on the mineralization of 10 ..mu..g DCP/L. In comparison, degradation of 10 and 25 mg DCP/L stopped after a few days. Yeast nitrogen base appeared to overcome the lack of nutrient regeneration, a function attributed to protozoa. The additional nutrients increased toxicant mineralization, especially when seeded with appropriate species. Thus, protozoa may limit growth of added cells but appear to be needed for mineralization of higher concentrations of DCP.

  3. Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii

    PubMed Central

    Ogier, Jean-Claude; Pagès, Sylvie; Bisch, Gaëlle; Chiapello, Hélène; Médigue, Claudine; Rouy, Zoé; Teyssier, Corinne; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2014-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the absence of its nematode host. We sequenced the genome of the X. poinarii strain G6 and the closely related but virulent X. doucetiae strain FRM16. G6 had a smaller genome (500–700 kb smaller) than virulent Xenorhabdus strains and lacked genes encoding potential virulence factors (hemolysins, type 5 secretion systems, enzymes involved in the synthesis of secondary metabolites, and toxin–antitoxin systems). The genomes of all the X. poinarii strains analyzed here had a similar small size. We did not observe the accumulation of pseudogenes, insertion sequences or decrease in coding density usually seen as a sign of genomic erosion driven by genetic drift in host-adapted bacteria. Instead, genome reduction of X. poinarii seems to have been mediated by the excision of genomic blocks from the flexible genome, as reported for the genomes of attenuated free pathogenic bacteria and some facultative mutualistic bacteria growing exclusively within hosts. This evolutionary pathway probably reflects the adaptation of X. poinarii to specific host. PMID:24904010

  4. Biodegradation of PAHs by two bacterial species isolated from coal gasification sites

    SciTech Connect

    Schneider, J.; Grosser, R.J.; Jayasimhulu, K.; Warshawsky, D.

    1994-12-31

    Utilization of microbial processes for bioremediation requires measuring compound degradability as well as characterization of the intermediates formed. A Mycobacterium sp. and Xanthamonas sp. were isolated from coal gasification site soils using standard enrichment techniques. The Mycobacterium sp. was isolated for its ability to mineralize pyrene, but was also found to be capable of degrading other polycyclic aromatic compounds. The Xanthamonas sp. was isolated for its ability to mineralize carbazole and showed very high substrate specificity. The Xanthamonas sp. was incubated with carbazole as the sole added carbon source for approximately two weeks. Analysis of organic extracts show the presence of at least three cleavage products of carbazole. Two of these have been tentatively identified as 2-indole-acetic acid and 2-indole-acrylic acid. A pathway for carbazole degradation by this species is proposed in which the indole moiety is maintained. Analysis of metabolites formed during pyrene degradation were found to include 4,5-pyrene-dihydrodiol, 4-phenanthroic acid, and 4,5-diphenanthroic acid. This Mycobacterium sp. was also found to biodegrade benz(a)anthracene- and benzo(a)pyrene-producing ring cleavage products. For benz(a)anthracene, analysis of organic extracts of the growth medium show at least two dihydrodiol intermediates formed as well as a ring cleavage product. A dihydrodiol intermediate and three ring cleavage products were also found with benzo(a)pyrene. Fluorescence spectra of the benzo(a)pyrene dihydrodiol intermediate was characteristic of that for benz(a)anthracene.

  5. Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species

    PubMed Central

    Bisch, Gaëlle; Ogier, Jean-Claude; Médigue, Claudine; Rouy, Zoé; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2016-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Within Xenorhabdus bovienii species, the X. bovienii CS03 strain (Xb CS03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its Steinernema symbiont. The genome of Xb CS03 was sequenced and compared with the genome of a virulent strain, X. bovienii SS-2004 (Xb SS-2004). The genome size and content widely differed between the two strains. Indeed, Xb CS03 had a large genome containing several specific loci involved in the inhibition of competitors, including a few NRPS-PKS loci (nonribosomal peptide synthetases and polyketide synthases) producing antimicrobial molecules. Consistently, Xb CS03 had a greater antimicrobial activity than Xb SS-2004. The Xb CS03 strain contained more pseudogenes than Xb SS-2004. Decay of genes involved in the host invasion and exploitation (toxins, invasins, or extracellular enzymes) was particularly important in Xb CS03. This may provide an explanation for the nonvirulence of the strain when injected into an insect host. We suggest that Xb CS03 and Xb SS-2004 followed divergent evolutionary scenarios to cope with their peculiar life cycle. The fitness strategy of Xb CS03 would involve competitor inhibition, whereas Xb SS-2004 would quickly and efficiently kill the insect host. Hence, Xenorhabdus strains would have widely divergent host exploitation strategies, which impact their genome structure. PMID:26769959

  6. Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly.

    PubMed

    Zhang, Fen-Guo; Zhang, Quan-Guo

    2015-01-01

    The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.

  7. Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly

    PubMed Central

    Zhang, Fen-Guo; Zhang, Quan-Guo

    2015-01-01

    The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations. PMID:25961300

  8. Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes

    PubMed Central

    Bolotin, Evgeni; Hershberg, Ruth

    2016-01-01

    Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment. PMID:27734920

  9. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    PubMed

    Davis, Ian J; Wallis, Corrin; Deusch, Oliver; Colyer, Alison; Milella, Lisa; Loman, Nick; Harris, Stephen

    2013-01-01

    Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss). In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.

  10. Evaluation of the DiversiLab system for detection of hospital outbreaks of infections by different bacterial species.

    PubMed

    Fluit, A C; Terlingen, A M; Andriessen, L; Ikawaty, R; van Mansfeld, R; Top, J; Cohen Stuart, J W; Leverstein-van Hall, M A; Boel, C H E

    2010-11-01

    Many bacterial typing methods are specific for one species only, time-consuming, or poorly reproducible. DiversiLab (DL; bioMérieux) potentially overcomes these limitations. In this study, we evaluated the DL system for the identification of hospital outbreaks of a number bacterial species. Appropriately typed clinical isolates were tested with DL. DL typing agreed with pulsed-field gel electrophoresis (PFGE) for Acinetobacter (n = 26) and Stenotrophomonas maltophilia (n = 13) isolates. With two exceptions, DL typing of Klebsiella isolates (n = 23) also correlated with PFGE, and in addition, PFGE-nontypeable (PFGE-NT) isolates could be typed. Enterobacter (n = 28) results also correlated with PFGE results; also, PFGE-NT isolates could be clustered. In a larger study (n = 270), a cluster of 30 isolates was observed that could be subdivided by PFGE. The results for Escherichia coli (n = 38) correlated less well with an experimental multilocus variable number of tandem repeats analysis (MLVA) scheme. Pseudomonas aeruginosa (n = 52) showed only a limited number of amplification products for most isolates. When multiple Pseudomonas isolates were assigned to a single type in DL, all except one showed multiple multilocus sequence types. Methicillin-resistant Staphylococcus aureus generally also showed a limited number of amplification products. Isolates that belonged to different outbreaks by other typing methods, including PFGE, spa typing, and MLVA, were grouped together in a number of cases. For Enterococcus faecium, the limited variability of the amplification products obtained made interpretation difficult and correlation with MLVA and esp gene typing was poor. All of the results are reflected in Simpson's index of diversity and adjusted Rand's and Wallace's coefficients. DL is a useful tool to help identify hospital outbreaks of Acinetobacter spp., S. maltophilia, the Enterobacter cloacae complex, Klebsiella spp., and, to a somewhat lesser extent, E. coli. In our

  11. Effect of high pressure on mesophilic lactic fermentation streptococci

    NASA Astrophysics Data System (ADS)

    Reps, A.; Kuźmicka, M.; Wiśniewska, K.

    2008-07-01

    The research concerned the effect of high pressure on mesophilic lactic fermentation streptococci, present in two cheese-making commercial inocula produced by Christian-Hansen. Water solutions of inocula were pressurized at 50-800 MPa, at room temperature, for 30-120 min. Pressurization at 50-100 MPa slightly increased or reduced the number of lactic streptococci, depending on the inoculum and pressurization time. Pressurization at 200 MPa caused a reduction in the number of streptococci by over 99.9%, whereas the pressure of 400 MPa and above almost completely inactivated streptococci. Pressurization also reduced the dynamics of microorganism growth and acidification, to the degree depending on the pressure.

  12. Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species.

    PubMed

    Artursson, Veronica; Finlay, Roger D; Jansson, Janet K

    2005-12-01

    High numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal-restriction fragment length polymorphism (T-RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth.

  13. Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae.

    PubMed

    Pollo, Stephen M J; Zhaxybayeva, Olga; Nesbø, Camilla L

    2015-09-01

    Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.

  14. 16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species).

    PubMed

    Makonde, Huxley M; Boga, Hamadi I; Osiemo, Zipporah; Mwirichia, Romano; Mackenzie, Lucy M; Göker, Markus; Klenk, Hans-Peter

    2013-11-01

    The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60 %) were the most abundant group in Odontotermes while those of Spirochaetes (29 %) and Firmicutes (23 %) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites' guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.

  15. Antimicrobial activity of plant essential oils against bacterial and fungal species involved in food poisoning and/or food decay.

    PubMed

    Lixandru, Brînduşa-Elena; Drăcea, Nicoleta Olguţa; Dragomirescu, Cristiana Cerasella; Drăgulescu, Elena Carmina; Coldea, Ileana Luminiţa; Anton, Liliana; Dobre, Elena; Rovinaru, Camelia; Codiţă, Irina

    2010-01-01

    The currative properties of aromatic and medicinal plants have been recognized since ancient times and, more recently, the antimicrobial activity of plant essential oils has been used in several applications, including food preservation. The purpose of this study was to create directly comparable, quantitative data on the antimicrobial activity of some plant essential oils prepared in the National Institute of Research-Development for Chemistry and Petrochemistry, Bucharest to be used for the further development of food packaging technology, based on their antibacterial and antifungal activity. The essential oils extracted from thyme (Thymus vulgaris L.), basil (Ocimum basilicum L.), coriander (Coriandrum sativum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.), fennel (Foeniculum vulgare L.), spearmint (Mentha spicata L.) and carraway (Carum carvi L.) were investigated for their antimicrobial activity against eleven different bacterial and three fungal strains belonging to species reported to be involved in food poisoning and/or food decay: S. aureus ATCC 25923, S. aureus ATCC 6538, S. aureus ATCC 25913, E. coli ATCC 25922, E. coli ATCC 35218, Salmonella enterica serovar Enteritidis Cantacuzino Institute Culture Collection (CICC) 10878, Listeria monocytogenes ATCC 19112, Bacillus cereus CIP 5127, Bacillus cereus ATCC 11778, Candida albicans ATCC 10231, Aspergillus niger ATCC 16404, Penicillium spp. CICC 251 and two E. coli and Salmonella enterica serovar Enteritidis clinical isolates. The majority of the tested essential oils exibited considerable inhibitory capacity against all the organisms tested, as supported by growth inhibition zone diameters, MICs and MBC's. Thyme, coriander and basil oils proved the best antibacterial activity, while thyme and spearmint oils better inhibited the fungal species. PMID:21462837

  16. A Case Control Study of Bacterial Species and Colony Count in Milk of Breastfeeding Women with Chronic Pain

    PubMed Central

    Mason, Mary Jane; Burgess, Kelly; Flocke, Susan; Zyzanski, Steven

    2014-01-01

    Abstract Background: An infectious etiology for chronic breast pain in breastfeeding women continues to be debated. Although recent data suggest that Staphylococcus aureus and coagulase-negative Staphylococcus (CNS) may cause chronic breast pain, no studies have used quantitative cultures to address this question. In this study we compared bacterial species and colony counts between breastfeeding women with (cases) and without (controls) chronic pain. Subjects and Methods: We enrolled 114 breastfeeding women in a prospective cohort study. Cases (n=61), breastfeeding women with breast pain for >1 week and no signs of acute infection, were matched with controls (n=53) by weeks postpartum and parity. Results: More cases had a history of mastitis (14% vs. 2%, p=0.036), cracked nipples (64% vs. 17%, p=0.001), and other breastfeeding difficulties. Enterobacter species growth was less likely in cases (0% vs. 7.5%, p=0.029). Cases had a significantly higher growth of S. aureus (19.7% vs. 1.9%, p=0.003). CNS frequency was similar between groups (75% vs. 79%, p=0.626), but median colony count growth was significantly lower in cases (900 colony-forming units/mL vs. 5,000 colony-forming units/ml, p=0.003). Growth of CNS and S. aureus was negatively correlated (r=–0.265, p=0.004). Conclusions: Higher S. aureus growth in cases supports a pathogenic role for S. aureus and reinforces the need for future antibiotic treatment studies in breastfeeding women with chronic pain. In contrast, similar CNS frequency between groups, lower CNS colony counts in cases, and a negative correlation between S. aureus and CNS growth suggest that neither CNS, nor its overgrowth, causes chronic breast pain. PMID:23789831

  17. Bacterial Profiling Reveals Novel “Ca. Neoehrlichia”, Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks

    PubMed Central

    Gofton, Alexander W.; Doggett, Stephen; Ratchford, Andrew; Oskam, Charlotte L.; Paparini, Andrea; Ryan, Una; Irwin, Peter

    2015-01-01

    In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279), Amblyomma triguttatum (n = 167), Haemaphysalis bancrofti (n = 7), and H. longicornis (n = 7) ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel “Candidatus Neoehrlichia” spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2%) ticks and a single I. holocyclus (0.6%) tick. Further phylogenetic analysis of novel “Ca. Neoehrlichia”, Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation. PMID:26709826

  18. Monoclonal antibodies specific for Escherichia coli J5 lipopolysaccharide: cross-reaction with other gram-negative bacterial species.

    PubMed Central

    Mutharia, L M; Crockford, G; Bogard, W C; Hancock, R E

    1984-01-01

    Four monoclonal antibodies against Escherichia coli J5 were studied. Each of these monoclonal antibodies reacted with purified lipopolysaccharides from E. coli J5, the deep rough mutant Salmonella minnesota Re595, Agrobacterium tumefaciens, and Pseudomonas aeruginosa PAO1 as well as with the purified lipid A of P. aeruginosa. Enzyme-linked immunosorbent assays using the outer membranes from a variety of gram-negative bacteria demonstrated that these lipid A-specific monoclonal antibodies interacted with between 84 and 97% of the gram-negative bacterial species tested. One of the monoclonal antibodies, 5E4, was shown to interact with 34 of the 35 outer membrane or lipopolysaccharide antigens tested. Immunoenzymatic staining of Western electrophoretic blots of separated P. aeruginosa outer membrane components was used to demonstrate that antibody 5E4 interacted with a similar fast-migrating band, corresponding to rough lipopolysaccharide, from all 17 serotype strains and all 14 clinical isolates of P. aeruginosa. Similarly, iodinated goat anti-mouse immunoglobulin was used to detect the binding of monoclonal antibody 8A1 to a fast-migrating band on Western electrophoretic blots of purified lipopolysaccharides from Klebsiella pneumoniae and both smooth and rough strains of E. coli, Salmonella typhimurium, and S. minnesota. These results suggest considerable conservation of single antigenic sites in the lipid A of gram-negative bacteria. Images PMID:6381310

  19. A Rich Morphological Diversity of Biosaline Drying Patterns Is Generated by Different Bacterial Species, Different Salts and Concentrations: Astrobiological Implications

    NASA Astrophysics Data System (ADS)

    Gómez Gómez, José María; Medina, Jesús; Rull, Fernando

    2016-07-01

    Biosaline formations (BSFs) are complex self-organized biomineral patterns formed by "hibernating" bacteria as the biofilm that contains them dries out. They were initially described in drying biofilms of Escherichia coli cells + NaCl. Due to their intricate 3-D morphology and anhydrobiosis, these biomineralogical structures are of great interest in astrobiology. Here we report experimental data obtained with various alkali halide salts (NaF, NaCl, NaBr, LiCl, KCl, CsCl) on BSF formation with E. coli and Bacillus subtilis bacteria at two saline concentrations: 9 and 18 mg/mL. Our results indicate that, except for LiCl, which is inactive, all the salts assayed are active during BSF formation and capable of promoting the generation of distinctive drying patterns at each salt concentration. Remarkably, the BSFs produced by these two bacterial species produce characteristic architectural hallmarks as the BSF dries. The potential biogenicity of these biosaline drying patterns is studied, and the astrobiological implications of these findings are discussed.

  20. Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels.

    PubMed

    Feng, Shi; Powell, Shane M; Wilson, Richard; Bowman, John P

    2015-09-01

    The extremely psychrophilic proteorhodopsin-containing bacterial species Psychroflexus torquis is considered to be a model sea-ice microorganism, which has adapted to an epiphytic lifestyle. So far, not much is known about proteorhodopsin-based phototrophy and associated life strategies of sea ice bacteria, although it has been previously shown that P. torquis can gain growth advantage from light using a proteorhodopsin proton pump, the activity of which is influenced by environmental salinity. The comprehensive quantitative proteomic study performed here indicated that P. torquis responds to changing salinity and illumination conditions. Proteins in the electron-transfer chain were down-regulated at a suboptimal salinity level, TonB-dependent transporters increased in abundance under supra-optimal salinity and decreased under suboptimal salinity. In addition, several anaplerotic CO2 fixation proteins and three putative light sensing proteins that contain PAS and GAF domains became more abundant under illumination. Furthermore, central metabolic pathways (TCA and glycolysis) were also induced by both salinity stress and illumination. The data suggest that P. torquis responded to changes in both light energy and salinity to modulate membrane and central metabolic proteins that are involved in energy production as well as nutrient uptake and gliding motility processes that would be especially advantageous during the polar summer ice algal bloom.

  1. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain.

    PubMed

    Pascual, Javier; García-López, Marina; Bills, Gerald F; Genilloud, Olga

    2015-02-01

    During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770(T) was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770(T) belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis, P. koreensis, P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770(T) in the genus Pseudomonas. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770(T) ( = DSM 28040(T) = LMG 27940(T)).

  2. Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures

    PubMed Central

    Suryavanshi, Mangesh V.; Bhute, Shrikant S.; Jadhav, Swapnil D.; Bhatia, Manish S.; Gune, Rahul P.; Shouche, Yogesh S.

    2016-01-01

    Hyperoxaluria due to endogenously synthesized and exogenously ingested oxalates is a leading cause of recurrent oxalate stone formations. Even though, humans largely rely on gut microbiota for oxalate homeostasis, hyperoxaluria associated gut microbiota features remain largely unknown. Based on 16S rRNA gene amplicons, targeted metagenomic sequencing of formyl-CoA transferase (frc) gene and qPCR assay, we demonstrate a selective enrichment of Oxalate Metabolizing Bacterial Species (OMBS) in hyperoxaluria condition. Interestingly, higher than usual concentration of oxalate was found inhibitory to many gut microbes, including Oxalobacter formigenes, a well-characterized OMBS. In addition a concomitant enrichment of acid tolerant pathobionts in recurrent stone sufferers is observed. Further, specific enzymes participating in oxalate metabolism are found augmented in stone endures. Additionally, hyperoxaluria driven dysbiosis was found to be associated with oxalate content, stone episodes and colonization pattern of Oxalobacter formigenes. Thus, we rationalize the first in-depth surveillance of OMBS in the human gut and their association with hyperoxaluria. Our findings can be utilized in the treatment of hyperoxaluria associated recurrent stone episodes. PMID:27708409

  3. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.

    PubMed

    Bolaños, Luis M; Rosenblueth, Mónica; Castillo-Ramírez, Santiago; Figuier-Huttin, Gilles; Martínez-Romero, Esperanza

    2016-05-01

    Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species. PMID:26058415

  4. Response in soil of Cupriavidus necator and other copper-resistant bacterial predators of bacteria to addition of water, soluble nutrients, various bacterial species, or Bacillus thuringiensis spores and crystals

    SciTech Connect

    Casida, L.E. Jr. )

    1988-09-01

    Soil was incubated with various species of bacteria, Bacillus subtilis, or Bacillus thuringiensis spores and crystals. These were added to serve as potential prey for indigenous, copper-resistant, nonobligate bacterial predators of bacteria in the soil. Alternatively, the soil was incubated with soluble nutrients or water only to cause potential indigenous prey cells to multiply so the predator cells would multiply. All of these incubation procedures caused excessive multiplication of some gram-negative bacteria in soil. Even greater multiplication, however, often occurred for certain copper-resistant bacterial predators of bacteria that made up a part of the gram-negative response. Incubation of the soil with copper per se did not give these responses. In most cases, the copper-resistant bacteria that responded were Cupriavidus necator, bacterial predator L-2, or previously unknown bacteria that resembled them. The results suggest that, under various conditions of soil incubation, gram-negative bacterial predators of bacteria multiply and that several copper-resistant types among them can be detected, counted, and isolated by plating dilutions of the soil onto media containing excess copper.

  5. Oceanobacillus endoradicis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.

    PubMed

    Yang, Ling-Ling; Tang, Shu-Kun; Chu, Xiao; Jiang, Zhao; Xu, Li-Hua; Zhi, Xiao-Yang

    2016-07-01

    A bacterial strain, py1294(T), isolated from a root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, southwest China, was characterised by using a polyphasic approach to clarify its taxonomic position. Strain py1294(T) was found to be Gram-positive, aerobic, spore-forming, peritrichous flagella and rod shaped. Growth was found to occur in the presence of 0-8 % (w/v) NaCl (optimum 1-3 %), at pH 6.5-9.5 (optimum 8.0) and at 10-42 °C (optimum 30 °C). The major cellular fatty acids were identified as anteiso-C15:0, anteiso-C17:0, iso-C16:0 and iso-C14:0. The predominant quinone was identified as MK-7 and a minor amount of MK-6 was detected. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain py1294(T) forms a well-supported clade with Oceanobacillus damuensis PT-20(T) (97.9 % sequence similarity) within the genus Oceanobacillus, although it also shares a high sequence similarity with Ornithinibacillus contaminans (97.5 %). Crucially, the DNA-DNA relatedness value between strain py1294(T) and O. damuensis PT-20(T) was 29.7 ± 3.2 %. The G+C content was determined to be 42.3 mol%. On the basis of the phylogenetic and phenotypic data, a novel species Oceanobacillus endoradicis sp. nov. is proposed, with py1294(T) (=DSM 100726(T) = KCTC 33731(T)) as the type strain. PMID:27059624

  6. Solving the supply of resveratrol tetramers from Papua New Guinean rainforest anisoptera species that inhibit bacterial type III secretion systems.

    PubMed

    Davis, Rohan A; Beattie, Karren D; Xu, Min; Yang, Xinzhou; Yin, Sheng; Holla, Harish; Healy, Peter C; Sykes, Melissa; Shelper, Todd; Avery, Vicky M; Elofsson, Mikael; Sundin, Charlotta; Quinn, Ronald J

    2014-12-26

    The supply of (-)-hopeaphenol (1) was achieved via enzymatic biotransformation in order to provide material for preclinical investigation. High-throughput screening of a prefractionated natural product library aimed to identify compounds that inhibit the bacterial virulence type III secretion system (T3SS) identified several fractions derived from two Papua New Guinean Anisoptera species, showing activity against Yersinia pseudotuberculosis outer proteins E and H (YopE and YopH). Bioassay-directed isolation from the leaves of A. thurifera, and similarly A. polyandra, resulted in three known resveratrol tetramers, (-)-hopeaphenol (1), vatalbinoside A (2), and vaticanol B (3). Compounds 1-3 displayed IC50 values of 8.8, 12.5, and 9.9 μM in a luminescent reporter-gene assay (YopE) and IC50 values of 2.9, 4.5, and 3.3 μM in an enzyme-based YopH assay, respectively, which suggested that they could potentially act against the T3SS in Yersinia. The structures of 1-3 were confirmed through a combination of spectrometric, chemical methods, and single-crystal X-ray structure determinations of the natural product 1 and the permethyl ether analogue of 3. The enzymatic hydrolysis of the β-glycoside 2 to the aglycone 1 was achieved through biotransformation using the endogenous leaf enzymes. This significantly enhanced the yield of the target bioactive natural product from 0.08% to 1.3% and facilitates ADMET studies of (-)-hopeaphenol (1).

  7. Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India.

    PubMed

    Jeyaram, K; Romi, W; Singh, Th Anand; Devi, A Ranjita; Devi, S Soni

    2010-09-30

    Soidon is a non-salted acidic fermented food prepared from the succulent bamboo shoot tip of Schizostachyum capitatum Munro by using a traditional liquid starter called "soidon mahi" in Manipur state of India. In this study, 163 bacterial isolates associated with this starter samples were identified and their population distribution was investigated by amplified ribosomal DNA restriction analysis (ARDRA), 16S rDNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. This acidic starter (pH 4.5+/-0.15) was dominated by a characteristic association of Bacillus and lactic acid bacteria (LAB) together. The population distribution of dominant species were Bacillus subtilis 29.3%, Bacillus cereus 35.7%, Bacillus pumilus 2.6%, Lactobacillus brevis 9.6%, Lactobacillus plantarum 5.1%, Carnobacterium sp. 11.9%, Enterococcus faecium 1.2% and Pseudomonas fluorescens 4.6%. Alarming population load (10(6)-10(7)cfu/ml) of B. cereus in 87% of starter samples studied should raise concern regarding biosafety of soidon consumption. PCR amplification of 16S-23S rDNA intergenic transcribed spacer (ITS) region and ITS-RFLP profiles revealed a high diversity with eight subgroups in B. subtilis, five subgroups in B. cereus and three subgroups in L. brevis isolates. The most abundant B. subtilis subgroup IB.1 distributed in most of the samples showed very less clonal variability during RAPD analysis. The molecular methods used in this study identified the dominant strains of Bacillus and LAB distributed in most of the starter samples. These dominant strains of B. subtilis, L. brevis and L. plantarum would allow for developing a defined starter culture for the production of quality soidon.

  8. The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp.

    PubMed Central

    Vilanova, Cristina; Baixeras, Joaquín; Latorre, Amparo; Porcar, Manuel

    2016-01-01

    Some specialist insects feed on plants rich in secondary compounds, which pose a major selective pressure on both the phytophagous and the gut microbiota. However, microbial communities of toxic plant feeders are still poorly characterized. Here, we show the bacterial communities of the gut of two specialized Lepidoptera, Hyles euphorbiae and Brithys crini, which exclusively feed on latex-rich Euphorbia sp. and alkaloid-rich Pancratium maritimum, respectively. A metagenomic analysis based on high-throughput sequencing of the 16S rRNA gene revealed that the gut microbiota of both insects is dominated by the phylum Firmicutes, and especially by the common gut inhabitant Enterococcus sp. Staphylococcus sp. are also found in H. euphorbiae though to a lesser extent. By scanning electron microscopy, we found a dense ring-shaped bacterial biofilm in the hindgut of H. euphorbiae, and identified the most prominent bacterium in the biofilm as Enterococcus casseliflavus through molecular techniques. Interestingly, this species has previously been reported to contribute to the immobilization of latex-like molecules in the larvae of Spodoptera litura, a highly polyphagous lepidopteran. The E. casseliflavus strain was isolated from the gut and its ability to tolerate natural latex was tested under laboratory conditions. This fact, along with the identification of less frequent bacterial species able to degrade alkaloids and/or latex, suggest a putative role of bacterial communities in the tolerance of specialized insects to their toxic diet. PMID:27446044

  9. Identification and characterization of Clostridium paraputrificum M-21, a chitinolytic, mesophilic and hydrogen-producing bacterium.

    PubMed

    Evvyernie, D; Yamazaki, S; Morimoto, K; Karita, S; Kimura, T; Sakka, K; Ohmiya, K

    2000-01-01

    A strictly anaerobic, mesophilic and chitinolytic bacterial strain, M-21, was isolated from a soil sample collected from Mie University campus and identified as Clostridium paraputrificum based on morphological and physiological characteristics, and 16S rRNA sequence analysis. C. paraputrificum M-21 utilized chitin and N-acetyl-D-glucosamine (GlcNAc), a constituent monosaccharide of chitin, to produce a large amount of gas along with acetic acid and propionic acid as major fermentation products. Hydrogen and carbon dioxide accounted for 65% and 35% of the gas evolved, respectively. The conditions for 1 l batch culture of C. paraputrificum, including pH of the medium, incubation temperature and agitation speed, were optimized for hydrogen production with GlcNAc as the carbon source. The bacterium grew rapidly on GlcNAc with a doubling time of around 30 min, and produced hydrogen gas with a yield of 1.9 mol H2/mol GlcNAc under the following cultivation conditions: initial medium pH of 6.5, incubation temperature of 45 degrees C, agitation speed of 250 rpm, and working volume of 50% of the fermentor. The dry cell weight harvested from this culture was 2.0 g/l.

  10. Anaerobic mesophilic treatment of cattle manure in an upflow anaerobic sludge blanket reactor with prior pasteurization.

    PubMed

    Marañón, Elena; Castrillón, Leonor; Fernández, Juan José; Fernández, Yolanda; Peláez, Ana Isabel; Sánchez, Jesús

    2006-02-01

    Different autonomous communities located in northern Spain have large populations of dairy cattle. In the case of Asturias, the greatest concentration of dairy farms is found in the areas near the coast, where the elimination of cattle manure by means of its use as a fertilizer may lead to environmental problems. The aim of the present research work was to study the anaerobic treatment of the liquid fraction of cattle manure at mesophilic temperature using an upflow anaerobic sludge blanket (UASB) reactor combined with a settler after a pasteurization process at 70 degrees C for 2 hr. The manure used in this study came from two different farms, with 40 and 200 cows, respectively. The manure from the smaller farm was pretreated in the laboratory by filtration through a 1-mm mesh, and the manure from the other farm was pretreated on the farm by filtration through a separator screw press (0.5-mm mesh). The pasteurization process removed the pathogenic microorganisms lacking spores, such as Enterococcus, Yersinia, Pseudomonas, and coliforms, but bacterial spores are only reduced by this treatment, not removed. The combination of a UASB reactor and a settler proved to be effective for the treatment of cattle manure. In spite of the variation in the organic loading rate and total solids in the influent during the experiment, the chemical oxygen demand (COD) of the effluent from the settler remained relatively constant, obtaining reductions in the COD of approximately 85%.

  11. Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.).

    PubMed

    Trébaol, G; Gardan, L; Manceau, C; Tanguy, J L; Tirilly, Y; Boury, S

    2000-07-01

    A bacterial disease of artichoke (Cynara scolymus L.) was first observed in 1954 in Brittany and the Loire Valley, France. This disease causes water-soaked spots on bracts and depreciates marketability of the harvest. Ten strains of the pathogen causing bacterial spot of artichoke, previously identified as a member of the genus Xanthomonas, were characterized and compared with type and pathotype strains of the 20 Xanthomonas species using a polyphasic study including both phenotypic and genomic methods. The ten strains presented general morphological, biochemical and physiological traits and G+C content characteristic of the genus Xanthomonas. Sequencing of the 165 rRNA gene confirmed that this bacterium belongs to the genus Xanthomonas, and more precisely to the Xanthomonas campestris core. DNA-DNA hybridization results showed that the strains that cause bacterial spot of artichoke were 92-100% related to the proposed type strain CFBP 4188T and constituted a discrete DNA homology group that was distinct from the 20 previously described Xanthomonas species. The results of numerical analysis were in accordance with DNA-DNA hybridization data. Strains causing the bacterial bract spot of artichoke exhibited consistent determinative biochemical characteristics, which distinguished them from the 20 other Xanthomonas species previously described. Furthermore, pathogenicity tests allowed specific identification of this new phytopathogenic bacterium. Thus, it is concluded that this bacterium is a new species belonging to the genus Xanthomonas, for which the name Xanthomonas cynarae is proposed. The type strain, CFBP 4188T, has been deposited in the Collection Française des Bactéries Phytopathogènes (CFBP).

  12. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

    PubMed

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K E; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

  13. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

    PubMed

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K E; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes. PMID

  14. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

    PubMed Central

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K. E.; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes

  15. Mesophilic Actinomycetes in the natural and reconstructed sand dune vegetation zones of Fraser Island, Australia.

    PubMed

    Kurtböke, D I; Neller, R J; Bellgard, S E

    2007-08-01

    The natural coastal habitat of Fraser Island located in the State of Queensland, Australia, has been disturbed in the past for mining of the mineral sand ilmenite. Currently, there is no information available on whether these past mining disturbances have affected the distribution, diversity, and survival of beneficial soil microorganisms in the sand dunes of the island. This in turn could deleteriously affect the success of the natural regeneration, plant growth, and establishment on the sand dunes. To support ongoing restoration efforts at sites like these mesophilic actinomycetes were isolated using conventional techniques, with particular emphasis on the taxa previously reported to produce plant-growth-promoting substances and providing support to mycorrhizal fungi, were studied at disturbed sites and compared with natural sites. In the natural sites, foredunes contained higher densities of micromonosporae replaced by increasing numbers of streptomycete species in the successional dune and finally leading to complex actinomycete communities in the mature hind dunes. Whereas in the disturbed zones affected by previous mining activities, which are currently being rehabilitated, no culturable actinomycete communities were detected. These findings suggest that the paucity of beneficial microflora in the rehabilitated sand dunes may be limiting the successful colonization by pioneer plant species. Failure to establish a cover of plant species would result in the mature hind dune plants being exposed to harsh salt and climatic conditions. This could exacerbate the incidence of wind erosion, resulting in the destabilization of well-defined and vegetated successional dunal zones.

  16. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    PubMed

    Davis, Ian J; Wallis, Corrin; Deusch, Oliver; Colyer, Alison; Milella, Lisa; Loman, Nick; Harris, Stephen

    2013-01-01

    Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss). In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease. PMID:24349448

  17. Population density profiles of nasopharyngeal carriage of 5 bacterial species in pre-school children measured using quantitative PCR offer potential insights into the dynamics of transmission

    PubMed Central

    Thors, Valtyr; Morales-Aza, Begonia; Pidwill, Grace; Vipond, Ian; Muir, Peter; Finn, Adam

    2016-01-01

    Bacterial vaccines can reduce carriage rates. Colonization is usually a binary endpoint. Real time quantitative PCR (qPCR) can quantify bacterial DNA in mucosal samples over a wide range. Using culture and single-gene species-specific qPCRs for Streptococcus pneumoniae (lytA), Streptococcus pyogenes (ntpC), Moraxella catarrhalis (ompJ), Haemophilus influenzae (hdp) and Staphylococcus aureus (nuc) and standard curves against log-phase reference strain broth cultures we described frequency and peak density distributions of carriage in nasopharyngeal swabs from 161 healthy 2–4 y old children collected into STGG broth. In general, detection by qPCR and culture was consistent. Discordance mostly occurred at lower detection thresholds of both methods, although PCR assays for S. pyogenes and S. aureus were less sensitive. Density varied across 5-7 orders of magnitude for the 5 species with the abundant species skewed toward high values (modes: S. pneumoniae log3-4, M. catarrhalis & H. influenzae log4-5 CFU/ml broth). Wide ranges of bacterial DNA concentrations in healthy children carrying these bacteria could mean that different individuals at different times vary greatly in infectiousness. Understanding the host, microbial and environmental determinants of colonization density will permit more accurate prediction of vaccine effectiveness. PMID:26367344

  18. Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

    PubMed Central

    Xu, Wenjing; Shi, Lingling; Chan, Onchim; Li, Jiao; Casper, Peter; Zou, Xiaoming

    2013-01-01

    Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well. PMID:24367682

  19. Population density profiles of nasopharyngeal carriage of 5 bacterial species in pre-school children measured using quantitative PCR offer potential insights into the dynamics of transmission.

    PubMed

    Thors, Valtyr; Morales-Aza, Begonia; Pidwill, Grace; Vipond, Ian; Muir, Peter; Finn, Adam

    2016-01-01

    Bacterial vaccines can reduce carriage rates. Colonization is usually a binary endpoint. Real time quantitative PCR (qPCR) can quantify bacterial DNA in mucosal samples over a wide range. Using culture and single-gene species-specific qPCRs for Streptococcus pneumoniae (lytA), Streptococcus pyogenes (ntpC), Moraxella catarrhalis (ompJ), Haemophilus influenzae (hdp) and Staphylococcus aureus (nuc) and standard curves against log-phase reference strain broth cultures we described frequency and peak density distributions of carriage in nasopharyngeal swabs from 161 healthy 2-4 y old children collected into STGG broth. In general, detection by qPCR and culture was consistent. Discordance mostly occurred at lower detection thresholds of both methods, although PCR assays for S. pyogenes and S. aureus were less sensitive. Density varied across 5-7 orders of magnitude for the 5 species with the abundant species skewed toward high values (modes: S. pneumoniae log3-4, M. catarrhalis & H. influenzae log4-5 CFU/ml broth). Wide ranges of bacterial DNA concentrations in healthy children carrying these bacteria could mean that different individuals at different times vary greatly in infectiousness. Understanding the host, microbial and environmental determinants of colonization density will permit more accurate prediction of vaccine effectiveness.

  20. Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

    PubMed Central

    Adams, Heather E.; Crump, Byron C.; Kling, George W.

    2014-01-01

    To understand mechanisms linking ecosystem processes and microbial diversity in freshwater ecosystems, bacterial productivity and the metacommunity dynamics of species sorting and mass effects were investigated in an 18 ha headwater lake in northern Alaska. On most sampling dates, the phylogenetic composition of bacterial communities in inflowing streams (inlets) was strikingly different than that in the lake and the outflowing stream (outlet) (16S DGGE fingerprinting), demonstrating the shift in composition that occurs as these communities transit the lake. Outlet and downstream communities were also more productive than inlet and upstream communities (14C-leucine incorporation). Inlet bacteria transplanted to the outlet stream in dialysis bags were equally or less productive than control bacteria, suggesting that the inlet bacteria are capable of growing under lake conditions, but do not remain abundant because of species sorting in the lake. Outlet bacteria (representative of epilimnetic bacteria) transplanted to the inlet stream were less productive than control bacteria, suggesting that lake bacteria are not as well adapted to growing under inlet conditions. Based on water density, inlet stream water and bacteria generally entered the lake at the base of the epilimnion. However, during low to medium flow in the inlet stream the residence time of the epilimnion was too long relative to bacterial doubling times for these allochthonous bacteria to have a mass effect on the composition of outlet bacteria. The highest community similarity between inlet and outlet bacteria was detected after a large rain event in 2003, with over 61% similarity (average non-storm similarities were 39 ± 8%). While mass effects may be important during large storm events, species sorting appears to be the predominant mechanism structuring bacterial communities within the lake, leading to the assembly of a lake community that has lost some ability to function in stream habitats. PMID

  1. Identification of airborne bacterial and fungal species in the clinical microbiology laboratory of a university teaching hospital employing ribosomal DNA (rDNA) PCR and gene sequencing techniques.

    PubMed

    Nagano, Yuriko; Walker, Jim; Loughrey, Anne; Millar, Cherie; Goldsmith, Colin; Rooney, Paul; Elborn, Stuart; Moore, John

    2009-06-01

    Universal or "broad-range" PCR-based ribosomal DNA (rDNA) was performed on a collection of 58 isolates (n = 30 bacteria + 28 fungi), originating from environmental air from several locations within a busy clinical microbiology laboratory, supporting a university teaching hospital. A total of 10 bacterial genera were identified including both Gram-positive and Gram-negative genera. Gram-positive organisms accounted for 27/30 (90%) of total bacterial species, consisting of seven genera and included (in descending order of frequency) Staphylococcus, Micrococcus, Corynebacterium, Paenibacillus, Arthrobacter, Janibacter and Rothia. Gram-negative organisms were less frequently isolated 3/30 (10%) and comprised three genera, including Moraxella, Psychrobacter and Haloanella. Eight fungal genera were identified among the 28 fungal organisms isolated, including (in descending order of frequency) Cladosporium, Penicillium, Aspergillus, Thanatephorus, Absidia, Eurotium, Paraphaeosphaeria and Tritirachium, with Cladosporium accounting for 10/28 (35.7%) of the total fungal isolates. In conclusion, this study identified the presence of 10 bacterial and eight fungal genera in the air within the laboratory sampled. Although this reflected diversity of the microorganisms present, none of these organisms have been described previously as having an inhalational route of laboratory-acquired infection. Therefore, we believe that the species of organisms identified and the concentration levels of these airborne contaminants determined, do not pose a significant health and safety threat for immunocompotent laboratory personnel and visitors. PMID:20183192

  2. Evaluation of the bacterial microbiome of two flea species using different DNA-isolation techniques provides insights into flea host ecology.

    PubMed

    Lawrence, Andrea L; Hii, Sze-Fui; Chong, Rowena; Webb, Cameron E; Traub, Rebecca; Brown, Graeme; Šlapeta, Jan

    2015-12-01

    Fleas (Siphonaptera) are ubiquitous blood-sucking pests of animals worldwide and are vectors of zoonotic bacteria such as Rickettsia and Bartonella. We performed Ion Torrent PGM amplicon sequencing for the bacterial 16S rRNA gene to compare the microbiome of the ubiquitous cat flea (Ctenocephalides f. felis) and the host-specific echidna stickfast flea (Echidnophaga a. ambulans) and evaluated potential bias produced during common genomic DNA-isolation methods. We demonstrated significant differences in the bacterial community diversity between the two flea species but not between protocols combining surface sterilisation with whole flea homogenisation or exoskeleton retention. Both flea species were dominated by obligate intracellular endosymbiont Wolbachia, and the echidna stickfast fleas possessed the endosymbiont Cardinium. Cat fleas that were not surface sterilised showed presence of Candidatus 'Rickettsia senegalensis' DNA, the first report of its presence in Australia. In the case of Rickettsia, we show that sequencing depth of 50 000 was required for comparable sensitivity with Rickettsia qPCR. Low-abundance bacterial genera are suggested to reflect host ecology. The deep-sequencing approach demonstrates feasibility of pathogen detection with simultaneous quantitative analysis and evaluation of the inter-relationship of microbes within vectors. PMID:26542076

  3. Isolation and identification of a new tetrodotoxin-producing bacterial species, Raoultella terrigena, from Hong Kong marine puffer fish Takifugu niphobles.

    PubMed

    Yu, Vincent Chung-Him; Yu, Peter Hoi-Fu; Ho, Kin-Chung; Lee, Fred Wang-Fat

    2011-01-01

    Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF). Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  4. Isolation and Identification of a New Tetrodotoxin-Producing Bacterial Species, Raoultella terrigena, from Hong Kong Marine Puffer Fish Takifugu niphobles

    PubMed Central

    Yu, Vincent Chung-Him; Yu, Peter Hoi-Fu; Ho, Kin-Chung; Lee, Fred Wang-Fat

    2011-01-01

    Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF). Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species. PMID:22163191

  5. Unifying mechanism for bacterial cell signalers (4,5-dihydroxy-2,3-pentanedione, lactones and oligopeptides): electron transfer and reactive oxygen species. Practical medical features.

    PubMed

    Kovacic, Peter

    2007-01-01

    Cell signaling has attracted much attention involving higher organisms, and more recently is of considerable interest concerning involvement in the bacterial realm. Many aspects can apply, including quorum sensing. Of the participating molecules, designated autoinducers, 4,5-dihydroxy-2,3-pentanedione (DPD) is one of the most important. It is in equilibrium with a furanone and a furanosyl-borate diester (AI-2). A prior hypothesis for cell signaling in higher organisms invoked a key role for electron transfer (ET) and reactive oxygen species (ROS), as well as conduits, relays and electrical effects. The principal ET functionalities are quinones, metal complexes, ArNO(2), and iminium species. A lesser known type is the alpha-dicarbonyl class. Diacetyl, a member, as well as its imine derivatives, can serve as a model for DPD, since the parent possesses a reduction potential amenable to ET in the biological domain. Hence, it is conceivable that DPD and its imine derivatives may be involved in ET-ROS processes. Presence of hydroxy groups should facilitate ET by DPD vs. diacetyl. Extensive prior literature supports participation of ET functionalities in action of therapeutic drugs, toxins and various illnesses. This biochemical behavior also applies to the alpha-dicarbonyl parent models. A second important bacterial autoinducer is the lactone category. Although ET functionality is lacking, the presence of the 1,3-dicarbonyl structure can provide a site for avid chelation with redox metal, e.g., iron or copper, followed by ET-ROS. Findings with added iron furnish support for the proposal. Oligopeptides comprise the third principal type of bacterial signaling agent. A prior review incorporates these within the theoretical framework based on ET by redox amino acids and redox enzymes. In recent years there has been a rapid increase in resistance to antibiotics by pathogenic bacteria. Infectious diseases are the leading cause of death worldwide and the third leading cause in

  6. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

    PubMed Central

    Frappier, Vincent; Najmanovich, Rafael

    2015-01-01

    We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering. PMID:25367089

  7. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering.

    PubMed

    Frappier, Vincent; Najmanovich, Rafael

    2015-04-01

    We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering.

  8. The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?

    PubMed

    Zeigler, Daniel R

    2014-01-01

    The genus Geobacillus comprises endospore-forming obligate thermophiles. These bacteria have been isolated from cool soils and even cold ocean sediments in anomalously high numbers, given that the ambient temperatures are significantly below their minimum requirement for growth. Geobacilli are active in environments such as hot plant composts, however, and examination of their genome sequences reveals that they are endowed with a battery of sensors, transporters and enzymes dedicated to hydrolysing plant polysaccharides. Although they appear to be relatively minor members of the plant biomass-degrading microbial community, Geobacillus bacteria have achieved a significant population with a worldwide distribution, probably in large part due to adaptive features of their spores. First, their morphology and resistance properties enable them to be mobilized in the atmosphere and transported long distances. Second, their longevity, which in theory may be extreme, enables them to lie quiescent but viable for long periods of time, accumulating gradually over time to achieve surprisingly high population densities.

  9. Characterization of culturable vaginal Lactobacillus species among women with and without bacterial vaginosis from the United States and India: a cross-sectional study.

    PubMed

    Madhivanan, Purnima; Raphael, Eva; Rumphs, Alnecia; Krupp, Karl; Ravi, Kavitha; Srinivas, Vijaya; Arun, Anjali; Reingold, Arthur L; Klausner, Jeffrey D; Riley, Lee W

    2014-07-01

    Lactobacillus species play an integral part in the health of the vaginal microbiota. We compared vaginal Lactobacillus species in women from India and the USA with and without bacterial vaginosis (BV). Between July 2009 and November 2010, a cross-sectional study was conducted among 40 women attending a women's health clinic in Mysore, India, and a sexually transmitted diseases clinic in San Francisco, USA. Women were diagnosed with BV using Amsel's criteria and the Nugent score. Lactobacillus 16S rDNA was sequenced to speciate the cultured isolates. Ten Indian and 10 US women without BV were compared with an equal number of women with BV. Lactobacilli were isolated from all healthy women, but from only 10% of Indian and 50% of US women with BV. 16S rDNA from 164 Lactobacillus colonies was sequenced from healthy women (126 colonies) and women with BV (38 colonies). Seven cultivable Lactobacillus species were isolated from 11 Indian women and nine species from 15 US women. The majority of Lactobacillus species among Indian women were L. crispatus (25.0%), L. jensenii (25.0%) and L. reuteri (16.7%). Among US women, L. crispatus (32.0%), L. jensenii (20.0%) and L. coleohominis (12.0%) predominated. L. jensenii and L. crispatus dominated the vaginal flora of healthy Indian and US women. Indian women appeared to have a higher percentage of obligate heterofermentative species, suggesting the need for a larger degree of metabolic flexibility and a more challenging vaginal environment.

  10. Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation.

    PubMed

    Wang, Yubo; Xia, Yu; Ju, Feng; Zhang, Tong

    2015-12-01

    Improvement on the bioconversion of cellulosic biomass depends much on the expanded knowledge on the underlying microbial structure and the relevant genetic information. In this study, metagenomic analysis was applied to characterize an enriched mesophilic cellulose-converting consortium, to explore its cellulose-hydrolyzing genes, and to discern genes involved in methanogenesis. Cellulose conversion efficiency of the mesophilic consortium enriched in this study was around 70 %. Apart from methane, acetate was the major fermentation product in the liquid phase, while propionate and butyrate were also detected at relatively high concentrations. With the intention to uncover the biological factors that might shape the varying cellulose conversion efficiency at different temperatures, results of this mesophilic consortium were then compared with that of a previously reported thermophilic cellulose-converting consortium. It was found that the mesophilic consortium harbored a larger pool of putative carbohydrate-active genes, with 813 of them in 54 GH modules and 607 genes in 13 CBM modules. Methanobacteriaceae and Methanosaetaceae were the two methanogen families identified, with a preponderance of the hydrogenotrophic Methanobacteriaceae. In contrast to its relatively high diversity and high abundance of carbohydrate-active genes, the abundance of genes involved in the methane metabolism was comparatively lower in the mesophilic consortium. A biological enhancement on the methanogenic process might serve as an effective option for the improvement of the cellulose bioconversion at mesophilic temperature. PMID:26359182

  11. Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation.

    PubMed

    Wang, Yubo; Xia, Yu; Ju, Feng; Zhang, Tong

    2015-12-01

    Improvement on the bioconversion of cellulosic biomass depends much on the expanded knowledge on the underlying microbial structure and the relevant genetic information. In this study, metagenomic analysis was applied to characterize an enriched mesophilic cellulose-converting consortium, to explore its cellulose-hydrolyzing genes, and to discern genes involved in methanogenesis. Cellulose conversion efficiency of the mesophilic consortium enriched in this study was around 70 %. Apart from methane, acetate was the major fermentation product in the liquid phase, while propionate and butyrate were also detected at relatively high concentrations. With the intention to uncover the biological factors that might shape the varying cellulose conversion efficiency at different temperatures, results of this mesophilic consortium were then compared with that of a previously reported thermophilic cellulose-converting consortium. It was found that the mesophilic consortium harbored a larger pool of putative carbohydrate-active genes, with 813 of them in 54 GH modules and 607 genes in 13 CBM modules. Methanobacteriaceae and Methanosaetaceae were the two methanogen families identified, with a preponderance of the hydrogenotrophic Methanobacteriaceae. In contrast to its relatively high diversity and high abundance of carbohydrate-active genes, the abundance of genes involved in the methane metabolism was comparatively lower in the mesophilic consortium. A biological enhancement on the methanogenic process might serve as an effective option for the improvement of the cellulose bioconversion at mesophilic temperature.

  12. Rapid establishment of thermophilic anaerobic microbial community during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester.

    PubMed

    Tian, Zhe; Zhang, Yu; Li, Yuyou; Chi, Yongzhi; Yang, Min

    2015-02-01

    The purpose of this study was to explore how fast the thermophilic anaerobic microbial community could be established during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester. Stable thermophilic anaerobic digestion was achieved within 20 days from a mesophilic digester treating sewage sludge by adopting the one-step startup strategy. The succession of archaeal and bacterial populations over a period of 60 days after the temperature increment was followed by using 454-pyrosequencing and quantitative PCR. After the increase of temperature, thermophilic methanogenic community was established within 11 days, which was characterized by the fast colonization of Methanosarcina thermophila and two hydrogenotrophic methanogens (Methanothermobacter spp. and Methanoculleus spp.). At the same time, the bacterial community was dominated by Fervidobacterium, whose relative abundance rapidly increased from 0 to 28.52 % in 18 days, followed by other potential thermophilic genera, such as Clostridium, Coprothermobacter, Anaerobaculum and EM3. The above result demonstrated that the one-step startup strategy could allow the rapid establishment of the thermophilic anaerobic microbial community.

  13. Conversion of cellulose to ethanol by mesophilic bacteria. Progress report and second year budget

    SciTech Connect

    Canale-Parola, E.

    1981-11-27

    Eight strains of anaerobic mesophilic cellulolytic bacteria were isolated from the mud of a freshwater pond and swamp. The isolation procedure involved serial dilution of the mud into cellulose-containing agar media. The isolates were rod-shaped and formed terminal, spherical to oval spores that swelled the sporangium. All strains fermented cellulose producing primarily ethanol, acetate, CO/sub 2/, and H/sub 2/. Growth and cellulose fermentation occurred between 22/sup 0/ and 40/sup 0/C, but not at 15/sup 0/ and 45/sup 0/C. The isolates differed from thermophilic cellulolytic clostridia not only in growth temperature range, but also because they fermented five-carbon products of plant polysaccharide hydrolysis, such as D-xylose and L-arabinose. Other fermentable substrates included xylan, D-glucose, cellobiose and, for three strains, D-galactose. None of the strains utilized maltose, sucrose, D-galacturonate, or amino acids as growth substrates. All isolates had a Gram-negative reaction and were motile by means of peritrichous flagella. The substrate utilization characteristics and the growth temperature range of the isolates indicate that these bacteria contribute to the anaerobic degradation of plant materials in the environments they inhabit. The isolates apparently represent a previously undescribed species of free-living cellulolytic clostridia.

  14. Enrichment of acetogenic bacteria in high rate anaerobic reactors under mesophilic and thermophilic conditions.

    PubMed

    Ryan, P; Forbes, C; McHugh, S; O'Reilly, C; Fleming, G T A; Colleran, E

    2010-07-01

    The objective of the current study was to expand the knowledge of the role of acetogenic Bacteria in high rate anaerobic digesters. To this end, acetogens were enriched by supplying a variety of acetogenic growth supportive substrates to two laboratory scale high rate upflow anaerobic sludge bed (UASB) reactors operated at 37 degrees C (R1) and 55 degrees C (R2). The reactors were initially fed a glucose/acetate influent. Having achieved high operational performance and granular sludge development and activity, both reactors were changed to homoacetogenic bacterial substrates on day 373 of the trial. The reactors were initially fed with sodium vanillate as a sole substrate. Although % COD removal indicated that the 55 degrees C reactor out performed the 37 degrees C reactor, effluent acetate levels from R2 were generally higher than from R1, reaching values as high as 5023 mg l(-1). Homoacetogenic activity in both reactors was confirmed on day 419 by specific acetogenic activity (SAA) measurement, with higher values obtained for R2 than R1. Sodium formate was introduced as sole substrate to both reactors on day 464. It was found that formate supported acetogenic activity at both temperatures. By the end of the trial, no specific methanogenic activity (SMA) was observed against acetate and propionate indicating that the methane produced was solely by hydrogenotrophic Archaea. Higher SMA and SAA values against H(2)/CO(2) suggested development of a formate utilising acetogenic population growing in syntrophy with hydrogenotrophic methanogens. Throughout the formate trial, the mesophilic reactor performed better overall than the thermophilic reactor.

  15. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

    PubMed

    Yu, D; Kurola, J M; Lähde, K; Kymäläinen, M; Sinkkonen, A; Romantschuk, M

    2014-10-01

    Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

  16. Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan.

    PubMed

    Green-Saxena, A; Feyzullayev, A; Hubert, C R J; Kallmeyer, J; Krueger, M; Sauer, P; Schulz, H-M; Orphan, V J

    2012-12-01

    Terrestrial mud volcanoes (TMVs) represent geochemically diverse habitats with varying sulfur sources and yet sulfur cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in four TMVs in Azerbaijan. A combination of geochemical analyses, biological rate measurements and molecular diversity surveys (targeting metabolic genes aprA and dsrA and SSU ribosomal RNA) supported the presence of active sulfur-oxidizing and sulfate-reducing guilds in all four TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. The TMVs varied in potential sulfate reduction rates (SRR) by up to four orders of magnitude with highest SRR observed in sediments where in situ sulfate concentrations were highest. Maximum temperatures at which SRR were measured was 60°C in two TMVs. Corresponding with these trends in SRR, members of the potentially thermophilic, spore-forming, Desulfotomaculum were detected in these TMVs by targeted 16S rRNA analysis. Additional sulfate-reducing bacterial lineages included members of the Desulfobacteraceae and Desulfobulbaceae detected by aprA and dsrA analyses and likely contributing to the mesophilic SRR measured. Phylotypes affiliated with sulfide-oxidizing Gamma- and Betaproteobacteria were abundant in aprA libraries from low sulfate TMVs, while the highest sulfate TMV harboured 16S rRNA phylotypes associated with sulfur-oxidizing Epsilonproteobacteria. Altogether, the biogeochemical and microbiological data indicate these unique terrestrial habitats support diverse active sulfur-cycling microorganisms reflecting the in situ geochemical environment.

  17. Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan.

    PubMed

    Green-Saxena, A; Feyzullayev, A; Hubert, C R J; Kallmeyer, J; Krueger, M; Sauer, P; Schulz, H-M; Orphan, V J

    2012-12-01

    Terrestrial mud volcanoes (TMVs) represent geochemically diverse habitats with varying sulfur sources and yet sulfur cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in four TMVs in Azerbaijan. A combination of geochemical analyses, biological rate measurements and molecular diversity surveys (targeting metabolic genes aprA and dsrA and SSU ribosomal RNA) supported the presence of active sulfur-oxidizing and sulfate-reducing guilds in all four TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. The TMVs varied in potential sulfate reduction rates (SRR) by up to four orders of magnitude with highest SRR observed in sediments where in situ sulfate concentrations were highest. Maximum temperatures at which SRR were measured was 60°C in two TMVs. Corresponding with these trends in SRR, members of the potentially thermophilic, spore-forming, Desulfotomaculum were detected in these TMVs by targeted 16S rRNA analysis. Additional sulfate-reducing bacterial lineages included members of the Desulfobacteraceae and Desulfobulbaceae detected by aprA and dsrA analyses and likely contributing to the mesophilic SRR measured. Phylotypes affiliated with sulfide-oxidizing Gamma- and Betaproteobacteria were abundant in aprA libraries from low sulfate TMVs, while the highest sulfate TMV harboured 16S rRNA phylotypes associated with sulfur-oxidizing Epsilonproteobacteria. Altogether, the biogeochemical and microbiological data indicate these unique terrestrial habitats support diverse active sulfur-cycling microorganisms reflecting the in situ geochemical environment. PMID:23116231

  18. Impact of fluorochrome stains used to study bacterial transport in shallow aquifers on motility and chemotaxis of Pseudomonas species.

    PubMed

    Toepfer, J Amanda; Ford, Roseanne M; Metge, David; Harvey, Ronald W

    2012-07-01

    One of the most common methods of tracking movement of bacteria in groundwater environments involves a priori fluorescent staining. A major concern in using these stains to label bacteria in subsurface injection-and-recovery studies is the effect they may have on the bacterium's transport properties. Previous studies investigated the impact of fluorophores on bacterial surface properties (e.g. zeta potential). However, no previous study has looked at the impact of fluorescent staining on swimming speed and chemotaxis. It was found that DAPI lowered the mean population swimming speed of Pseudomonas putida F1 by 46% and Pseudomonas stutzeri by 55%. DAPI also inhibited the chemotaxis in both strains. The swimming speeds of P. putida F1 and P. stutzeri were diminished slightly by CFDA/SE, but not to a statistically significant extent. CFDA/SE had no effect on chemotaxis of either strain to acetate. SYBR(®) Gold had no effect on swimming speed or the chemotactic response to acetate for either strain. This research indicates that although DAPI may not affect sorption to grain surfaces, it adversely affects other potentially important transport properties such as swimming and chemotaxis. Consequently, bacterial transport studies conducted using DAPI are biased to nonchemotactic conditions and do not appear to be suitable for monitoring the effect of chemotaxis on bacterial transport in shallow aquifers.

  19. Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents

    PubMed Central

    Zwirglmaier, Katrin; Reid, William D K; Heywood, Jane; Sweeting, Christopher J; Wigham, Benjamin D; Polunin, Nicholas V C; Hawkes, Jeff A; Connelly, Douglas P; Pearce, David; Linse, Katrin

    2015-01-01

    We analyzed the diversity of bacterial epibionts and trophic ecology of a new species of Kiwa yeti crab discovered at two hydrothermal vent fields (E2 and E9) on the East Scotia Ridge (ESR) in the Southern Ocean using a combination of 454 pyrosequencing, Sanger sequencing, and stable isotope analysis. The Kiwa epibiont communities were dominated by Epsilon- and Gammaproteobacteria. About 454 sequencing of the epibionts on 15 individual Kiwa specimen revealed large regional differences between the two hydrothermal vent fields: at E2, the bacterial community on the Kiwa ventral setae was dominated (up to 75%) by Gammaproteobacteria, whereas at E9 Epsilonproteobacteria dominated (up to 98%). Carbon stable isotope analysis of both Kiwa and the bacterial epibionts also showed distinct differences between E2 and E9 in mean and variability. Both stable isotope and sequence data suggest a dominance of different carbon fixation pathways of the epibiont communities at the two vent fields. At E2, epibionts were putatively fixing carbon via the Calvin-Benson-Bassham and reverse tricarboxylic acid cycle, while at E9 the reverse tricarboxylic acid cycle dominated. Co-varying epibiont diversity and isotope values at E2 and E9 also present further support for the hypothesis that epibionts serve as a food source for Kiwa. PMID:25515351

  20. Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents.

    PubMed

    Zwirglmaier, Katrin; Reid, William D K; Heywood, Jane; Sweeting, Christopher J; Wigham, Benjamin D; Polunin, Nicholas V C; Hawkes, Jeff A; Connelly, Douglas P; Pearce, David; Linse, Katrin

    2015-02-01

    We analyzed the diversity of bacterial epibionts and trophic ecology of a new species of Kiwa yeti crab discovered at two hydrothermal vent fields (E2 and E9) on the East Scotia Ridge (ESR) in the Southern Ocean using a combination of 454 pyrosequencing, Sanger sequencing, and stable isotope analysis. The Kiwa epibiont communities were dominated by Epsilon- and Gammaproteobacteria. About 454 sequencing of the epibionts on 15 individual Kiwa specimen revealed large regional differences between the two hydrothermal vent fields: at E2, the bacterial community on the Kiwa ventral setae was dominated (up to 75%) by Gammaproteobacteria, whereas at E9 Epsilonproteobacteria dominated (up to 98%). Carbon stable isotope analysis of both Kiwa and the bacterial epibionts also showed distinct differences between E2 and E9 in mean and variability. Both stable isotope and sequence data suggest a dominance of different carbon fixation pathways of the epibiont communities at the two vent fields. At E2, epibionts were putatively fixing carbon via the Calvin-Benson-Bassham and reverse tricarboxylic acid cycle, while at E9 the reverse tricarboxylic acid cycle dominated. Co-varying epibiont diversity and isotope values at E2 and E9 also present further support for the hypothesis that epibionts serve as a food source for Kiwa.

  1. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions.

    PubMed

    Cheng, Lei; Shi, Shengbao; Li, Qiang; Chen, Jianfa; Zhang, Hui; Lu, Yahai

    2014-01-01

    Although methanogenic degradation of hydrocarbons has become a well-known process, little is known about which crude oil tend to be degraded at different temperatures and how the microbial community is responded. In this study, we assessed the methanogenic crude oil degradation capacity of oily sludge microbes enriched from the Shengli oilfield under mesophilic and thermophilic conditions. The microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes combined with cloning and sequencing. Enrichment incubation demonstrated the microbial oxidation of crude oil coupled to methane production at 35 and 55°C, which generated 3.7±0.3 and 2.8±0.3 mmol of methane per gram oil, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that crude oil n-alkanes were obviously degraded, and high molecular weight n-alkanes were preferentially removed over relatively shorter-chain n-alkanes. Phylogenetic analysis revealed the concurrence of acetoclastic Methanosaeta and hydrogenotrophic methanogens but different methanogenic community structures under the two temperature conditions. Candidate divisions of JS1 and WWE 1, Proteobacteria (mainly consisting of Syntrophaceae, Desulfobacteraceae and Syntrophorhabdus) and Firmicutes (mainly consisting of Desulfotomaculum) were supposed to be involved with n-alkane degradation in the mesophilic conditions. By contrast, the different bacterial phylotypes affiliated with Caldisericales, "Shengli Cluster" and Synergistetes dominated the thermophilic consortium, which was most likely to be associated with thermophilic crude oil degradation. This study revealed that the oily sludge in Shengli oilfield harbors diverse uncultured microbes with great potential in methanogenic crude oil degradation over a wide temperature range, which extend our previous understanding of methanogenic degradation of crude oil alkanes.

  2. Assessment of bacterial diversity during composting of agricultural byproducts

    PubMed Central

    2013-01-01

    Background Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts. Results The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 105 to 109 cfu g-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts. Conclusion The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost

  3. Start-up phase of an anaerobic full-scale farm reactor - Appearance of mesophilic anaerobic conditions and establishment of the methanogenic microbial community.

    PubMed

    Goux, Xavier; Calusinska, Magdalena; Fossépré, Marie; Benizri, Emile; Delfosse, Philippe

    2016-07-01

    The goal of this study was to investigate how the microbial community structure establishes during the start-up phase of a full-scale farm anaerobic reactor inoculated with stale and cold cattle slurry. The 16S/18S high-throughput amplicon sequencing results showed an increase of the bacterial, archaeal and eukaryotic diversity, evenness and richness during the settlement of the mesophilic anaerobic conditions. When a steady performing digestion process was reached, the microbial diversity, evenness and richness decreased, indicating the establishment of a few dominant microbial populations, best adapted to biogas production. Interestingly, among the environmental parameters, the temperature, alkalinity, free-NH3, total solids and O2 content were found to be the main drivers of microbial dynamics. Interactions between eukaryotes, characterized by a high number of unknown organisms, and the bacterial and archaeal communities were also evidenced, suggesting that eukaryotes might play important roles in the anaerobic digestion process. PMID:27099947

  4. Activation of the Complement Classical Pathway (C1q Binding) by Mesophilic Aeromonas hydrophila Outer Membrane Protein

    PubMed Central

    Merino, Susana; Nogueras, Maria Mercedes; Aguilar, Alicia; Rubires, Xavier; Albertí, Sebastian; Benedí, Vicente Javier; Tomás, Juan M.

    1998-01-01

    The mechanism of killing of Aeromonas hydrophila serum-sensitive strains in nonimmune serum by the complement classical pathway has been studied. The bacterial cell surface component that binds C1q more efficiently was identified as a major outer membrane protein of 39 kDa, presumably the porin II described by D. Jeanteur, N. Gletsu, F. Pattus, and J. T. Buckley (Mol. Microbiol. 6:3355–3363, 1992), of these microorganisms. We have demonstrated that the purified form of porin II binds C1q and activates the classical pathway in an antibody-independent manner, with the subsequent consumption of C4 and reduction of the serum total hemolytic activity. Activation of the classical pathway has been observed in human nonimmune serum and agammaglobulinemic serum (both depleted of factor D). Binding of C1q to other components of the bacterial outer membrane, in particular to rough lipopolysaccharide, could not be demonstrated. Activation of the classical pathway by this lipopolysaccharide was also much less efficient than activation by the outer membrane protein. The strains possessing O-antigen lipopolysaccharide bind less C1q than the serum-sensitive strains, because the outer membrane protein is less accessible, and are resistant to complement-mediated killing. Finally, a similar or identical outer membrane protein (presumably porin II) that binds C1q was shown to be present in strains from the most common mesophilic Aeromonas O serogroups. PMID:9673268

  5. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters.

    PubMed

    Kirkegaard, Rasmus Hansen; Dueholm, Morten Simonsen; McIlroy, Simon Jon; Nierychlo, Marta; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

    2016-10-01

    Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life.

  6. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

    PubMed Central

    Kirkegaard, Rasmus Hansen; Dueholm, Morten Simonsen; McIlroy, Simon Jon; Nierychlo, Marta; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

    2016-01-01

    Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life. PMID:27058503

  7. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters.

    PubMed

    Kirkegaard, Rasmus Hansen; Dueholm, Morten Simonsen; McIlroy, Simon Jon; Nierychlo, Marta; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

    2016-10-01

    Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life. PMID:27058503

  8. Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.

    PubMed

    Sauer, C; Stackebrandt, E; Gadau, J; Hölldobler, B; Gross, R

    2000-09-01

    The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.

  9. Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.

    PubMed

    Sauer, C; Stackebrandt, E; Gadau, J; Hölldobler, B; Gross, R

    2000-09-01

    The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'. PMID:11034499

  10. Association of sexually transmitted infections, Candida species, gram-positive flora and perianal flora with bacterial vaginosis.

    PubMed

    Vahidnia, Ali; Tuin, Hellen; Bliekendaal, Harry; Spaargaren, Joke

    2015-10-01

    Bacterial vaginosis (BV) is characterised by depletion of the normal Lactobacillus spp. and overgrowth of commensal anaerobic bacteria. We investigated the composition of vaginal microbiota and their association with BV in women of reproductive age. Vaginal samples from 1197 women were analysed, whereby n=451 patients had normal flora and n=614 were diagnosed with BV, the remaining patients were diagnosed with having either intermediate flora (n=42) or dysbacteriosis (n=90). The reported results show that pathogens are associated with BV. This knowledge will further expand our understanding of events leading to BV, which may lead to more effective prevention and treatment strategies.

  11. Association of sexually transmitted infections, Candida species, gram-positive flora and perianal flora with bacterial vaginosis.

    PubMed

    Vahidnia, Ali; Tuin, Hellen; Bliekendaal, Harry; Spaargaren, Joke

    2015-10-01

    Bacterial vaginosis (BV) is characterised by depletion of the normal Lactobacillus spp. and overgrowth of commensal anaerobic bacteria. We investigated the composition of vaginal microbiota and their association with BV in women of reproductive age. Vaginal samples from 1197 women were analysed, whereby n=451 patients had normal flora and n=614 were diagnosed with BV, the remaining patients were diagnosed with having either intermediate flora (n=42) or dysbacteriosis (n=90). The reported results show that pathogens are associated with BV. This knowledge will further expand our understanding of events leading to BV, which may lead to more effective prevention and treatment strategies. PMID:26485014

  12. Culture-independent analysis of bacterial species from an anaerobic mat from Lake Fryxell, Antarctica: prokaryotic diversity revisited.

    PubMed

    Stackebrandt, E; Brambilla, E; Cousin, S; Dirks, W; Pukall, R

    2004-07-01

    Using a lake sediment mat sample from Lake Fryxell, Antarctica, different DNA extraction and purification methods were compared by denaturing gradient gel electrophoresis (DGGE). Based on the analyses of cloned 16S rRNA gene sequences a high degree of as yet uncultured prokaryotes have been reported in this sample. Although the vast majority of these as yet uncultured organisms seem to be classified as representatives of Firmicutes, Proteobacteria and Bacteriodetes, many of these taxa should be regarded novel species as judged from the distance of their gene sequences to those of their nearest cultured phylogenetic neighbours. The physiological properties of cultured strains from Lake Fryxell and of those of described species that are phylogenetically affiliated to the as yet uncultured species from this environment, suggest the presence of a well developed food web of primary producers, anaerobic degraders and fermenters, and aerobes. The few novel species described from this sample add to the increasing number of species characterized from various Antarctic habitats. Determination of the phylogenetic relatedness of the mat clone sequences of Clostridia with recent entries into public databases revealed that many of the putative species are closely related to other putative species detected in a broad range of environments, ranging from rumen and gut, anaerobic and polluted soil to sediment and groundwater samples.

  13. Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids.

    PubMed

    Jousselin, Emmanuelle; Desdevises, Yves; Coeur d'acier, Armelle

    2009-01-01

    Aphids harbour an obligatory symbiont, Buchnera aphidicola, providing essential amino acids not supplied by their diet. These bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. We investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus Brachycaudus. We used DNA-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and Buchnera species and to infer association patterns without the presumption of a specific interaction. Our results call into question certain 'taxonomic' species of Brachycaudus and suggest that B. aphidicola has diversified into independently evolving entities, each specific to a 'phylogenetic' Brachycaudus species. We also found that Buchnera and their hosts simultaneously diversified, in parallel. These results validate the use of Buchnera DNA data for inferring the evolutionary history of their host. The Buchnera genome evolves rapidly, making it the perfect tool for resolving ambiguities in aphid taxonomy. This study also highlights the usefulness of species delimitation methods in cospeciation studies involving species difficult to conceptualize--as is the case for bacteria--and in cases in which the taxonomy of the interacting organisms has not been determined independently and species definition depends on host association.

  14. Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes.

    PubMed

    Qiu, Yan-Ling; Hanada, Satoshi; Kamagata, Yoichi; Guo, Rong-Bo; Sekiguchi, Yuji

    2014-06-01

    A mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7(T), was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7(T) were motile, curved rods (0.7-1.0×5.0-8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25-40 °C) and pH 7.0 (pH 6.0-7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864(T), strain 7WAY-8-7(T) could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, L-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called 'PD-UASB-13' in the Greengenes database) in the bacterial phylum Synergistetes, showing less than 90% sequence similarity with closely related described species such as Aminivibrio pyruvatiphilus and Aminobacterium colombiense (89.7% and 88.7%, respectively). The major cellular fatty acids were iso-C(13 : 0), iso-C(15 : 0), anteiso-C(15 : 0), C(18 : 1), C(19 : 1), C(20 : 1) and C(21 : 1). A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7(T) ( = JCM 17151(T

  15. Effect of various carbon and nitrogen sources on decolorization of textile dye remazol golden yellow using bacterial species.

    PubMed

    Palanivelan, R; Rajakumar, S; Ayyasamy, P M

    2014-09-01

    Textile dyes with different chemical structures are consistently used in textile industries and they are being recalcitrant xenobiotic in nature. The aim of present research is directed to finding the preference of striking carbon and nitrogen sources on remazol golden yellow decolorization. Bacterial strains were isolated, screened and tested for dye degradation of remazol golden yellow in basal medium amended with different carbon and nitrogen sources. This study was carried out for the period of 12 d at 37 degrees C. Among various carbon and nitrogen sources, starch and yeast extracts promote maximum decolorization in the medium inoculated with Bacillus. sp. (ESL-52). Nevertheless, the rate of decolorization was less in the medium amended with various carbon and nitrogen sources in the presence of Bacillus sp. (TSL-9), Micrococcus sp. (TSL-7), Pseudomonas sp. (M-1) and Staphylococcus sp. (ES-37) respectively. The results clearly showed that addition of significant organic carbon and nitrogen sources are only desirable co-substrates for bacterial dye decolorization process.

  16. The widespread plant-colonizing bacterial species Pseudomonas syringae detects and exploits an extracellular pool of choline in hosts.

    PubMed

    Chen, Chiliang; Li, Shanshan; McKeever, Dana R; Beattie, Gwyn A

    2013-09-01

    The quaternary ammonium compound (QAC) choline is a major component of membrane lipids in eukaryotes and, if available to microbial colonists of plants, could provide benefits for growth and protection from stress. Free choline is found in homogenized plant tissues, but its subcellular location and availability to plant microbes are not known. Whole-cell bacterial bioreporters of the phytopathogen Pseudomonas syringae were constructed that couple a QAC-responsive transcriptional fusion with well-characterized bacterial QAC transporters. These bioreporters demonstrated the presence of abundant free choline compounds released from germinating seeds and seedlings of the bean Phaseolus vulgaris, and a smaller but consistently detectable amount of QACs, probably choline, from leaves. The localization of P. syringae bioreporter cells to the surface and intercellular sites of plant tissues demonstrated the extracellular location of these QAC pools. Moreover, P. syringae mutants that were deficient in the uptake of choline compounds exhibited reduced fitness on leaves, highlighting the importance of extracellular choline to P. syringae on leaves. Our data support a model in which this choline pool is derived from the phospholipid phosphatidylcholine through plant-encoded phospholipases that release choline into the intercellular spaces of plant tissues, such as for membrane lipid recycling. The consequent extracellular release of choline compounds enables their interception and exploitation by plant-associated microbes, and thus provides a selective advantage for microbes such as P. syringae that are adapted to maximally exploit choline.

  17. Architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron.

    PubMed

    Breugelmans, Philip; Barken, Kim Bundvig; Tolker-Nielsen, Tim; Hofkens, Johan; Dejonghe, Winnie; Springael, Dirk

    2008-05-01

    Members of a triple-species 3-(3,4-dichlorophenyl)-1-methoxy-1-methyl urea (linuron)-mineralizing consortium, i.e. the linuron- and 3,4-dichloroaniline-degrading Variovorax sp. WDL1, the 3,4-dichloroaniline-degrading Comamonas testosteroni WDL7 and the N,O-dimethylhydroxylamine-degrading Hyphomicrobium sulfonivorans WDL6, were cultivated as mono- or multi-species biofilms in flow cells irrigated with selective or nonselective media, and examined with confocal laser scanning microscopy. In contrast to mono-species biofilms of Variovorax sp. WDL1, the triple-species consortium biofilm degraded linuron completely through apparent synergistic interactions. The triple-species linuron-fed consortium biofilm displayed a heterogeneous structure with an irregular surface topography that most resembled the topography of linuron-fed mono-species WDL1 biofilms, indicating that WDL1 had a dominating influence on the triple-species biofilm architecture. This architecture was dependent on the carbon source supplied, as the biofilm architecture of WDL1 growing on alternative carbon sources was different from that observed under linuron-fed conditions. Linuron-fed triple-species consortium biofilms consisted of mounds composed of closely associated WDL1, WDL7 and WDL6 cells, while this association was lost when the consortium was grown on a nonselective carbon source. In addition, under linuron-fed conditions, microcolonies displaying associated growth developed rapidly after inoculation. These observations indicate that the spatial organization in the linuron-fed consortium biofilm reflected the metabolic interactions within the consortium. PMID:18373685

  18. Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir.

    PubMed

    Grabowski, Agnès; Tindall, Brian J; Bardin, Véronique; Blanchet, Denis; Jeanthon, Christian

    2005-05-01

    A mesophilic, anaerobic, fermentative bacterium, strain BN3(T), was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15-40 degrees C, with optimum growth at 37-40 degrees C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO(2) were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G + C content of the genomic DNA was 40.8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum 'Bacteroidetes', distantly related to the genera Bacteroides and Tannerella (similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3(T) could be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Petrimonas gen. nov., of which Petrimonas sulfuriphila sp. nov. is the type species. The type strain is BN3(T) (= DSM 16547(T) = JCM 12565(T)). PMID:15879242

  19. The enteric bacterial metabolite propionic acid alters brain and plasma phospholipid molecular species: further development of a rodent model of autism spectrum disorders

    PubMed Central

    2012-01-01

    Gastrointestinal symptoms and altered blood phospholipid profiles have been reported in patients with autism spectrum disorders (ASD). Most of the phospholipid analyses have been conducted on the fatty acid composition of isolated phospholipid classes following hydrolysis. A paucity of information exists on how the intact phospholipid molecular species are altered in ASD. We applied ESI/MS to determine how brain and blood intact phospholipid species were altered during the induction of ASD-like behaviors in rats following intraventricular infusions with the enteric bacterial metabolite propionic acid. Animals were infused daily for 8 days, locomotor activity assessed, and animals killed during the induced behaviors. Propionic acid infusions increased locomotor activity. Lipid analysis revealed treatment altered 21 brain and 30 blood phospholipid molecular species. Notable alterations were observed in the composition of brain SM, diacyl mono and polyunsaturated PC, PI, PS, PE, and plasmalogen PC and PE molecular species. These alterations suggest that the propionic acid rat model is a useful tool to study aberrations in lipid metabolism known to affect membrane fluidity, peroxisomal function, gap junction coupling capacity, signaling, and neuroinflammation, all of which may be associated with the pathogenesis of ASD. PMID:22747852

  20. Biochemical changes induced by salt stress in halotolerant bacterial isolates are media dependent as well as species specific.

    PubMed

    Joghee, Nidhya Nadarajan; Jayaraman, Gurunathan

    2016-01-01

    Halophilic bacteria respond to salt stress by regulating the cytosolic pools of organic solutes to achieve osmotic equilibrium. In order to understand the metabolic regulation of these organic solutes, for the first time, we have investigated the effect of salt on growth and biochemical changes in four major moderately halophilic bacterial strains isolated from a saltern region of the Kumta coast, India. The strains under study were Halomonas hydrothermalis VITP9, Bacillus aquimaris VITP4, Planococcus maritimus VITP21, and Virgibacillus dokdonensis VITP14, which exhibited similar salt tolerance (0% to 10% w/v NaCl) with optimal growth at 5% w/v NaCl. Biochemical analysis showed that the total intracellular organic solutes increased significantly with increasing NaCl concentration in the growth medium, and the compositions of the solutes were dependent on the type of strain and also on the nutrient richness of the growth medium. Glutamic acid levels increased in all the strains under salt stress, indicating the significance of glutamic acid as the anionic counterpart of K(+)/Na(+) ions and precursor for other synthesized nitrogenous osmolytes. Though initial studies were performed with thin-layer chromatography, mass spectrometry was used to identify the major solutes accumulated by the strains under salt stress, such as proline (VITP4), ectoine (VITP14 and VITP9), and sugars (VITP21) under minimal medium and glycine betaine (by all the strains under study) under complex growth medium conditions. Such comparative study on the stress-dependent metabolic differences of different microbes, under identical experimental condition, helps to identify possible bacterial sources for the production of industrially important solutes. PMID:25286020

  1. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

    PubMed

    Ramond, Jean-Baptiste; Lako, Joseph D W; Stafford, William H L; Tuffin, Marla I; Cowan, Don A

    2015-08-01

    Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils.

  2. Chemometric Analysis of Multiple Species of Bacillus Bacterial Endospores Using Infrared Spectroscopy: Discrimination to the Strain Level

    SciTech Connect

    Forrester, Joel B.; Valentine, Nancy B.; Su, Yin-Fong; Johnson, Timothy J.

    2009-09-28

    Previous work using infrared spectroscopy has shown potential for rapid discrimination between bacteria in either their sporulated or vegetative states, as well as between bacteria and other common interferents. For species within one physiological state, however, distinction is far more challenging, and requires chemometrics. In the current study, we have narrowed the field of study by eliminating the confounding issues of vegetative cells as well as growth media and focused on using IR spectra to distinguish between different species all in the sporulated state. Using principal component analysis (PCA) and a classification method based upon similarity measurements, we demonstrate a successful identification rate to the species level of 85% for Bacillus spores grown and sporulated in a glucose broth medium.

  3. Ecology of mesophilic Aeromonas spp. in aquatic environments of a temperate region and relationship with some biotic and abiotic environmental parameters.

    PubMed

    Chowdhury, M A; Yamanaka, H; Miyoshi, S; Shinoda, S

    1990-10-01

    The Ecology of mesophilic Aeromonas species has been investigated since January 1988 to examine their occurrence and distribution in aquatic environments of Okayama Prefecture. Water and plankton samples were quantitatively as well as qualitatively analyzed throughout the seasons from five selected stations including fresh, brackish, and saline environments. Analysis of variance and correlation coefficients among the biotic and abiotic parameters were sought. The organisms were found in all the environs with high densities through all the seasons. Plankton samples yielded higher counts of Aeromonas than the water samples in all the environs. Water temperature seemed to play a significant role on their growth during the winter months, however, no significant seasonal variation nor any correlation with fecal pollution were observed in most of the environments. A reciprocal relationship was seen with salt concentration in the saline environment. Among the currently recognized mesophilic species; A. caviae, A. hydrophila, A. sobria, and A. media were isolated with the predominance of anaerobic biovar. The present study reveals that Aeromonas are widely distributed in fresh, brackish and saline environments of this region. The study also reveals that Aeromonas are autochthonous members in aquatic ecosystems and are indigenous to these environs. Aeromonas species isolated from our environments were found to exhibit drug resistance potential which differed from that of isolates from diverse geographical locales. The high incidence of clinically significant Aeromonas species in this aquatic region could be of public health significance for the inhabitants of this region, as well as a challenge to their dependence on aquatic resources.

  4. Osteomyelitis Caused by Staphylococcus schleiferi and Evidence of Misidentification of This Staphylococcus Species by an Automated Bacterial Identification System

    PubMed Central

    Calvo, Jorge; Hernández, José L.; Fariñas, Maria C.; García-Palomo, Daniel; Agüero, Jesús

    2000-01-01

    We report a case of sternal osteomyelitis due to Staphylococcus schleiferi in a patient who underwent thoracic surgery. This constitutes the first documented case of osteomyelitis caused by this Staphylococcus species. We also relate our experience in the utilization of commercially available MicroScan panels for the identification of this microorganism. PMID:11015429

  5. Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes.

    PubMed

    Duarte, G F; Rosado, A S; Seldin, L; de Araujo, W; van Elsas, J D

    2001-03-01

    The selective effects of sulfur-containing hydrocarbons, with respect to changes in bacterial community structure and selection of desulfurizing organisms and genes, were studied in soil. Samples taken from a polluted field soil (A) along a concentration gradient of sulfurous oil and from soil microcosms treated with dibenzothiophene (DBT)-containing petroleum (FSL soil) were analyzed. Analyses included plate counts of total bacteria and of DBT utilizers, molecular community profiling via soil DNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and detection of genes that encode enzymes involved in the desulfurization of hydrocarbons, i.e., dszA, dszB, and dszC. Data obtained from the A soil showed no discriminating effects of oil levels on the culturable bacterial numbers on either medium used. Generally, counts of DBT degraders were 10- to 100-fold lower than the total culturable counts. However, PCR-DGGE showed that the numbers of bands detected in the molecular community profiles decreased with increasing oil content of the soil. Analysis of the sequences of three prominent bands of the profiles generated with the highly polluted soil samples suggested that the underlying organisms were related to Actinomyces sp., Arthrobacter sp., and a bacterium of uncertain affiliation. dszA, dszB, and dszC genes were present in all A soil samples, whereas a range of unpolluted soils gave negative results in this analysis. Results from the study of FSL soil revealed minor effects of the petroleum-DBT treatment on culturable bacterial numbers and clear effects on the DBT-utilizing communities. The molecular community profiles were largely stable over time in the untreated soil, whereas they showed a progressive change over time following treatment with DBT-containing petroleum. Direct PCR assessment revealed the presence of dszB-related signals in the untreated FSL soil and the apparent selection of dszA- and dszC-related sequences by the petroleum-DBT treatment

  6. The Immune Strategy and Stress Response of the Mediterranean Species of the Bemisia tabaci Complex to an Orally Delivered Bacterial Pathogen

    PubMed Central

    Xia, Jun; Li, Fang-Fang; Xia, Wen-Qiang; Liu, Shu-Sheng; Wang, Xiao-Wei

    2014-01-01

    Background The whitefly, Bemisia tabaci, a notorious agricultural pest, has complex relationships with diverse microbes. The interactions of the whitefly with entomopathogens as well as its endosymbionts have received great attention, because of their potential importance in developing novel whitefly control technologies. To this end, a comprehensive understanding on the whitefly defense system is needed to further decipher those interactions. Methodology/Principal Findings We conducted a comprehensive investigation of the whitefly's defense responses to infection, via oral ingestion, of the pathogen, Pseudomonas aeruginosa, using RNA-seq technology. Compared to uninfected whiteflies, 6 and 24 hours post-infected whiteflies showed 1,348 and 1,888 differentially expressed genes, respectively. Functional analysis of the differentially expressed genes revealed that the mitogen associated protein kinase (MAPK) pathway was activated after P. aeruginosa infection. Three knottin-like antimicrobial peptide genes and several components of the humoral and cellular immune responses were also activated, indicating that key immune elements recognized in other insect species are also important for the response of B. tabaci to pathogens. Our data also suggest that intestinal stem cell mediated epithelium renewal might be an important component of the whitefly's defense against oral bacterial infection. In addition, we show stress responses to be an essential component of the defense system. Conclusions/Significance We identified for the first time the key immune-response elements utilized by B. tabaci against bacterial infection. This study provides a framework for future research into the complex interactions between whiteflies and microbes. PMID:24722540

  7. Comparison of mesophilic and thermophilic anaerobic digestion of sugar beet pulp: performance, dewaterability and foam control.

    PubMed

    Suhartini, Sri; Heaven, Sonia; Banks, Charles J

    2014-01-01

    Digestion of sugar beet pulp was assessed in relation to biogas and methane production, foaming potential, and digestate dewaterability. Four 4-litre working volume digesters were operated mesophilically (37±0.5 °C) and four thermophilically (55±0.5 °C) over three hydraulic retention times. Digesters were operated in duplicate at organic loading rates (OLR) of 4 and 5 g volatile solids l(-1) day(-1) without water addition. Thermophilic digestion gave higher biogas and methane productivity than mesophilic and was able to operate at the higher OLR, where mesophilic digestion showed signs of instability. Digestate dewaterability was assessed using capillary suction time and frozen image centrifugation. The occurrence of, or potential for, stable foam formation was assessed using a foaming potential test. Thermophilic operation allowed higher loadings to be applied without loss of performance, and gave a digestate with superior dewatering characteristics and very little foaming potential.

  8. On the relation of pore-scale heterogeneities and bacterial mobility to bioavailability and in-situ biodegradation of chemical species in porous media: a numerical modeling approach

    NASA Astrophysics Data System (ADS)

    Gharasoo, M. G.; Centler, F.; Fetzer, I.; Thullner, M.

    2010-12-01

    Reactive processes, for example nutrient cycling or degradation of organic contaminants, in subsurface environments like soils or aquifers are driven by microorganisms residing in these porous environments. These natural porous media are characterized by heterogeneities at various scales and the heterogeneous structure of the medium shapes both the transport of chemical species and the distribution of microorganisms, both of which are altering the accessibility and availability of the chemical species to the located microorganisms within the medium. Effective reaction rates that describe the biodegradation of contaminants and resulted microbial distribution patterns thus depend not only on the growth and degradation capacity of the indigenous microbial population but also on the pore-scale heterogeneities of a medium and on the ability of microorganisms to relocate within the medium. The interaction of these properties will control the bacterial distribution patterns and in consequence the bioavailability and realized biodegradation rate of chemical species. To obtain a better and quantitative understanding of the bioavailability of biodegradable compounds in porous media, a numerical pore-network model has been developed, which is capable of considering the transport of an arbitrary number of chemical species, as well as their consumption/production by an arbitrary number of (bio)geochemical reactions. These simulations are further combined with the individual-based simulation of the growth and chemotactic mobility of microbial cells within the pore network. The model allows for considering various ranges of heterogeneities as well as pore-specific limitations of intra-pore bioavailability. Simulations are performed for studying the link between pore-scale heterogeneity and the distribution of bacteria, which will allow assess the bioavailability of biodegradable species and their effective biodegradation rates in such media.

  9. Hygienic treatment and energy recovery of dead animals by high solid co-digestion with vinasse under mesophilic condition: feasibility study.

    PubMed

    Dai, Xiaohu; Chen, Sisi; Xue, Yonggang; Dai, Lingling; Li, Ning; Takahashi, Junichi; Zhao, Wentao

    2015-10-30

    In the present study, the feasibility of hygienic treatment and energy recovery of dead animals (pork as an experimental alternative) by high solid co-digestion with vinasse under mesophilic condition was investigated. A lab-scale digester was operated for 125 days with SRT of 20 days. The volatile solid (VS) reduction, biogas yield, and CH4 content finally achieved stability after two obvious fluctuations, and were 55±1%, 0.40±0.02 m(3)/kg VS feed and 68%, respectively. Meanwhile, the shifts of microbial communities of the samples taken on typical days with different performance (day 40 (stable), day 65 (deteriorated), day 75 (in recovery), day 90 (recovered) and day 110 (stable)) were monitored by the application of pyrosequencing technology and the bioinformatical analysis with QIIME 1.8. In consequence, the details of changes in bacterial and archaeal communities elaborately explained the intrinsic reasons for the deterioration and recovery of the digester, and provided the proofs for the feasibility of hygienic treatment and energy recovery of dead animals by high solid co-digestion with vinasse under mesophilic condition. PMID:26026851

  10. Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects.

    PubMed

    Tobler, Dominique J; Benning, Liane G

    2011-07-01

    The microbial ecology associated with siliceous sinters was studied in five geochemically diverse Icelandic geothermal systems. Bacterial 16S rRNA clone libraries were constructed from water-saturated precipitates from each site resulting in a total of 342 bacterial clone sequences and 43 species level phylotypes. In near-neutral, saline (2.6-4.7% salinity) geothermal waters where sinter growth varied between 10 and ~300 kg year(-1) m(-2), 16S rRNA gene analyses revealed very low (no OTUs could be detected) to medium (9 OTUs) microbial activity. The most dominant phylotypes found in these waters belong to marine genera of the Proteobacteria. In contrast, in alkaline (pH = 9-10), meteoric geothermal waters with temperature = 66-96°C and <1-20 kg year(-1)m(-2) sinter growth, extensive biofilms (a total of 34 OTUs) were observed within the waters and these were dominated by members of the class Aquificae (mostly related to Thermocrinis), Deinococci (Thermus species) as well as Proteobacteria. The observed phylogenetic diversity (i.e., number and composition of detected OTUs) is argued to be related to the physico-chemical regime prevalent in the studied geothermal waters; alkaliphilic thermophilic microbial communities with phylotypes related to heterotrophic and autotrophic microorganisms developed in alkaline high temperature waters, whereas halophilic mesophilic communities dominated coastal geothermal waters.

  11. Bacterial catabolism of threonine. Threonine degradation initiated by l-threonine hydrolyase (deaminating) in a species of Corynebacterium

    PubMed Central

    Bell, Stephen C.; Turner, John M.

    1977-01-01

    1. Three bacterial isolates capable of growth on l-threonine medium only when supplemented with branched-chain amino acids, and possessing high l-threonine dehydratase activity, were examined to elucidate the catabolic route for the amino acid. 2. Growth, manometric, radiotracer and enzymic experiments indicated that l-threonine was catabolized by initial deamination to 2-oxobutyrate and thence to propionate. No evidence was obtained for the involvement of l-threonine 3-dehydrogenase or l-threonine aldolase in threonine catabolism. 3. l-Threonine dehydratase of Corynebacterium sp. F5 (N.C.I.B. 11102) was partially purified and its kinetic properties were examined. The enzyme exhibited a sigmoid kinetic response to substrate concentration. The concentration of substrate giving half the maximum velocity, [S0.5], was 40mm and the Hill coefficient (h) was 2.0. l-Isoleucine inhibited enzyme activity markedly, causing 50% inhibition at 60μm, but did not affect the Hill constant. At the fixed l-threonine concentration of 10mm, the effect of l-valine was biphasic, progressive activation occurring at concentrations up to 2mm-l-valine, but was abolished by higher concentrations. Substrate-saturation plots for the l-valine-activated enzyme exhibited normal Michaelis–Menten kinetics with a Hill coefficient (h) of 1.0. The kinetic properties of the enzyme were thus similar to those of the `biosynthetic' isoenzyme from Rhodopseudomonas spheroides rather than those of the enteric bacteria. 4. The synthesis of l-threonine dehydratase was constitutive and was not subject to multivalent repression by l-isoleucine or other branched-chain amino acids either singly or in combination. 5. The catabolism of l-threonine, apparently initiated by a `biosynthetic' l-threonine dehydratase in the isolates studied, depended on the concomitant catabolism of branched-chain amino acids. The biochemical basis of this dependence appeared to lie in the further catabolism of 2-oxobutyrate by enzymes

  12. Microtus species as new herbivorous laboratory animals: reproduction; bacterial flora and fermentation in the digestive tracts; and nutritional physiology.

    PubMed

    Kudo, H; Oki, Y

    1984-05-01

    In a study of the possible introduction of Japanese field vole (Microtus montebelli ) and Hungarian voles (M. arvalis) as herbivorous experimental animals, the following biological characteristics were investigated: breeding and reproductive performance; bacterial flora and fermentation in the digestive tracts; and nutritional physiology. The animals are polyestrus , show postpartum estrus on the day of parturition, and there is little or no delay in implantation due to lactation, especially in M. arvalis. On examination of vaginal smears, Japanese field vole did not show any definite pattern, whereas most Hungarian voles showed 6- to 18- day cycles. From the esophageal sac of voles fed rations with a high fiber content, cellulolytic bacteria similar to Ruminococcus albus, Ruminococcus flavefaciens , and Bacteroides succinogenes were isolated. More than 1 000 000/g anaerobic bacteria were present in the esophageal sac and the pattern and the types of bacteria resembled those found in the rumen. Gastric fermentation took place in the esophageal sac. The pH and total VFAs were much smaller in the fundic and pyloric regions of the stomach than in the esophageal sac. Acetic and lactic acids were the major fermentation products in the esophageal sac. Following deficiency or lowering of the cellulose decomposing abilities, a decrease of VFAs and an increase in lactic acid production in the esophageal sac were observed. These effects resulted in high glucose, FFA and ketone bodies in the blood, and a higher incidence of glucosuria. Diabetes induced by administrations of drugs such as alloxan, streptozotocin and phloridzin were compared using Microtus and mice. Microtus had low sensitivity to alloxan but high sensitivity to streptozotocin. The influence of monensin on Microtus was also investigated by using diets containing 20 and 80 mg/kg monensin. Diets containing 80 mg/kg monensin led to 50 % mortality in 7 weeks and growth was hindered. Gas production from the

  13. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species.

    PubMed

    Hasan, Nur A; Grim, Christopher J; Lipp, Erin K; Rivera, Irma N G; Chun, Jongsik; Haley, Bradd J; Taviani, Elisa; Choi, Seon Young; Hoq, Mozammel; Munk, A Christine; Brettin, Thomas S; Bruce, David; Challacombe, Jean F; Detter, J Chris; Han, Cliff S; Eisen, Jonathan A; Huq, Anwar; Colwell, Rita R

    2015-05-26

    Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea. PMID:25964331

  14. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species

    PubMed Central

    Hasan, Nur A.; Grim, Christopher J.; Lipp, Erin K.; Rivera, Irma N. G.; Chun, Jongsik; Haley, Bradd J.; Taviani, Elisa; Choi, Seon Young; Hoq, Mozammel; Munk, A. Christine; Brettin, Thomas S.; Bruce, David; Challacombe, Jean F.; Detter, J. Chris; Han, Cliff S.; Eisen, Jonathan A.; Huq, Anwar; Colwell, Rita R.

    2015-01-01

    Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea. PMID:25964331

  15. Thermodynamic assessment of domain-domain interactions and in vitro activities of mesophilic and thermophilic ribosome recycling factors.

    PubMed

    Uchiyama, Susumu; Ohshima, Atsushi; Yoshida, Takuya; Ohkubo, Tadayasu; Kobayashi, Yuji

    2013-07-01

    Ribosome recycling factor (RRF) is essential for bacterial growth. Structural studies revealed that RRF consists of two domains connected by two short polypeptides at the hinge region. Here, we evaluated the intrinsic stabilities (ΔG*s) of the two domains and the free energy of the domain-domain interactions (ΔG(int)) for mesophilic RRF (RRF from Escherichia coli, EcRRF) and thermophilic RRF (RRF from Thermus thermophilus, TtRRF) by using differential scanning calorimetry and circular dichroic spectroscopy. Despite single endothermic peaks, a higher than unity value for the ratio of calorimetric enthalpy to van't Hoff enthalpy of the unfolding indicated the presence of unfolding intermediates for both RRFs. Deconvolution analysis based on statistical thermodynamics employing multiple states of the unfolding process with domain-domain interactions allowed us to determine ΔG*s of each domain and ΔG(int). The results indicated that domain I has a higher unfolding temperature than domain II and that it stabilizes domain II through ΔG(int), giving rise to an apparent single peak of unfolding. Interestingly, the estimated ΔG(int) values of 6.28 kJ/mol for EcRRF and 26.28 kJ/mol for TtRRF reflect the observation that only EcRRF has recycling activity at ambient temperature. Our present study suggests the importance of a moderate ΔG(int) for biological activity of multidomain proteins.

  16. [Biodiversity of mesophilic microbial community BYND-8 capability of lignocellulose degradation and its effect on biogas production].

    PubMed

    Wang, Wei-Dong; Song, Ya-Bin; Wang, Yan-Jie; Gao, Ya-Mei; Jing, Rui-Yong; Cui, Zong-Jun

    2011-01-01

    The biodiversity of a mesophilic microbial community BYND-8 capable of degrading lignocellulose at 30 degrees C was detected using denaturing gradient gel electrophoresis (DGGE) and the isolation of pure cultures, and the effect of the liquid of rice straw degradation by BYND-8 on biogas production was measured. Six bacterial strains were isolated using peptone cellulose solution medium, and the highest similarities of their 16S rDNA gene sequences to Serratia sp. PSGB 13, S. marcescens strain UFLA-25LS, S. marcescens strain DAP33, Alcaligenes sp. YcX-20, Stenotrophomonas maltophilia strain C6, Bacillus cereus isolate BRL02-71 were 99%, 100%, 96%, 100%, 100% and 99%, respectively. In addition, one band was detected besides six bands of cultured isolates on the DGGE gel, and it showed 100% sequence similarity to uncultured bacterium clone ATB-KS-1446. The cumulative biogas and methane productions of biogas fermentation system added with the liquid of rice straw degraded by BYND-8 were 13 167 mL and 7 248 mL, 44.5% and 95.3% higher than those of the control, respectively, in the early 15 days of fermentation. The results showed that the biodiversity of microbial community BYND-8 was very high, and the time of producing biogas was put forward and biogas production was increased with application of microbial community for rice straw pretreatment during the biogas fermentation.

  17. Effect of increasing total solids contents on anaerobic digestion of food waste under mesophilic conditions: performance and microbial characteristics analysis.

    PubMed

    Yi, Jing; Dong, Bin; Jin, Jingwei; Dai, Xiaohu

    2014-01-01

    The total solids content of feedstocks affects the performances of anaerobic digestion and the change of total solids content will lead the change of microbial morphology in systems. In order to increase the efficiency of anaerobic digestion, it is necessary to understand the role of the total solids content on the behavior of the microbial communities involved in anaerobic digestion of organic matter from wet to dry technology. The performances of mesophilic anaerobic digestion of food waste with different total solids contents from 5% to 20% were compared and the microbial communities in reactors were investigated using 454 pyrosequencing technology. Three stable anaerobic digestion processes were achieved for food waste biodegradation and methane generation. Better performances mainly including volatile solids reduction and methane yield were obtained in the reactors with higher total solids content. Pyrosequencing results revealed significant shifts in bacterial community with increasing total solids contents. The proportion of phylum Chloroflexi decreased obviously with increasing total solids contents while other functional bacteria showed increasing trend. Methanosarcina absolutely dominated in archaeal communities in three reactors and the relative abundance of this group showed increasing trend with increasing total solids contents. These results revealed the effects of the total solids content on the performance parameters and the behavior of the microbial communities involved in the anaerobic digestion of food waste from wet to dry technologies.

  18. Effect of Increasing Total Solids Contents on Anaerobic Digestion of Food Waste under Mesophilic Conditions: Performance and Microbial Characteristics Analysis

    PubMed Central

    Jin, Jingwei; Dai, Xiaohu

    2014-01-01

    The total solids content of feedstocks affects the performances of anaerobic digestion and the change of total solids content will lead the change of microbial morphology in systems. In order to increase the efficiency of anaerobic digestion, it is necessary to understand the role of the total solids content on the behavior of the microbial communities involved in anaerobic digestion of organic matter from wet to dry technology. The performances of mesophilic anaerobic digestion of food waste with different total solids contents from 5% to 20% were compared and the microbial communities in reactors were investigated using 454 pyrosequencing technology. Three stable anaerobic digestion processes were achieved for food waste biodegradation and methane generation. Better performances mainly including volatile solids reduction and methane yield were obtained in the reactors with higher total solids content. Pyrosequencing results revealed significant shifts in bacterial community with increasing total solids contents. The proportion of phylum Chloroflexi decreased obviously with increasing total solids contents while other functional bacteria showed increasing trend. Methanosarcina absolutely dominated in archaeal communities in three reactors and the relative abundance of this group showed increasing trend with increasing total solids contents. These results revealed the effects of the total solids content on the performance parameters and the behavior of the microbial communities involved in the anaerobic digestion of food waste from wet to dry technologies. PMID:25051352

  19. The Bacterial Fermentation Product Butyrate Influences Epithelial Signaling via Reactive Oxygen Species-Mediated Changes in Cullin-1 Neddylation1

    PubMed Central

    Kumar, Amrita; Wu, Huixia; Collier-Hyams, Lauren S.; Kwon, Young-Man; Hanson, Jason M.; Neish, Andrew S.

    2010-01-01

    The human enteric flora plays a significant role in intestinal health and disease. Populations of enteric bacteria can inhibit the NF-κB pathway by blockade of IκB-α ubiquitination, a process catalyzed by the E3-SCFβ-TrCP ubiquitin ligase. The activity of this ubiquitin ligase is regulated via covalent modification of the Cullin-1 subunit by the ubiquitin-like protein NEDD8. We previously reported that interaction of viable commensal bacteria with mammalian intestinal epithelial cells resulted in a rapid and reversible generation of reactive oxygen species (ROS) that modulated neddylation of Cullin-1 and resulted in suppressive effects on the NF-κB pathway. Herein, we demonstrate that butyrate and other short chain fatty acids supplemented to model human intestinal epithelia in vitro and human tissue ex vivo results in loss of neddylated Cul-1 and show that physiological concentrations of butyrate modulate the ubiquitination and degradation of a target of the E3-SCFβ-TrCP ubiquitin ligase, the NF-κB inhibitor IκB-α. Mechanistically, we show that physiological concentrations of butyrate induces reactive oxygen species that transiently alters the intracellular redox balance and results in inactivation of the NEDD8-conjugating enzyme Ubc12 in a manner similar to effects mediated by viable bacteria. Because the normal flora produces significant amounts of butyrate and other short chain fatty acids, these data provide a functional link between a natural product of the intestinal normal flora and important epithelial inflammatory and proliferative signaling pathways. PMID:19109186

  20. Anaerobic digestion in mesophilic and room temperature conditions: Digestion performance and soil-borne pathogen survival.

    PubMed

    Chen, Le; Jian, Shanshan; Bi, Jinhua; Li, Yunlong; Chang, Zhizhou; He, Jian; Ye, Xiaomei

    2016-05-01

    Tomato plant waste (TPW) was used as the feedstock of a batch anaerobic reactor to evaluate the effect of anaerobic digestion on Ralstonia solanacearum and Phytophthora capsici survival. Batch experiments were carried out for TS (total solid) concentrations of 2%, 4% and 6% respectively, at mesophilic (37±1°C) and room (20-25°C) temperatures. Results showed that higher digestion performance was achieved under mesophilic digestion temperature and lower TS concentration conditions. The biogas production ranged from 71 to 416L/kg VS (volatile solids). The inactivation of anaerobic digestion tended to increase as digestion performance improved. The maximum log copies reduction of R. solanacearum and P. capsici detected by quantitative PCR (polymerase chain reaction) were 3.80 and 4.08 respectively in reactors with 4% TS concentration at mesophilic temperatures. However, both in mesophilic and room temperature conditions, the lowest reduction of R. solanacearum was found in the reactors with 6% TS concentration, which possessed the highest VFA (volatile fatty acid) concentration. These findings indicated that simple accumulation of VFAs failed to restrain R. solanacearum effectively, although the VFAs were considered poisonous. P. capsici was nearly completely dead under all conditions. Based on the digestion performance and the pathogen survival rate, a model was established to evaluate the digestate biosafety. PMID:27155428

  1. Mesophilic-hydrothermal-thermophilic (M-H-T) digestion of green corn straw.

    PubMed

    Li, Dong; Wang, Qingjing; Li, Jiang; Li, Zhidong; Yuan, Yuexiang; Yan, Zhiying; Mei, Zili; Liu, Xiaofeng

    2016-02-01

    Mesophilic-hydrothermal (80-160 °C, 30 min)-thermophilic (M-H-T) digestion and control tests of mesophilic (M), thermophilic (T), hydrothermal-mesophilic (H-M), and mesophilic-thermophilic digestion (M-T) of green corn straw were conducted for a 20-day fermentation period. The results indicate that M-H-T is an efficient method to improve methane production. A maximum methane yield of 371.74 mL/g volatile solid was obtained by the M (3 days)-H (140 °C)-T (17 days) process, which was 20.44%, 16.55%, 31.44%, and 14.31% higher than the yields of the M, T, 140-M, and M-T processes. The enhanced methane production was attributed to (1) the improved hemicellulose degradation and lignin disorganization; (2) prevention of the degradation of soluble sugar, easily hydrolyzed hemicellulose and cellulose into furfural and methylfurfural; and (3) lack of formation of Maillard reaction products during initial hydrothermal treatment.

  2. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

    PubMed Central

    Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

    2016-01-01

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. PMID:26741367

  3. The elimination of Salmonella typhimurium in sewage sludge by aerobic mesophilic stabilization and lime hydrated stabilization.

    PubMed

    Plachá, Iveta; Venglovský, Ján; Maková, Zuzana; Martinéz, José

    2008-07-01

    This study observed the effects of two methods, aerobic mesophilic stabilization and lime hydrated stabilization of sewage sludge upon the survival of Salmonella typhimurium. Raw (primary) sludges from the mechanical biological municipal sewage treatment plant were used. Aerobic stabilization and lime hydrated stabilization were carried out in a laboratory fermentor. Aerobic stabilization was carried out in the mesophilic temperature range (from 25.70+/-0.40 to 37.82+/-1.38 degrees C). Lime hydrated was used at an amount of 10 kg/m(3) for the stabilization. Sludge samples were inoculated with a broth culture of S. typhimurium. Quantitative and qualitative examinations of the presence of S. typhimurium were carried out. Aerobic mesophilic stabilization caused elimination S. typhimurium within 48 h. The T(90) value of S. typhimurium was 6.66+/-0.20 h. During the lime hydrated stabilization pH values significantly increased from 5.66+/-0.07 to 12.12+/-0.02 (P<0.01). S. typhimurium was inactivated within 1h and the T(90) value was 0.19+/-0.01 h. Our study confirmed that the treatment of sewage sludge with lime hydrated was significantly more effective than the aerobic mesophilic stabilization, (P<0.01). PMID:17931859

  4. Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

    DOE PAGESBeta

    Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

    2016-01-07

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

  5. Acyl Carrier Protein Synthases from Gram-Negative, Gram-Positive, and Atypical Bacterial Species: Biochemical and Structural Properties and Physiological Implications

    PubMed Central

    McAllister, Kelly A.; Peery, Robert B.; Zhao, Genshi

    2006-01-01

    Acyl carrier protein (ACP) synthase (AcpS) catalyzes the transfer of the 4′-phosphopantetheine moiety from coenzyme A (CoA) onto a serine residue of apo-ACP, resulting in the conversion of apo-ACP to the functional holo-ACP. The holo form of bacterial ACP plays an essential role in mediating the transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and phospholipids. AcpS is therefore an attractive target for therapeutic intervention. In this study, we have purified and characterized the AcpS enzymes from Escherichia coli, Streptococcus pneumoniae, and Mycoplasma pneumoniae, which exemplify gram-negative, gram-positive, and atypical bacteria, respectively. Our gel filtration column chromatography and cross-linking studies demonstrate that the AcpS enzyme from M. pneumoniae, like E. coli enzyme, exhibits a homodimeric structure, but the enzyme from S. pneumoniae exhibits a trimeric structure. Our biochemical studies show that the AcpS enzymes from M. pneumoniae and S. pneumoniae can utilize both short- and long-chain acyl CoA derivatives but prefer long-chain CoA derivatives as substrates. On the other hand, the AcpS enzyme from E. coli can utilize short-chain CoA derivatives but not the long-chain CoA derivatives tested. Finally, our biochemical studies show that M. pneumoniae AcpS is kinetically a very sluggish enzyme compared with those from E. coli and S. pneumoniae. Together, the results of these studies show that the AcpS enzymes from different bacterial species exhibit different native structures and substrate specificities with regard to the utilization of CoA and its derivatives. These findings suggest that AcpS from different microorganisms plays a different role in cellular physiology. PMID:16788183

  6. Dry co-digestion of sewage sludge and rice straw under mesophilic and thermophilic anaerobic conditions.

    PubMed

    Chu, Xiangqian; Wu, Guangxue; Wang, Jiaquan; Hu, Zhen-Hu

    2015-12-01

    Dry anaerobic digestion of sewage sludge can recover biogas as energy; however, its low C/N ratio limits it as a single substrate in the anaerobic digestion. Rice straw is an abundant agricultural residue in China, which is rich in carbon and can be used as carbon source. In the present study, the performance of dry co-digestion of sewage sludge and rice straw was investigated under mesophilic (35 °C) and thermophilic (55 °C) conditions. The operational factors impacting dry co-digestion of sewage sludge and rice straw such as C/N ratio, moisture content, and initial pH were explored under mesophilic conditions. The results show that low C/N ratios resulted in a higher biogas production rate, but a lower specific biogas yield; low moisture content of 65 % resulted in the instability of the digestion system and a low specific biogas yield. Initial pH ranging 7.0-9.0 did not affect the performance of the anaerobic digestion. The C/N ratio of 26-29:1, moisture content of 70-80 %, and pH 7.0-9.0 resulted in good performance in the dry mesophilic co-digestion of sewage sludge and rice straw. As compared with mesophilic digestion, thermophilic co-digestion of sewage sludge and rice straw significantly enhanced the degradation efficiency of the substrates and the specific biogas yield (p < 0.05) at the conditions of C/N ratio 26:1, moisture content 80 %, and natural initial pH. Although high concentrations of ammonia-nitrogen (NH4-N, 1500 mg/kg wet weight) were formed during thermophilic digestion, there was no obvious inhibition occurred. The results indicated that rice straw can be used as carbon source for the dry co-digestion of sewage sludge under mesophilic and thermophilic conditions.

  7. Mesophilic and thermophilic biotreatment of BTEX-polluted air in reactors.

    PubMed

    Mohammad, Balsam T; Veiga, María C; Kennes, Christian

    2007-08-15

    This study compares the removal of a mixture of benzene, toluene, ethylbenzene, and all three xylene isomers (BTEX) in mesophilic and thermophilic (50 degrees C) bioreactors. In the mesophilic reactor fungi became dominant after long-term operation, while bacteria dominated in the thermophilic unit. Microbial acclimation was achieved by exposing the biofilters to initial BTEX loads of 2-15 g m(-3) h(-1), at an empty bed residence time of 96 s. After adaptation, the elimination capacities ranged from 3 to 188 g m(-3) h(-1), depending on the inlet load, for the mesophilic biofilter with removal efficiencies reaching 96%. On the other hand, in the thermophilic reactor the average removal efficiency was 83% with a maximum elimination capacity of 218 g m(-3) h(-1). There was a clear positive relationship between temperature gradients as well as CO(2) production and elimination capacities across the biofilters. The gas phase was sampled at different depths along the reactors observing that the percentage pollutant removal in each section was strongly dependant on the load applied. The fate of individual alkylbenzene compounds was checked, showing the unusually high biodegradation rate of benzene at high loads under thermophilic conditions (100%) compared to its very low removal in the mesophilic reactor at such load (<10%). Such difference was less pronounced for the other pollutants. After 210 days of operation, the dry biomass content for the mesophilic and thermophilic reactors were 0.300 and 0.114 g g(-1) (support), respectively, reaching higher removals under thermophilic conditions with a lower biomass accumulation, that is, lower pressure drop.

  8. Antibiotic Multiresistance Analysis of Mesophilic and Psychrotrophic Pseudomonas spp. Isolated from Goat and Lamb Slaughterhouse Surfaces throughout the Meat Production Process

    PubMed Central

    Lavilla Lerma, Leyre; Benomar, Nabil; Casado Muñoz, María del Carmen; Gálvez, Antonio

    2014-01-01

    The aim of this study was to investigate the phenotypic and genotypic antibiotic resistance profiles of pseudomonads isolated from surfaces of a goat and lamb slaughterhouse, which were representative of areas that are possible sources of meat contamination. Mesophilic (85 isolates) and psychrotrophic (37 isolates) pseudomonads identified at the species level generally were resistant to sulfamethoxazole, erythromycin, amoxicillin, ampicillin, chloramphenicol, trimethoprim, rifampin, and ceftazidime (especially mesophiles), as well as colistin and tetracycline (especially psychrotrophes). However, they generally were sensitive to ciprofloxacin, gentamicin, imipenem, and kanamycin regardless of species identity. Worryingly, in the present study, we found multidrug resistance (MDR) to up to 13 antibiotics, which was related to intrinsic and acquired resistance mechanisms. Furthermore, a link between various antimicrobial resistance genes was shown for beta-lactams and tetracycline, trimethoprim, and sulfonamides. The distribution and resistome-based analysis of MDR pseudomonads in different slaughterhouse zones indicated that the main sources of the identical or related pseudomonad strains were the animals (feet and wool) and the slaughterhouse environment, being disseminated from the beginning, or entrance environment, to the environment of the finished meat products. Those facts must be taken into consideration to avoid cross-contamination with the subsequent flow of mobile resistance determinants throughout all slaughterhouse zones and then to humans and the environment by the application of adequate practices of hygiene and disinfection measures, including those for animal wool and feet and also the entrance environment. PMID:25172860

  9. Differentiation of Methanosaeta concilii and Methanosarcina barkeri in Anaerobic Mesophilic Granular Sludge by Fluorescent In Situ Hybridization and Confocal Scanning Laser Microscopy†

    PubMed Central

    Rocheleau, Sylvie; Greer, Charles W.; Lawrence, John R.; Cantin, Christiane; Laramée, Louise; Guiot, Serge R.

    1999-01-01

    Oligonucleotide probes, designed from genes coding for 16S rRNA, were developed to differentiate Methanosaeta concilii, Methanosarcina barkeri, and mesophilic methanogens. All M. concilii oligonucleotide probes (designated MS1, MS2, and MS5) hybridized specifically with the target DNA, but MS5 was the most specific M. concilii oligonucleotide probe. Methanosarcina barkeri oligonucleotide probes (designated MB1, MB3, and MB4) hybridized with different Methanosarcina species. The MB4 probe specifically detected Methanosarcina barkeri, and the MB3 probe detected the presence of all mesophilic Methanosarcina species. These new oligonucleotide probes facilitated the identification, localization, and quantification of the specific relative abundance of M. concilii and Methanosarcina barkeri, which play important roles in methanogenesis. The combined use of fluorescent in situ hybridization with confocal scanning laser microscopy demonstrated that anaerobic granule topography depends on granule origin and feeding. Protein-fed granules showed no layered structure with a random distribution of M. concilii. In contrast, a layered structure developed in methanol-enriched granules, where M. barkeri growth was induced in an outer layer. This outer layer was followed by a layer composed of M. concilii, with an inner core of M. concilii and other bacteria. PMID:10224023

  10. Antibiotic multiresistance analysis of mesophilic and psychrotrophic Pseudomonas spp. isolated from goat and lamb slaughterhouse surfaces throughout the meat production process.

    PubMed

    Lavilla Lerma, Leyre; Benomar, Nabil; Casado Muñoz, María del Carmen; Gálvez, Antonio; Abriouel, Hikmate

    2014-11-01

    The aim of this study was to investigate the phenotypic and genotypic antibiotic resistance profiles of pseudomonads isolated from surfaces of a goat and lamb slaughterhouse, which were representative of areas that are possible sources of meat contamination. Mesophilic (85 isolates) and psychrotrophic (37 isolates) pseudomonads identified at the species level generally were resistant to sulfamethoxazole, erythromycin, amoxicillin, ampicillin, chloramphenicol, trimethoprim, rifampin, and ceftazidime (especially mesophiles), as well as colistin and tetracycline (especially psychrotrophes). However, they generally were sensitive to ciprofloxacin, gentamicin, imipenem, and kanamycin regardless of species identity. Worryingly, in the present study, we found multidrug resistance (MDR) to up to 13 antibiotics, which was related to intrinsic and acquired resistance mechanisms. Furthermore, a link between various antimicrobial resistance genes was shown for beta-lactams and tetracycline, trimethoprim, and sulfonamides. The distribution and resistome-based analysis of MDR pseudomonads in different slaughterhouse zones indicated that the main sources of the identical or related pseudomonad strains were the animals (feet and wool) and the slaughterhouse environment, being disseminated from the beginning, or entrance environment, to the environment of the finished meat products. Those facts must be taken into consideration to avoid cross-contamination with the subsequent flow of mobile resistance determinants throughout all slaughterhouse zones and then to humans and the environment by the application of adequate practices of hygiene and disinfection measures, including those for animal wool and feet and also the entrance environment.

  11. Differentiation of Methanosaeta concilii and Methanocarcina barkeri in anaerobic mesophilic granular sludge by fluorescent in situ hybridization and confocal scanning laser microscopy

    SciTech Connect

    Rocheleau, S.; Greer, C.W.; Cantin, C.; Laramee, L.; Guiot, S.R.; Lawrence, J.R.

    1999-05-01

    Oligonucleotide probes, designed from genes coding for 16S rRNA, were developed to differentiate Methanosaeta concilii, Methanosarcina barkeri, and mesophilic methanogens. All M. concilii oligonucleotide probes (designated MS1, MS2, and MS5) hybridized specifically with the target DNA, but MS5 was the most specific M. concilii oligonucleotide probe. Methanosarcina barkeri oligonucleotide probes (designated MB1, MB3, and MB4) hybridized with different Methanosarcina species. The MB4 probe specifically detected Methanosarcina barkeri, and the MB3 probe detected the presence of al mesophilic Methanosarcina species. These new oligonucleotide probes facilitated the identification, localization, and quantification of the specific relative abundance of M. concilii and Methanosarcina barkeri, which play important roles in methanogenesis. The combined use of fluorescent in situ hybridization with confocal scanning laser microscopy demonstrated that anaerobic granule topography depends on granule origin and feeding. Protein-fed granules showed no layered structure with a random distribution of M. concilii. In contrast, a layered structure developed in methanol-enriched granules, where M. barkeri growth was induced in an outer layer. This outer layer was followed by a layer composed of M. concilii, with an inner core of M. concilii and other bacteria.

  12. Extensive Gene Acquisition in the Extremely Psychrophilic Bacterial Species Psychroflexus torquis and the Link to Sea-Ice Ecosystem Specialism

    PubMed Central

    Feng, Shi; Powell, Shane M.; Wilson, Richard; Bowman, John P.

    2014-01-01

    Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755T, associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44T. Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism. PMID:24391155

  13. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning.

    PubMed

    Navarro, Ronald R; Hori, Tomoyuki; Inaba, Tomohiro; Matsuo, Kazuyuki; Habe, Hiroshi; Ogata, Atsushi

    2016-05-01

    Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn

  14. The incidence of virulence factors in mesophilic Aeromonas species isolated from farm animals and their environment.

    PubMed Central

    Gray, S. J.; Stickler, D. J.; Bryant, T. N.

    1990-01-01

    Sixty-one isolates of Aeromonas spp. from the faeces of pigs, cows and a variety of associated environmental sources were examined for the characteristics that are reputed to have roles in pathogenicity. Most isolates of Aeromonas hydrophila were cytotoxic (96.4%) and were capable of producing cell elongation factor (75%) and haemagglutinins (67.9%). In contrast few of the Aeromonas caviae isolates produced these three markers (13.6%, 27.3% and 36.4% respectively). In general, Aeromonas sobria occupied an intermediate position (36.4%, 27.3% and 54.5%), but they did produce the highest mean invasion index for HEp-2 cells. Statistical analysis revealed significant associations between the carriage of these factors and it was clear that many isolates of aeromonads from water and animals possessed the full battery of putative virulence factors. PMID:2209733

  15. Affinity of ribosomal protein S8 from mesophilic and (hyper)thermophilic archaea and bacteria for 16S rRNA correlates with the growth temperatures of the organisms.

    PubMed

    Gruber, Thomas; Köhrer, Caroline; Lung, Birgit; Shcherbakov, Dmitri; Piendl, Wolfgang

    2003-08-14

    The ribosomal protein S8 plays a pivotal role in the assembly of the 30S ribosomal subunit. Using filter binding assays, S8 proteins from mesophilic, and (hyper)thermophilic species of the archaeal genus Methanococcus and from the bacteria Escherichia coli and Thermus thermophilus were tested for their affinity to their specific 16S rRNA target site. S8 proteins from hyperthermophiles exhibit a 100-fold and S8 from thermophiles exhibit a 10-fold higher affinity than their mesophilic counterparts. Thus, there is a striking correlation of affinity of S8 proteins for their specific RNA binding site and the optimal growth temperatures of the respective organisms. The stability of individual rRNA-protein complexes might modulate the stability of the ribosome, providing a maximum of thermostability and flexibility at the growth temperature of the organism.

  16. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    PubMed Central

    Esfandiari, Leyla; Wang, Siqing; Wang, Siqi; Banda, Anisha; Lorenzini, Michael; Kocharyan, Gayane; Monbouquette, Harold G.; Schmidt, Jacob J.

    2016-01-01

    A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100–1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids. PMID:27455337

  17. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor.

    PubMed

    Esfandiari, Leyla; Wang, Siqing; Wang, Siqi; Banda, Anisha; Lorenzini, Michael; Kocharyan, Gayane; Monbouquette, Harold G; Schmidt, Jacob J

    2016-07-22

    A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

  18. Sequence-Based Identification of Mycobacterium Species Using the MicroSeq 500 16S rDNA Bacterial Identification System

    PubMed Central

    Patel, Jean Baldus; Leonard, Debra G. B.; Pan, Xai; Musser, James M.; Berman, Richard E.; Nachamkin, Irving

    2000-01-01

    We evaluated the MicroSeq 500 16S rDNA Bacterial Sequencing Kit (PE Applied Biosystems), a 500-bp sequence-based identification system, for its ability to identify clinical Mycobacterium isolates. The organism identity was determined by comparing the 16S rDNA sequence to the MicroSeq database, which consists primarily of type strain sequences. A total of 113 isolates (18 different species), previously recovered and identified by routine methods from two clinical laboratories, were analyzed by the MicroSeq method. Isolates with discordant results were analyzed by hsp65 gene sequence analysis and in some cases repeat phenotypic identification, AccuProbe rRNA hybridization (Gen-Probe, Inc., San Diego, Calif.), or high-performance liquid chromatography of mycolic acids. For 93 (82%) isolates, the MicroSeq identity was concordant with the previously reported identity. For 18 (16%) isolates, the original identification was discordant with the MicroSeq identification. Of the 18 discrepant isolates, 7 (six unique sequences) were originally misidentified by phenotypic analysis or the AccuProbe assay but were correctly identified by the MicroSeq assay. Of the 18 discrepant isolates, 11 (seven unique sequences) were unusual species that were difficult to identify by phenotypic methods and, in all but one case, by molecular methods. The remaining two isolates (2%) failed definitive phenotypic identification, but the MicroSeq assay was able to definitively identify one of these isolates. The MicroSeq identification system is an accurate and rapid method for the identification of Mycobacterium spp. PMID:10618095

  19. A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species.

    PubMed

    Sakai, Yoriko; Ogawa, Naoto; Shimomura, Yumi; Fujii, Takeshi

    2014-03-01

    Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium Burkholderia sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from Burkholderia sp. YI23 and pBVIE01 from Burkholderia sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven Burkholderia strains and a strain of Cupriavidus, which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.

  20. Binding interface between the Salmonella σS/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl

    PubMed Central

    Cavaliere, Paola; Sizun, Christina; Levi-Acobas, Fabienne; Nowakowski, Mireille; Monteil, Véronique; Bontems, François; Bellalou, Jacques; Mayer, Claudine; Norel, Françoise

    2015-01-01

    In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σS accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σS binding to the Crl protein increases σS activity by favouring its association to E. Taking advantage of evolution of the σS sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σS to the S. Typhimurium σS-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σS and to generate in silico models of the σS-Crl complex constrained by mutational analysis. The σS-Crl models suggest that the identified arginine in σS interacts with an aspartate of Crl that is required for σS binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σS-Crl complex. PMID:26338235

  1. Extremophiles in Mineral Sulphide Heaps: Some Bacterial Responses to Variable Temperature, Acidity and Solution Composition

    PubMed Central

    Watling, Helen R.; Shiers, Denis W.; Collinson, David M.

    2015-01-01

    In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity. PMID:27682094

  2. Extremophiles in Mineral Sulphide Heaps: Some Bacterial Responses to Variable Temperature, Acidity and Solution Composition.

    PubMed

    Watling, Helen R; Shiers, Denis W; Collinson, David M

    2015-07-09

    In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity.

  3. Extremophiles in Mineral Sulphide Heaps: Some Bacterial Responses to Variable Temperature, Acidity and Solution Composition

    PubMed Central

    Watling, Helen R.; Shiers, Denis W.; Collinson, David M.

    2015-01-01

    In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity.

  4. Cognitive skills and bacterial load: comparative evidence of costs of cognitive proficiency in birds

    NASA Astrophysics Data System (ADS)

    Soler, Juan José; Peralta-Sánchez, Juan Manuel; Martín-Vivaldi, Manuel; Martín-Platero, Antonio Manuel; Flensted-Jensen, Einar; Møller, Anders Pape

    2012-02-01

    Parasite-mediated selection may affect the evolution of cognitive abilities because parasites may influence development of the brain, but also learning capacity. Here, we tested some predictions of this hypothesis by analyzing the relationship between complex behaviours (feeding innovations (as a measure of behavioural flexibility) and ability to detect foreign eggs in their nests (i.e. a measure of discriminatory ability)) and abundance of microorganisms in different species of birds. A positive relationship would be predicted if these cognitive abilities implied a larger number of visited environments, while if these skills favoured detection and avoidance of risky environments, a negative relationship would be the prediction. Bacterial loads of eggshells, estimated for mesophilic and potentially pathogenic bacteria (i.e. Enterococcus, Staphylococcus and Enterobacteriaceae), were used as a surrogate of probability of contact with pathogenic bacteria. We found that bird species with higher feeding innovation rates and rejection rates of experimental brood parasitic eggs had higher density of bacteria on their eggshells than the average species. Since the analysed groups of microorganisms include pathogenic bacteria, these results suggest that both feeding innovation and ability to recognize foreign eggs are costly and highlight the importance of parasite-mediated selection in explaining the evolution of cognitive abilities in animals.

  5. Microbial community structure in a thermophilic aerobic digester used as a sludge pretreatment process for the mesophilic anaerobic digestion and the enhancement of methane production.

    PubMed

    Jang, Hyun Min; Park, Sang Kyu; Ha, Jeong Hyub; Park, Jong Moon

    2013-10-01

    An effective two-stage sewage sludge digestion process, consisting of thermophilic aerobic digestion (TAD) followed by mesophilic anaerobic digestion (MAD), was developed for efficient sludge reduction and methane production. Using TAD as a biological pretreatment, the total volatile suspended solid reduction (VSSR) and methane production rate (MPR) in the MAD reactor were significantly improved. According to denaturing gradient gel electrophoresis (DGGE) analysis, the results indicated that the dominant bacteria species such as Ureibacillus thermophiles and Bacterium thermus in TAD were major routes for enhancing soluble organic matter. TAD pretreatment using a relatively short SRT of 1 day showed highly increased soluble organic products and positively affected an increment of bacteria populations which performed interrelated microbial metabolisms with methanogenic species in the MAD; consequently, a quantitative real-time PCR indicated greatly increased Methanosarcinales (acetate-utilizing methanogens) in the MAD, resulting in enhanced methane production.

  6. Comparative performance of mesophilic and thermophilic anaerobic digestion for high-solid sewage sludge.

    PubMed

    Hidaka, Taira; Wang, Feng; Togari, Taketo; Uchida, Tsutomu; Suzuki, Yutaka

    2013-12-01

    In local cities, many small sewage and waste treatment facilities are operated independently. To encourage processing by anaerobic digestion at a centralized sewage treatment plant (STP), high-solid sewage sludge is helpful because it reduces the energy and cost required for transporting the sludge from other STPs. Mesophilic and thermophilic anaerobic digestion of sewage sludge at total solids concentrations (TS) of 7.5% and 10% were evaluated using laboratory-scale continuous reactors. Under the mesophilic condition, sewage sludge of 10% TS was successfully treated. Under the thermophilic condition, sewage sludge of 7.5% TS was not successfully treated when the total ammonia concentration was over 2000 mg N/L. Batch experiments showed that it takes a few weeks for the methane fermentation activity to recover after being inhibited. The effectiveness of adding easily biodegradable organic matter was confirmed. These results show that high-solid sewage sludge is suitable for small facilities by controlling the operating conditions.

  7. Comparison of dry medium culture plates for mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products.

    PubMed

    Park, Junghyun; Kim, Myunghee

    2013-12-01

    This study was performed to compare the performance of Sanita-Kun dry medium culture plate with those of traditional culture medium and Petrifilm dry medium culture plate for the enumeration of the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet. Mesophilic aerobic bacteria were comparatively evaluated in milk, ice cream, ham, and codfish fillet using Sanita-Kun aerobic count (SAC), Petrifilm aerobic count (PAC), and traditional plate count agar (PCA) media. According to the results, all methods showed high correlations of 0.989~1.000 and no significant differences were observed for enumerating the mesophilic aerobic bacteria in the tested food products. SAC method was easier to perform and count colonies efficiently as compared to the PCA and PAC methods. Therefore, we concluded that the SAC method offers an acceptable alternative to the PCA and PAC methods for counting the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products. PMID:24551829

  8. Comparison of dry medium culture plates for mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products.

    PubMed

    Park, Junghyun; Kim, Myunghee

    2013-12-01

    This study was performed to compare the performance of Sanita-Kun dry medium culture plate with those of traditional culture medium and Petrifilm dry medium culture plate for the enumeration of the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet. Mesophilic aerobic bacteria were comparatively evaluated in milk, ice cream, ham, and codfish fillet using Sanita-Kun aerobic count (SAC), Petrifilm aerobic count (PAC), and traditional plate count agar (PCA) media. According to the results, all methods showed high correlations of 0.989~1.000 and no significant differences were observed for enumerating the mesophilic aerobic bacteria in the tested food products. SAC method was easier to perform and count colonies efficiently as compared to the PCA and PAC methods. Therefore, we concluded that the SAC method offers an acceptable alternative to the PCA and PAC methods for counting the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products.

  9. Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes

    SciTech Connect

    Karpinets, Tatiana V; Obraztsova, Anna Y; Wang, Yanbin; Schmoyer, Denise D; Kora, Guruprasad H; Kothe, T Brett; Serres, Margrethe H.; Romine, Margaret F; Fredrickson, Jim K; Nealson, Kenneth H.; Uberbacher, Edward C; Land, Miriam L

    2009-01-01

    In spite of a rapid growth in the number of sequenced bacteria and significant progress in the annotation of their genomes, current computational technologies are limited in their capability to associate the genotype of a sequenced bacterial organism with its phenotypic traits. We evaluated two novel, complimentary approaches that can facilitate this task. They are based on correlation between the numbers of the trait-specific protein families or Pfam domains and a quantitative characteristic of the phenotypic trait among different bacterial species. Our first, a top-down approach, involves quantification and comparison of a higher-level characteristic, a bacterial phenotype, to reveal genomic characteristics and specific genes related to the phenotype. The second, a bottom-up approach, predicts phenotypes by quantification of molecular functions in the genomes of closely related bacterial species and by following pair-wise correlation of the molecular functions enrichments and their network clustering. The approach is implemented using network analysis tools. The approaches were validated by a comparison of 19 sequenced Shewanella species. Using the first approach, we were able to identify specific domains and gene clusters associated with cold tolerance of these mesophilic species and to predict some novel cellular mechanisms underlying the phenotype. We find that in three tested species both cold and salt tolerance relate to presence in their genome of a specific Na+/H+ antiporter. By using the second approach we identified genomic clusters predicting several environmentally relevant phenotypes in the newly sequenced Shewanella species including degradation of aromatic compounds by an aerobic hybrid pathway, utilization of ethanolamine, and arsenic and copper resistance. Results of the study confirm validity of the approaches and their utility for (i) computational predictions of phenotypic traits in the sequenced organisms, (ii) revealing genomic determinants

  10. Differences in the catalytic mechanisms of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures

    SciTech Connect

    Zaccardi, Margot J.; Mannweiler, Olga; Boehr, David D.

    2012-02-10

    Highlights: Black-Right-Pointing-Pointer Catalytic mechanisms of thermophilic-mesophilic enzymes may differ. Black-Right-Pointing-Pointer Product release is rate-determining for thermophilic IGPS at low temperatures. Black-Right-Pointing-Pointer But at higher temperatures, proton transfer from the general acid is rate-limiting. Black-Right-Pointing-Pointer Rate-determining step is different still for mesophilic IGPS. Black-Right-Pointing-Pointer Both chemical and physical steps of catalysis are important for temperature adaptation. -- Abstract: Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An alternative hypothesis, however, is that complementary thermophilic-mesophilic enzyme pairs simply operate through different evolutionary-optimized catalytic mechanisms. In this communication, we present evidence that while the steps of the catalytic mechanisms for mesophilic and thermophilic indole-3-glycerol phosphate synthase (IGPS) enzymes are fundamentally similar, the identity of the rate-determining step changes as a function of temperature. Our findings indicate that while product release is rate-determining at 25 Degree-Sign C for thermophilic IGPS, near its adaptive temperature (75 Degree-Sign C), a proton transfer event, involving a general acid, becomes rate-determining. The rate-determining steps for thermophilic and mesophilic IGPS enzymes are also different at their respective, adaptive temperatures with the mesophilic IGPS-catalyzed reaction being rate-limited before irreversible CO{sub 2} release, and the thermophilic IGPS

  11. Enhancing ethanol production from thermophilic and mesophilic solid digestate using ozone combined with aqueous ammonia pretreatment.

    PubMed

    Wang, Dianlong; Xi, Jiang; Ai, Ping; Yu, Liang; Zhai, Hong; Yan, Shuiping; Zhang, Yanlin

    2016-05-01

    Pretreatment with ozone combined with aqueous ammonia was used to recover residual organic carbon from recalcitrant solid digestate for ethanol production after anaerobic digestion (AD) of rice straw. Methane yield of AD at mesophilic and thermophilic conditions, and ethanol production of solid digestate were investigated. The results showed that the methane yield at thermophilic temperature was 72.2% higher than that at mesophilic temperature under the same conditions of 24days and 17% solid concentration. And also the ethanol production efficiency of solid digestate after thermophilic process was 24.3% higher than that of solid digestate after mesophilic process. In this study, the optimal conditions for integrated methane and ethanol processes were determined as 55°C, 17% solid concentration and 24days. 58.6% of glucose conversion, 142.8g/kg of methane yield and 65.2g/kg of ethanol yield were achieved, and the highest net energy balance was calculated as 6416kJ/kg.

  12. A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding.

    PubMed

    Longo, Liam M; Tenorio, Connie A; Kumru, Ozan S; Middaugh, C Russell; Blaber, Michael

    2015-01-01

    The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate "cradle" for proteogenesis. In this viewpoint, a subsequent halophile-to-mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original "prebiotic" set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile-to-mesophile transition by hydrophobic core-packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a "primitive" designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)-having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a "primitive" polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile-to-mesophile protein folding adaptation-identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.

  13. Performance comparison between mesophilic and thermophilic anaerobic reactors for treatment of palm oil mill effluent.

    PubMed

    Jeong, Joo-Young; Son, Sung-Min; Pyon, Jun-Hyeon; Park, Joo-Yang

    2014-08-01

    The anaerobic digestion of palm oil mill effluent (POME) was carried out under mesophilic (37°C) and thermophilic (55°C) conditions without long-time POME storage in order to compare the performance of each condition in the field of Sumatra Island, Indonesia. The anaerobic treatment system was composed of anaerobic hybrid reactor and anaerobic baffled filter. Raw POME was pretreated by screw decanter to reduce suspended solids and residual oil. The total COD removal rate of 90-95% was achieved in both conditions at the OLR of 15kg[COD]/m(3)/d. The COD removal in thermophilic conditions was slightly better, however the biogas production was much higher than that in the mesophilic one at high OLR. The organic contents in pretreated POME were highly biodegradable in mesophilic under the lower OLRs. The biogas production was 13.5-20.0l/d at the 15kg[COD]/m(3)/d OLR, and the average content of carbon dioxide was 5-35% in both conditions. PMID:24797939

  14. Performance comparison between mesophilic and thermophilic anaerobic reactors for treatment of palm oil mill effluent.

    PubMed

    Jeong, Joo-Young; Son, Sung-Min; Pyon, Jun-Hyeon; Park, Joo-Yang

    2014-08-01

    The anaerobic digestion of palm oil mill effluent (POME) was carried out under mesophilic (37°C) and thermophilic (55°C) conditions without long-time POME storage in order to compare the performance of each condition in the field of Sumatra Island, Indonesia. The anaerobic treatment system was composed of anaerobic hybrid reactor and anaerobic baffled filter. Raw POME was pretreated by screw decanter to reduce suspended solids and residual oil. The total COD removal rate of 90-95% was achieved in both conditions at the OLR of 15kg[COD]/m(3)/d. The COD removal in thermophilic conditions was slightly better, however the biogas production was much higher than that in the mesophilic one at high OLR. The organic contents in pretreated POME were highly biodegradable in mesophilic under the lower OLRs. The biogas production was 13.5-20.0l/d at the 15kg[COD]/m(3)/d OLR, and the average content of carbon dioxide was 5-35% in both conditions.

  15. Comparison of mesophilic and thermophilic feruloyl esterases: characterization of their substrate specificity for methyl phenylalkanoates.

    PubMed

    Topakas, Evangelos; Christakopoulos, Paul; Faulds, Craig B

    2005-02-23

    The active sites of feruloyl esterases from mesophilic and thermophilic sources were probed using methyl esters of phenylalkanoic acids. Only 13 out of 26 substrates tested were significant substrates for all the enzymes. Lengthening or shortening the aliphatic side chain while maintaining the same aromatic substitutions completely abolished activity for both enzymes, which demonstrates the importance of the correct distance between the aromatic group and the ester bond. Maintaining the phenylpropanoate structure but altering the substitutions of the aromatic ring demonstrated that the type-A esterase from the mesophilic fungus Fusarium oxysporum (FoFaeA) showed a preference for methoxylated substrates, in contrast to the type-B esterase from the same source (FoFaeB) and the thermophilic type-B (StFaeB) and type-C (StFaeC) from Sporotrichum thermophile, which preferred hydroxylated substrates. All four esterases hydrolyzed short chain aliphatic acid (C2-C4) esters of p-nitrophenol, but not the C12 ester of laurate. All the feruloyl esterases were able to release ferulic acid from the plant cell wall material in conjunction with a xylanase, but only the type-A esterase FoFaeA was effective in releasing the 5,5' form of diferulic acid. The thermophilic type-B esterase had a lower catalytic efficiency than its mesophilic counterpart, but released more ferulic acid from plant cell walls.

  16. Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.

    PubMed

    Gunnigle, Eoin; Nielsen, Jeppe L; Fuszard, Matthew; Botting, Catherine H; Sheahan, Jerome; O'Flaherty, Vincent; Abram, Florence

    2015-12-01

    Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD.

  17. Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.

    PubMed

    Gunnigle, Eoin; Nielsen, Jeppe L; Fuszard, Matthew; Botting, Catherine H; Sheahan, Jerome; O'Flaherty, Vincent; Abram, Florence

    2015-12-01

    Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD. PMID:26507125

  18. Mesophilic, Circumneutral Anaerobic Iron Oxidation as a Remediation Mechanism for Radionuclides, Nitrate and Perchlorate

    NASA Astrophysics Data System (ADS)

    Bose, S.; Thrash, J. C.; Coates, J. D.

    2008-12-01

    Iron oxidation is a novel anaerobic metabolism where microorganisms obtain reducing equivalents from the oxidization of Fe(II) and assimilate carbon from organic carbon compounds or CO2. Recent evidence indicates that in combination with the activity of dissimilatory Fe(III)-reducing bacteria, anaerobic microbial Fe(II) oxidation can also contribute to the global iron redox cycle. Studies have also proved that Fe(II)- oxidation is ubiquitous in diverse environments and produce a broad range of insoluble iron forms as end products. These biogenic Fe(III)-oxides and mixed valence Fe minerals have a very high adsorption capacity of heavy metals and radionuclides. Adsorption and immobilization by these biogenic Fe phases produced at circumneutral pH, is now considered a very effective mode of remediation of radionuclides like Uranium, especially under variable redox conditions. By coupling soluble and insoluble Fe(II) oxidation with nitrate and perchlorate as terminal electron acceptors in-situ, anaerobic Fe-oxidation can also be used for environmental cleanup of Fe through Fe-mineral precipitation, as well as nitrate and perchlorate through reduction. Coupling of Fe as the sole electron and energy source to the reduction of perchlorate or nitrate boosts the metabolism without building up biomass hence also taking care of biofouling. To understand the mechanisms by which microorganisms can grow at circumneutral pH by mesophilic, anaerobic iron oxidation and the ability of microorganisms to reduce nitrate and perchlorate coupled to iron oxidation recent work in our lab involved the physiological characterization of Dechlorospirillum strain VDY which was capable of anaerobic iron-oxidation with either nitrate or perchlorate serving as terminal electron acceptor. Under non-growth conditions, VDY oxidized 3mM Fe(II) coupled to nitrate reduction, and 2mM Fe(II) coupled to perchlorate reduction, in 24 hours. It contained a copy of the RuBisCO cbbM subunit gene which was

  19. Mechanisms of bacterial pathogenicity

    PubMed Central

    Wilson, J; Schurr, M; LeBlanc, C; Ramamurthy, R; Buchanan, K; Nickerson, C

    2002-01-01

    Pathogenic bacteria utilise a number of mechanisms to cause disease in human hosts. Bacterial pathogens express a wide range of molecules that bind host cell targets to facilitate a variety of different host responses. The molecular strategies used by bacteria to interact with the host can be unique to specific pathogens or conserved across several different species. A key to fighting bacterial disease is the identification and characterisation of all these different strategies. The availability of complete genome sequences for several bacterial pathogens coupled with bioinformatics will lead to significant advances toward this goal. PMID:11930024

  20. Correlation between antibiotic and biocide resistance in mesophilic and psychrotrophic Pseudomonas spp. isolated from slaughterhouse surfaces throughout meat chain production.

    PubMed

    Lavilla Lerma, Leyre; Benomar, Nabil; Casado Muñoz, María del Carmen; Gálvez, Antonio; Abriouel, Hikmate

    2015-10-01

    The aim of this study was to evaluate biocide susceptibility in mesophilic and psychrotrophic pseudomonads isolated from surfaces of a goat and lamb slaughterhouse, which was representative of the region. To determine biocide resistance in pseudomonads, we determined for the first time the epidemiological cut-off values (ECOFFs) of benzalkonium, cetrimide, chlorhexidine, hexachlorophene, P3 oxonia, polyhexamethylene guanidine hydrochloride (PHMG), topax 66 and triclosan being generally very similar in different Pseudomonas spp. with some exceptions. Thus, resistance of pseudomonads was mainly shown to triclosan, and in lesser extent to cetrimide and benzalkonium chloride depending on the species, however they were highly susceptible to industrial formulations of biocides. By means of statistical analysis, positive correlations between antibiotics, biocides and both antimicrobials in pseudomonads were detected suggesting a co- or cross resistance between different antimicrobials in goat and lamb slaughterhouse environment. Cross-resistance between biocides and antibiotics in pseudomonads were especially detected between PHMG or triclosan and different antibiotics depending on the biocide and the population type. Thus, the use of those biocides as disinfectant in slaughterhouse zones must be carefully evaluated because of the selection pressure effect of antimicrobials on the emergence of resistant bacteria which could be spread to the consumer. It is noteworthy that specific industrial formulations such as topax 66 and oxonia P3 showed few correlations with antibiotics (none or 1-2 antibiotics) which should be taken into consideration for disinfection practices in goat and lamb slaughterhouse. PMID:26187825

  1. Bioenergy production from diluted poultry manure and microbial consortium inside Anaerobic Sludge Bed Reactor at sub-mesophilic conditions.

    PubMed

    Jaxybayeva, Aigerim; Yangin-Gomec, Cigdem; Cetecioglu, Zeynep; Ozbayram, E Gozde; Yilmaz, Fatih; Ince, Orhan

    2014-01-01

    In this study, anaerobic treatability of diluted chicken manure (with an influent feed ratio of 1 kg of fresh chicken manure to 6 L of tap water) was investigated in a lab-scale anaerobic sludge bed (ASB) reactor inoculated with granular seed sludge. The ASB reactor was operated at ambient temperature (17-25°C) in order to avoid the need of external heating up to higher operating temperatures (e.g., up to 35°C for mesophilic digestion). Since heat requirement for raising the temperature of incoming feed for digestion is eliminated, energy recovery from anaerobic treatment of chicken manure could be realized with less operating costs. Average biogas production rates were calculated ca. 210 and 242 L per kg of organic matter removed from the ASB reactor at average hydraulic retention times (HRTs) of 13 and 8.6 days, respectively. Moreover, average chemical oxygen demand (COD) removal of ca. 89% was observed with suspended solids removal more than 97% from the effluent of the ASB reactor. Influent ammonia, on the other hand, did not indicate any free ammonia inhibition due to dilution of the raw manure while pH and alkalinity results showed stability during the study. Microbial quantification results indicated that as the number of bacterial community decreased, the amount of Archaea increased through the effective digestion volume of the ASB reactor. Moreover, the number of methanogens displayed an uptrend like archaeal community and a strong correlation (-0.645) was found between methanogenic community and volatile fatty acid (VFA) concentration especially acetate. PMID:25065830

  2. Bacterial Sialidase

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Data shows that elevated sialidase in bacterial vaginosis patients correlates to premature births in women. Bacterial sialidase also plays a significant role in the unusual colonization of Pseudomonas aeruginosa in cystic fibrosis patients. Crystals of Salmonella sialidase have been reproduced and are used for studying the inhibitor-enzyme complexes. These inhibitors may also be used to inhibit a trans-sialidase of Trypanosome cruzi, a very similar enzyme to bacterial sialidase, therefore preventing T. cruzi infection, the causitive agent of Chagas' disease. The Center for Macromolecular Crystallography suggests that inhibitors of bacterial sialidases can be used as prophylactic drugs to prevent bacterial infections in these critical cases.

  3. In vivo photosystem I reduction in thermophilic and mesophilic cyanobacteria: The thermal resistance of the process is limited by factors other than the unfolding of the partners

    SciTech Connect

    Duran, Raul V.; Hervas, Manuel; Rosa, Miguel A. de la; Navarro, Jose A. . E-mail: jnavarro@ibvf.csic.es

    2005-08-19

    Photosystem I reduction by plastocyanin and cytochrome c {sub 6} in cyanobacteria has been extensively studied in vitro, but much less information is provided on this process inside the cell. Here, we report an analysis of the electron transfer from both plastocyanin and cytochrome c {sub 6} to photosystem I in intact cells of several cyanobacterial species, including a comparative study of the temperature effect in mesophilic and thermophilic organisms. Our data show that cytochrome c {sub 6} reduces photosystem I by following a reaction mechanism involving complex formation, whereas the copper-protein follows a simpler collisional mechanism. These results contrast with previous kinetic studies in vitro. The effect of temperature on photosystem I reduction leads us to conclude that the thermal resistance of this process is determined by factors other than the proper stability of the protein partners.

  4. Intact Membrane Lipids of “Candidatus Nitrosopumilus maritimus,” a Cultivated Representative of the Cosmopolitan Mesophilic Group I Crenarchaeota▿

    PubMed Central

    Schouten, Stefan; Hopmans, Ellen C.; Baas, Marianne; Boumann, Henry; Standfest, Sonja; Könneke, Martin; Stahl, David A.; Sinninghe Damsté, Jaap S.

    2008-01-01

    In this study we analyzed the membrane lipid composition of “Candidatus Nitrosopumilus maritimus,” the only cultivated representative of the cosmopolitan group I crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of “Ca. Nitrosopumilus maritimus” consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belonging to the group I.1a crenarchaeota. Intact polar lipid analysis revealed that the GDGTs have hexose, dihexose, and/or phosphohexose head groups. Similar polar lipids were previously found in deeply buried sediments from the Peru margin, suggesting that they were in part synthesized by group I crenarchaeota. PMID:18296531

  5. Bacterial surface adaptation

    NASA Astrophysics Data System (ADS)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  6. Scouring Potential of Mesophile Acidic Proteases of Pseudomonas aeruginosa for Grey Cotton Fabrics

    NASA Astrophysics Data System (ADS)

    Saravanan, D.

    2013-04-01

    Mesophile, acidic proteases were produced using the microbial source, Pseudomonas aeruginosa, with wider thermal tolerances. Process conditions of scouring treatment were optimized using Taguchi method for optimum temperature, time, pH and concentration of protease. Treatment with the protease lower weight loss values compared to the alkali scouring, however, significant improvement in the absorbency compared to the grey samples was observed. Large amounts of pectin left out in the samples resulted in higher extractable impurities, substantiated by the FTIR results. Relatively, lower reduction in the tear strengths was observed in both warp and weft directions after protease treatment of the cotton fabrics.

  7. Bacterial Proteasomes

    PubMed Central

    Jastrab, Jordan B.; Darwin, K. Heran

    2015-01-01

    Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology. PMID:26488274

  8. Staining bacterial flagella easily.

    PubMed Central

    Heimbrook, M E; Wang, W L; Campbell, G

    1989-01-01

    A wet-mount technique for staining bacterial flagella is highly successful when a stable stain and regular slides and cover slips are used. Although not producing a permanent mount, the technique is simple for routine use when the number and arrangement of flagella are critical in identifying species of motile bacteria. Images PMID:2478573

  9. Identification of bacterial species associated with the sheep scab mite (Psoroptes ovis) by using amplified genes coding for 16S rRNA.

    PubMed

    Hogg, J C; Lehane, M J

    1999-09-01

    This was the first molecular study of the bacterial flora of the sheep scab mite (Psoroptes ovis). A sequence analysis of genes coding for 16S rRNA revealed that Serratia marcescens and bacteria closely related to Staphylococcus intermedius or Staphylococcus chromogens and Alloiococcus otitidis were present. These bacteria were associated with skin lesions, dermatitis, and otitis media caused by P. ovis.

  10. Gram-negative bacterial isolates from fresh-cut processing plants enhance the presence of Escherichia Coli O157:H7 in dual-species biofilms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biofilms formed by resident microflora may provide a microenvironment for foodborne bacterial pathogens to survive and cause cross-contamination in fresh-cut processing and handling facilities. The objective of this study is to determine the impact of individual bacteria strains isolated from two l...

  11. Study of the cellulases produced by three mesophilic actinomycetes grown on bagasse as substrate

    SciTech Connect

    Van Zyl, W.H.

    1985-09-01

    The cellulases that strains of Streptomyces albogrisolus, S. nitrosporeus, and Micromonospora melanosporea produce when grown on untreated ballmilled bagasse were investigated. Optimum conditions for extracellular cellulase production and activity were determined to be growth at pH 6.7-7.4 and 25-35 degrees C for 4-5 days and assay at pH 5.0-6.0 and 45-55 degrees C, respectively. The endoglucanases were thermally stable at 50 degrees C, but the Avicelases had a half-life of approximately 24 hours at this temperature. Nearly half of the endoglucanases and almost all of the Avicelases were absorbed on ballmilled bagasse after 15 minutes incubation at 50 degrees C. The ..beta..-glucosidases were found to be mainly intracellular or cell wall bound. These mesophilic actinomycetes concomitantly produced xylanases and ..beta..-xylosidases with cellulases that, apart from cellobiose and glucose, also release xylose from bagasse. This feature may be advantageous in the commercial application of the enzymes of mesophilic actinomycetes for the saccharification of natural cellulosic substrates.

  12. Strategies for changing temperature from mesophilic to thermophilic conditions in anaerobic CSTR reactors treating sewage sludge.

    PubMed

    Bousková, A; Dohányos, M; Schmidt, J E; Angelidaki, I

    2005-04-01

    Thermophilic anaerobic digestion presents an advantageous way for stabilization of sludge from wastewater treatment plants. Two different strategies for changing operational process temperature from mesophilic (37 degrees C) to thermophilic (55 degrees C) were tested using two continuous flow stirred tank reactors operated at constant organic loading rate of 1.38 g VS/l reactor/day and hydraulic retention time of 20 days. In reactor A, the temperature was increased step-wise: 37 degrees C-->42 degrees C-->47 degrees C-->51 degrees C-->55 degrees C. While in reactor B, the temperature was changed in one-step, from 37 degrees C to the desired temperature of 55 degrees C, The results showed that the overall adaptation of the process for the step-wise temperature increment took 70 days in total and a new change was applied when the process was stabilized as indicated by stable methane production and low volatile fatty acids concentrations. Although the one-step temperature increase caused a severe disturbance in all the process parameters, the system reached a new stable operation after only 30 days indicating that this strategy is the best in changing from mesophilic to thermophilic operation in anaerobic digestion plants.

  13. Double Mutation in Photosystem II Reaction Centers and Elevated CO2 Grant Thermotolerance to Mesophilic Cyanobacterium

    PubMed Central

    Dinamarca, Jorge; Shlyk-Kerner, Oksana; Kaftan, David; Goldberg, Eran; Dulebo, Alexander; Gidekel, Manuel; Gutierrez, Ana; Scherz, Avigdor

    2011-01-01

    Photosynthetic biomass production rapidly declines in mesophilic cyanobacteria grown above their physiological temperatures largely due to the imbalance between degradation and repair of the D1 protein subunit of the heat susceptible Photosystem II reaction centers (PSIIRC). Here we show that simultaneous replacement of two conserved residues in the D1 protein of the mesophilic Synechocystis sp. PCC 6803, by the analogue residues present in the thermophilic Thermosynechococcus elongatus, enables photosynthetic growth, extensive biomass production and markedly enhanced stability and repair rate of PSIIRC for seven days even at 43°C but only at elevated CO2 (1%). Under the same conditions, the Synechocystis control strain initially presented very slow growth followed by a decline after 3 days. Change in the thylakoid membrane lipids, namely the saturation of the fatty acids is observed upon incubation for the different strains, but only the double mutant shows a concomitant major change of the enthalpy and entropy for the light activated QA−→QB electron transfer, rendering them similar to those of the thermophilic strain. Following these findings, computational chemistry and protein dynamics simulations we propose that the D1 double mutation increases the folding stability of the PSIIRC at elevated temperatures. This, together with the decreased impairment of D1 protein repair under increased CO2 concentrations result in the observed photothermal tolerance of the photosynthetic machinery in the double mutant PMID:22216094

  14. Exploring local flexibility/rigidity in psychrophilic and mesophilic carbonic anhydrases.

    PubMed

    Chiuri, R; Maiorano, G; Rizzello, A; del Mercato, L L; Cingolani, R; Rinaldi, R; Maffia, M; Pompa, P P

    2009-02-18

    Molecular flexibility and rigidity are required to determine the function and specificity of protein molecules. Some psychrophilic enzymes demonstrate a higher catalytic efficiency at low temperatures, compared to the efficiency demonstrated by their meso/thermophilic homologous. The emerging picture suggests that such enzymes have an improved flexibility of the structural catalytic components, whereas other protein regions far from functional sites may be even more rigid than those of their mesophilic counterparts. To gain a deeper insight in the analysis of the activity-flexibility/rigidity relationship in protein structure, psychrophilic carbonic anhydrase of the Antarctic teleost Chionodraco hamatus has been compared with carbonic anhydrase II of Bos taurus through fluorescence studies, three-dimensional modeling, and activity analyses. Data demonstrated that the cold-adapted enzyme exhibits an increased catalytic efficiency at low and moderate temperatures and, more interestingly, a local flexibility in the region that controls the correct folding of the catalytic architecture, as well as a rigidity in the hydrophobic core. The opposite result was observed in the mesophilic counterpart. These results suggest a clear relationship between the activity and the presence of flexible and rigid protein substructures that may be useful in rational molecular and drug design of a class of enzymes playing a key role in pathologic processes.

  15. An analysis of temperature adaptation in cold active, mesophilic and thermophilic Bacillus α-amylases.

    PubMed

    Mahdavi, Atiyeh; Sajedi, Reza H; Asghari, S Mohsen; Taghdir, Majid; Rassa, Mehdi

    2011-12-01

    A comparative biochemical and structural study was performed on a cold active α-amylase from Bacillus cereus (BCA) and two well-known homologous mesophilic and thermophilic α-amylases from Bacillus amyloliquefaciens (BAA) and Bacillus licheniformis (BLA). In spite of a high degree of sequence and structural similarity, drastic variations were found for T(opt) as 50, 70 and 90°C for BCA, BAA and BLA, respectively. The half-lives of thermoinactivation were 1 and 9 min for BCA and BAA at 80°C respectively, whilst there was no inactivation for BLA at this temperature. Thermodynamic studies on inactivation process suggested that lower thermostability of BCA is due to lower inactivation slope of the Arrhenius plots and subsequently, lower E(a) and ΔH(#). Increased K(m) and accessible surface area for catalytic residues along with a decreased number of internal interactions in this region in BCA compared to BLA suggest that BCA substrate-binding site might be temperature sensitive and is probably more flexible. On the other hand, fewer ion pairs, destructive substitutions and disruption of aromatic interaction networks in structurally critical regions of Bacillus α-amylases result in a severe decrease in BCA thermostability compared to its mesophilic and thermophilic homologues.

  16. A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

    PubMed Central

    Jung, Man-Young; Park, Soo-Je; Kim, So-Jeong; Kim, Jong-Geol; Sinninghe Damsté, Jaap S.

    2014-01-01

    Soil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e., Nitrosopumilus maritimus and “Candidatus Nitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited ammonia oxidation, while ammonia oxidation itself was not inhibited in the presence of up to 5 mM ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those of N. maritimus and “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “Candidatus Nitrosotenuis chungbukensis” for the ammonia-oxidizing archaeal strain MY2. PMID:24705324

  17. Nest Material Shapes Eggs Bacterial Environment.

    PubMed

    Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

    2016-01-01

    Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

  18. Nest Material Shapes Eggs Bacterial Environment

    PubMed Central

    Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

    2016-01-01

    Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

  19. Bacterial glycosyltransferase toxins.

    PubMed

    Jank, Thomas; Belyi, Yury; Aktories, Klaus

    2015-12-01

    Mono-glycosylation of host proteins is a common mechanism by which bacterial protein toxins manipulate cellular functions of eukaryotic target host cells. Prototypic for this group of glycosyltransferase toxins are Clostridium difficile toxins A and B, which modify guanine nucleotide-binding proteins of the Rho family. However, toxin-induced glycosylation is not restricted to the Clostridia. Various types of bacterial pathogens including Escherichia coli, Yersinia, Photorhabdus and Legionella species produce glycosyltransferase toxins. Recent studies discovered novel unexpected variations in host protein targets and amino acid acceptors of toxin-catalysed glycosylation. These findings open new perspectives in toxin as well as in carbohydrate research.

  20. Ectopic Expression of Hrf1 Enhances Bacterial Resistance via Regulation of Diterpene Phytoalexins, Silicon and Reactive Oxygen Species Burst in Rice

    PubMed Central

    Zhong, Weigong; Yang, Jie; Okada, Kazunori; Yamane, Hisakazu; Zhang, Lei; Wang, Guang; Wang, Dong; Xiao, Shanshan; Chang, Shanshan; Qian, Guoliang; Liu, Fengquan

    2012-01-01

    Harpin proteins as elicitor derived from plant gram negative bacteria such as Xanthomonas oryzae pv. oryzae (Xoo), Erwinia amylovora induce disease resistance in plants by activating multiple defense responses. However, it is unclear whether phytoalexin production and ROS burst are involved in the disease resistance conferred by the expression of the harpinXoo protein in rice. In this article, ectopic expression of hrf1 in rice enhanced resistance to bacterial blight. Accompanying with the activation of genes related to the phytoalexin biosynthesis pathway in hrf1-transformed rice, phytoalexins quickly and consistently accumulated concurrent with the limitation of bacterial growth rate. Moreover, the hrf1-transformed rice showed an increased ability for ROS scavenging and decreased hydrogen peroxide (H2O2) concentration. Furthermore, the localization and relative quantification of silicon deposition in rice leaves was detected by scanning electron microscopy (SEM) and energy-dispersive X-ray spectrometer (EDS). Finally, the transcript levels of defense response genes increased in transformed rice. These results show a correlation between Xoo resistance and phytoalexin production, H2O2, silicon deposition and defense gene expression in hrf1-transformed rice. These data are significant because they provide evidence for a better understanding the role of defense responses in the incompatible interaction between bacterial disease and hrf1-transformed plants. These data also supply an opportunity for generating nonspecific resistance to pathogens. PMID:22970151

  1. Infectious prosthetic hip joint loosening: bacterial species involved in its aetiology and their antibiotic resistance profiles against antibiotics recommended for the therapy of implant-associated infections.

    PubMed

    Bogut, Agnieszka; Niedźwiadek, Justyna; Strzelec-Nowak, Dagmara; Blacha, Jan; Mazurkiewicz, Tomasz; Marczyński, Wojciech; Kozioł-Montewka, Maria

    2014-04-01

    Reliable microbiological diagnosis along with surgery and prolonged antibiotic therapy are key elements in the management of prosthetic-joint infections (PJIs). The purpose of this study was to characterize antibiotic resistance profiles of bacteria involved in the aetiology of PJIs. A total of 33 bacterial isolates cultured from 31 patients undergoing exchange of total hip prostheses were analyzed. The diagnostic approach toward isolation of prosthesis- associated microorganisms included sonication of retrieved implants and conventional cultures of periprosthetic tissues and synovial fluid. The in vitro resistance profiles of bacterial isolates were determined in relation to antibiotics recommended for the therapy of PJIs using the disc diffusion method, E-tests(®) and broth microdilution system. Coagulase-negative staphylococci (CNS) were predominant microorganisms followed by Staphylococcus aureus, Enterobacter cloacae, Streptococcus mitis, and Propionibacterium acnes. Twenty out of 30 and 12 out of 30 staphylococcal isolates were methicillin- and multi-drug resistant, respectively. Only two isolates were rifampicinresistant. All staphylococci were susceptible to glycopeptides and linezolid. This paper stresses the pathogenic role of staphylococci in patients suffering from implant loosening and reports high methicillin- and multidrug-resistance rates in these bacteria. Hence, antimicrobial susceptibility tests of individual bacterial isolates must always be performed to guide selection of the optimal therapeutic option.

  2. Bacterial Keratitis

    MedlinePlus

    ... very quickly, and if left untreated, can cause blindness. The bacteria usually responsible for this type of ... to intense ultraviolet radiation exposure, e.g. snow blindness or welder's arc eye). Next Bacterial Keratitis Symptoms ...

  3. Differential bioleaching of copper by mesophilic and moderately thermophilic acidophilic consortium enriched from same copper mine water sample.

    PubMed

    Marhual, N P; Pradhan, N; Kar, R N; Sukla, L B; Mishra, B K

    2008-11-01

    Three acidophilic enrichment consortium were developed from mine water sample of copper mine site at Khetri, India were compared for their copper leaching efficiency. Out of these one was mesophilic (35 degrees C) and two were moderately thermophilic (50 degrees C). Consortia were named as mesophilic acidophilic chemolithotrophic consortia (MACC), thermophilic acidophilic chemolithotrophic consortia (TACC), and Sulfobacillus acidophilic consortia (SAC). Copper extraction ability of both the thermophilic consortia (77-78% extraction) was almost double to that of mesophilic consortia (40% extraction) at 10% pulp density after 55 days. Both the thermophilic consortia were equally effective in leaching of other metals like Ni, Co, Zn, Mn. After 55 days, the percentage of extractions of copper by TACC was 76, 74, 67, 48 and 45 at 5%, 10%, 15%, 20% and 30% pulp density, respectively. Total number of bacteria was maximum at 5% pulp density which decreases with increase in pulp density. Sulfobacillus-like bacteria were seen in the Sulfobacillus enrichment cultures. Moderately thermophilic consortia proved to be better in leaching performance than the mesophilic counterpart.

  4. Digestion of cattle manure under mesophilic and thermophilic conditions: characterization of organic matter applying thermal analysis and 1H NMR.

    PubMed

    Gómez, X; Blanco, D; Lobato, A; Calleja, A; Martínez-Núñez, F; Martin-Villacorta, J

    2011-06-01

    Digestion of cattle manure collected from a livestock farm together with bedding material (straw) has been studied under mesophilic and thermophilic conditions in batch reactors. The digestion was carried out for a prolonged period with the aim of evaluating the changes undergone by the organic matter. The mesophilic digestion carried out revealed a greater capacity to produce gas and transform organic matter, while a higher conversion rate, but a lower gas yield, was obtained under thermophilic conditions. Degradation of the organic matter was evaluated by means of thermal analysis and (1)H NMR. Stabilisation through anaerobic digestion (either mesophilic or thermophilic) resulted in an increase in the quality of the organic matter, as characterised by an enrichment in thermostable compounds, and an accumulation of long chain aliphatic materials. The experiments performed demonstrated the transformation of organic matter into complex materials under anaerobic conditions with an accumulation of aliphatic components under both types of conditions tested. Degradation through mesophilic digestion, in comparison to the thermophilic process, resulted in a greater destruction of straw particles.

  5. Digestion of cattle manure under mesophilic and thermophilic conditions: characterization of organic matter applying thermal analysis and 1H NMR.

    PubMed

    Gómez, X; Blanco, D; Lobato, A; Calleja, A; Martínez-Núñez, F; Martin-Villacorta, J

    2011-06-01

    Digestion of cattle manure collected from a livestock farm together with bedding material (straw) has been studied under mesophilic and thermophilic conditions in batch reactors. The digestion was carried out for a prolonged period with the aim of evaluating the changes undergone by the organic matter. The mesophilic digestion carried out revealed a greater capacity to produce gas and transform organic matter, while a higher conversion rate, but a lower gas yield, was obtained under thermophilic conditions. Degradation of the organic matter was evaluated by means of thermal analysis and (1)H NMR. Stabilisation through anaerobic digestion (either mesophilic or thermophilic) resulted in an increase in the quality of the organic matter, as characterised by an enrichment in thermostable compounds, and an accumulation of long chain aliphatic materials. The experiments performed demonstrated the transformation of organic matter into complex materials under anaerobic conditions with an accumulation of aliphatic components under both types of conditions tested. Degradation through mesophilic digestion, in comparison to the thermophilic process, resulted in a greater destruction of straw particles. PMID:21082330

  6. Monitoring of thermophilic adaptation of mesophilic anaerobe fermentation of sugar beet pressed pulp.

    PubMed

    Tukacs-Hájos, Annamária; Pap, Bernadett; Maróti, Gergely; Szendefy, Judit; Szabó, Piroska; Rétfalvi, Tamás

    2014-08-01

    Anaerobe fermentation of sugar beet pressed pulp was investigated in pilot-scale digesters. Thermophilic adaptation of mesophilic culture was monitored using chemical analysis and metagenomic characterization of the sludge. Temperature adaptation was achieved by increasing the temperature gradually (2 °C day(-1)) and by greatly decreasing the OLR. During stable run, the OLR was increased gradually to 11.29 kg VS m(-3)d(-1) and biogas yield was 5% higher in the thermophilic reactor. VFA levels increased in the thermophilic reactor with increased OLR (acetic acid 646 mg L(-1), propionic acid 596 mg L(-1)), then VFA decreased and the operation was manageable beside the relative high tVFA (1300-2000 mg L(-1)). The effect of thermophilic adaptation on the microbial communities was studied using a sequencing-based metagenomic approach. Connections between physico-chemical parameters and populations of bacteria and methanogen archaea were revealed.

  7. Dry anaerobic digestion of food waste under mesophilic conditions: performance and methanogenic community analysis.

    PubMed

    Cho, Si-Kyung; Im, Wan-Taek; Kim, Dong-Hoon; Kim, Moon-Hwan; Shin, Hang-Sik; Oh, Sae-Eun

    2013-03-01

    The performance of dry anaerobic digestion (AD) of food waste was investigated under mesophilic conditions and the methanogenic community was investigated using 454 pyrosequencing. Stable dry AD was achieved by hydraulic retention time (HRT) control without the addition of alkali agents. The average CH4 production rate, CH4 content, and volatile solid reduction rate were 2.51±0.17m(3)/m(3)/d, 66±2.1%, and 65.8±1.22%, respectively, at an HRT of 40d. The methanogenic community of the seed sludge experienced a significant reduction in genus diversity from 18 to 4 and a dominant methanogenic shift from hydrogenotrophic to acetoclastic groups after the acclimation under dry condition. Almost all sequences of the dry anaerobic digester were closely related with those of Methanosarcina thermophila with similarity of 96.4-99.1%. The experimental results would serve as useful information to understand the dry AD system.

  8. High resolution structure of the large ribosomal subunit from a Mesophilic Eubacterium

    SciTech Connect

    Harms, Joerg; Schluenzen, Frank; Zarivach, Raz; Bashan, Anat; Gat, Sharon; Agmon, Ilana; Bartels, Heike; Franceschi, Francois; Yonath, Ada

    2009-10-07

    We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.

  9. Mesophilic anaerobic co-digestion of sewage sludge and orange peel waste.

    PubMed

    Serrano, Antonio; Siles López, José Angel; Chica, Arturo Francisco; Martín, M Angeles; Karouach, Fadoua; Mesfioui, Abdelaziz; El Bari, Hassan

    2014-01-01

    Mesophilic anaerobic digestion is a treatment that is widely applied for sewage sludge management but has several disadvantages such as low methane yield, poor biodegradability and nutrient imbalance. In this paper, we propose orange peel waste as an easily biodegradable co-substrate to improve the viability of the process. Sewage sludge and orange peel waste were mixed at a proportion of 70:30 (wet weight), respectively. The stability was maintained within correct parameters throughout the process, while the methane yield coefficient and biodegradability were 165 L/kg volatile solids (VS) (0 degrees C, 1 atm) and 76% (VS), respectively. The organic loading rate (OLR) increased from 0.4 to 1.6kg VS/m3 d. Nevertheless, the OLR and methane production rate decreased at the highest loads, suggesting the occurrence of an inhibition phenomenon. PMID:24645472

  10. Methane production in an UASB reactor operated under periodic mesophilic-thermophilic conditions.

    PubMed

    Bourque, J-S; Guiot, S R; Tartakovsky, B

    2008-08-15

    Methane production was studied in a laboratory-scale 10 L anaerobic upflow sludge bed (UASB) reactor with periodic variations of the reactor temperature. On a daily basis the temperature was varied between 35 and 45 degrees C or 35 and 55 degrees C with a heating period of 6 h. Each temperature increase was accompanied by an increase in methane production and a decrease in the concentration of soluble organic matter in the effluent. In comparison to a reactor operated at 35 degrees C, a net increase in methane production of up to 22% was observed. Batch activity tests demonstrated a tolerance of mesophilic methanogenic populations to short-term, 2-6 h, temperature increases, although activity of acetoclastic methanogens decreased after 6 h exposure to a temperature of 55 degrees C. 16S sequencing of DGGE bands revealed proliferation of temperature-tolerant Methanospirillum hungatii sp. in the reactor.

  11. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures

    PubMed Central

    2011-01-01

    Batch anaerobic digestion experiments using dairy manure as feedstocks were performed at moderate (25°C), mesophilic (37°C), and thermophilic (52.5°C) temperatures to understand E. coli, an indicator organism for pathogens, inactivation in dairy manure. Incubation periods at 25, 37, and 52.5°C, were 61, 41, and 28 days respectively. Results were used to develop models for predicting E. coli inactivation and survival in anaerobic digestion. For modeling we used the decay of E. coli at each temperature to calculate the first-order inactivation rate coefficients, and these rates were used to formulate the time - temperature - E. coli survival relationships. We found the inactivation rate coefficient at 52.5°C was 17 and 15 times larger than the inactivation rate coefficients at 25 and 37°C, respectively. Decimal reduction times (D10; time to achieve one log removal) at 25, 37, and 52.5°C, were 9 -10, 7 - 8 days, and < 1 day, respectively. The Arrhenius correlation between inactivation rate coefficients and temperatures over the range 25 -52.5°C was developed to understand the impacts of temperature on E. coli inactivation rate. Using this correlation, the time - temperature - E. coli survival relationships were derived. Besides E. coli inactivation, impacts of temperature on biogas production, methane content, pH change, ORP, and solid reduction were also studied. At higher temperatures, biogas production and methane content was greater than that at low temperatures. While at thermophilic temperature pH was increased, at mesophilic and moderate temperatures pH were reduced over the incubation period. These results can be used to understand pathogen inactivation during anaerobic digestion of dairy manure, and impacts of temperatures on performance of anaerobic digesters treating dairy manure. PMID:21906374

  12. Interaction between temperature and ammonia in mesophilic digesters for animal waste treatment.

    PubMed

    Garcia, Marcelo L; Angenent, Largus T

    2009-05-01

    Four anaerobic sequencing batch reactors (ASBRs) were operated during a period of 988 days to evaluate the effect of temperature, ammonia, and their interconnectivity on the methane yield of anaerobic processes for animal waste treatment. During period 1 (day 0-378), the methane yield was 0.31 L CH(4)/g volatile solids (VS) for all digesters (with no statistical differences among them) at a temperature and total ammonium-N levels of 25 degrees C and approximately 1200 mg NH(4)(+)-N/L, respectively. During period 2 (day 379-745), the methane yield at 25 degrees C decreased by 45% when total ammonium-N and ammonia-N were increased in two of the four ASBRs to levels >4000 mg NH(4)(+)-N/L and >80 mg NH(3)-N/L, respectively. During period 3 (day 746-988), this relative inhibition was reduced from 45% to 13% compared to the low-ammonia control reactors when the operating temperature was increased from 25 degrees C to 35 degrees C (while the free ammonia levels increased from approximately 100 to approximately 250 mg NH(3)-N/L). The 10 degrees C increase in temperature doubled the rate constant for methanogenesis, which overwhelmed the elevated toxicity effects caused by the increasing concentration of free ammonia. Thus, the farmer/operator may alleviate ammonia toxicity by increasing the operating temperature within the mesophilic range. We extrapolated our data to correlate temperature, ammonia, and methane yield and to hypothesize that the difference between high- and low-ammonia reactors is negligible at the optimum mesophilic temperature of 38 degrees C.

  13. Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function.

    PubMed

    Wells, Stephen A; Crennell, Susan J; Danson, Michael J

    2014-10-01

    Citrate synthase (CS) catalyses the entry of carbon into the citric acid cycle and is highly-conserved structurally across the tree of life. Crystal structures of dimeric CSs are known in both "open" and "closed" forms, which differ by a substantial domain motion that closes the substrate-binding clefts. We explore both the static rigidity and the dynamic flexibility of CS structures from mesophilic and extremophilic organisms from all three evolutionary domains. The computational expense of this wide-ranging exploration is kept to a minimum by the use of rigidity analysis and rapid all-atom simulations of flexible motion, combining geometric simulation and elastic network modeling. CS structures from thermophiles display increased structural rigidity compared with the mesophilic enzyme. A CS structure from a psychrophile, stabilized by strong ionic interactions, appears to display likewise increased rigidity in conventional rigidity analysis; however, a novel modified analysis, taking into account the weakening of the hydrophobic effect at low temperatures, shows a more appropriate decreased rigidity. These rigidity variations do not, however, affect the character of the flexible dynamics, which are well conserved across all the structures studied. Simulation trajectories not only duplicate the crystallographically observed symmetric open-to-closed transitions, but also identify motions describing a previously unidentified antisymmetric functional motion. This antisymmetric motion would not be directly observed in crystallography but is revealed as an intrinsic property of the CS structure by modeling of flexible motion. This suggests that the functional motion closing the binding clefts in CS may be independent rather than symmetric and cooperative.

  14. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures.

    PubMed

    Pandey, Pramod K; Soupir, Michelle L

    2011-01-01

    Batch anaerobic digestion experiments using dairy manure as feedstocks were performed at moderate (25°C), mesophilic (37°C), and thermophilic (52.5°C) temperatures to understand E. coli, an indicator organism for pathogens, inactivation in dairy manure. Incubation periods at 25, 37, and 52.5°C, were 61, 41, and 28 days respectively. Results were used to develop models for predicting E. coli inactivation and survival in anaerobic digestion. For modeling we used the decay of E. coli at each temperature to calculate the first-order inactivation rate coefficients, and these rates were used to formulate the time - temperature - E. coli survival relationships. We found the inactivation rate coefficient at 52.5°C was 17 and 15 times larger than the inactivation rate coefficients at 25 and 37°C, respectively. Decimal reduction times (D10; time to achieve one log removal) at 25, 37, and 52.5°C, were 9 -10, 7 - 8 days, and < 1 day, respectively. The Arrhenius correlation between inactivation rate coefficients and temperatures over the range 25 -52.5°C was developed to understand the impacts of temperature on E. coli inactivation rate. Using this correlation, the time - temperature - E. coli survival relationships were derived. Besides E. coli inactivation, impacts of temperature on biogas production, methane content, pH change, ORP, and solid reduction were also studied. At higher temperatures, biogas production and methane content was greater than that at low temperatures. While at thermophilic temperature pH was increased, at mesophilic and moderate temperatures pH were reduced over the incubation period. These results can be used to understand pathogen inactivation during anaerobic digestion of dairy manure, and impacts of temperatures on performance of anaerobic digesters treating dairy manure. PMID:21906374

  15. Conversion of cellulose to ethanol by mesophilic bacteria. Progress report and third year budget

    SciTech Connect

    Canale-Parola, E.

    1982-11-24

    Much of our research has dealt with eight strains of obligately anaerobic bacteria that we isolated from various natural environments as described in last year's progress report. These eight strains (referred to as C strains) are strains of mesophilic, spore-forming, rod-shaped bacteria that ferment cellulose with production of ethanol. We determined quantitatively the fermentation products formed by C strains from cellulose and various other carbohydrates. In all cases ethanol was produced, as well as acetate, CO/sub 2/ and H/sub 2/. The C strains utilized, for ethanol production and growth, a variety of cellulosic substrates ranging from paper to alpha-cellulose. Enzymatic assays and growth studies showed that C strains possessed a celluloase system consisting of endoglucanase, exoglucanase, and cellobiase components. Studies indicated that growth substrates have a regulatory effect(s) on components of the cellulase system of the C strains. another experimental approach is aimed at cloning cellobiase, endoglucanase and exoglucanase genes from the C strains into a suitable vector plasmid and, eventually, at introducing the plasmid into cells of Zymomonas mobilis. The objective of this part of our research is to obtain a Z. mobilis strain capable of fermenting cellobiose and/or cellulose. Plasmids that contained DNA inserts were used to transform E. coli C600 recA. E. coli transformants that had acquired the cellobiase gene were obtained by this procedure. At present, we are attempting to introduce into Z. mobilis cells the vector plasmid purified from the E. coli transformants. In another series of experiments, we have used a new selective procedure to isolate four additional strains of mesophilic, obligately anaerobic, cellulolytic bacteria from natural environments.

  16. Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments.

    PubMed

    Jehmlich, Nico; Schmidt, Frank; Taubert, Martin; Seifert, Jana; von Bergen, Martin; Richnow, Hans-Hermann; Vogt, Carsten

    2009-06-01

    We developed a concept for analysing carbon and nitrogen fluxes in microbial communities by employing protein-based stable isotope probing (Protein-SIP) in metabolic labelling experiments with stable isotope labelled substrates. For identification of microbial species intact protein profiling (IPP) can be used, whereas the assessment of their metabolic activity is achieved by shotgun mass mapping (SMM). Microbial cultures were grown on substrates containing (13)C or (15)N. For identification of species we tested both the IPP and the SMM approaches. Mass spectra (MALDI-MS) were taken from mixtures of either intact proteins or peptides from tryptic digestion for generating species-specific peak patterns. In the case of SMM, the fragmentation of peptides was additionally used to obtain sequence information for species identification. Mass spectra of peptide sequences allow calculation of the amount of (13)C or (15)N incorporation within peptides for determining metabolic activity of the specific species. The comparison of IPP and SMM revealed a higher robustness of species identification by SMM. In addition, the assessment of incorporation levels of (13)C and (15)N into peptides by SMM revealed a lower uncertainty (0.5-0.8 atom %) compared to IPP (6.4-8.9 atom %). The determination of metabolic activity and function of individual species by Protein-SIP can help to analyse carbon and nitrogen fluxes within microbial communities.

  17. Mono- and Dialkyl Glycerol Ether Lipids in Anaerobic Bacteria: Biosynthetic Insights from the Mesophilic Sulfate Reducer Desulfatibacillum alkenivorans PF2803T

    PubMed Central

    Mollex, Damien; Vinçon-Laugier, Arnauld; Hakil, Florence; Pacton, Muriel; Cravo-Laureau, Cristiana

    2015-01-01

    Bacterial glycerol ether lipids (alkylglycerols) have received increasing attention during the last decades, notably due to their potential role in cell resistance or adaptation to adverse environmental conditions. Major uncertainties remain, however, regarding the origin, biosynthesis, and modes of formation of these uncommon bacterial lipids. We report here the preponderance of monoalkyl- and dialkylglycerols (1-O-alkyl-, 2-O-alkyl-, and 1,2-O-dialkylglycerols) among the hydrolyzed lipids of the marine mesophilic sulfate-reducing proteobacterium Desulfatibacillum alkenivorans PF2803T grown on n-alkenes (pentadec-1-ene or hexadec-1-ene) as the sole carbon and energy source. Alkylglycerols account for one-third to two-thirds of the total cellular lipids (alkylglycerols plus acylglycerols), depending on the growth substrate, with dialkylglycerols contributing to one-fifth to two-fifths of the total ether lipids. The carbon chain distribution of the lipids of D. alkenivorans also depends on that of the substrate, but the chain length and methyl-branching patterns of fatty acids and monoalkyl- and dialkylglycerols are systematically congruent, supporting the idea of a biosynthetic link between the three classes of compounds. Vinyl ethers (1-alken-1′-yl-glycerols, known as plasmalogens) are not detected among the lipids of strain PF2803T. Cultures grown on different (per)deuterated n-alkene, n-alkanol, and n-fatty acid substrates further demonstrate that saturated alkylglycerols are not formed via the reduction of hypothetic alken-1′-yl intermediates. Our results support an unprecedented biosynthetic pathway to monoalkyl/monoacyl- and dialkylglycerols in anaerobic bacteria and suggest that n-alkyl compounds present in the environment can serve as the substrates for supplying the building blocks of ether phospholipids of heterotrophic bacteria. PMID:25724965

  18. Anaerobic co-digestion of food waste and chemically enhanced primary-treated sludge under mesophilic and thermophilic conditions.

    PubMed

    Obulisamy, Parthiba Karthikeyan; Chakraborty, Debkumar; Selvam, Ammaiyappan; Wong, Jonathan W C

    2016-12-01

    Anaerobic co-digestion of food waste with primary sewage sludge is beneficial for urban centers, while the optimized conditions reported in the literature are not locally suitable for Hong Kong. Therefore, the present study was aimed to develop an optimized mixing ratio of food waste to chemically enhanced primary-treated sewer sludge (CEPT) for co-digestion using batch tests under mesophilic (37°C) and thermophilic (55°C) conditions. The mixing ratios of 1:1, 1:2, 1:3, 2:1 and 3:1 (v v(-1)) of food waste to CEPT sludge was tested under the following conditions: temperature - 35°C and 55°C; pH - not regulated; agitation - 150 rpm and time - 20 days. The thermophilic incubations led a good hydrolysis rate and 2-12-fold higher enzyme activities than in mesophilic incubations for different mixing ratios. While the acidogenesis were found retarded that leading to 'sour and stuck' digestion for all mixing ratio of food waste to CEPT sludge from thermophilic incubations. The measured zeta potential was most favourable (-5 to -16.8 mV) for methane production under thermophilic incubations; however the CH4 recovery was less than that in mesophilic incubations. The results suggested that the quick hydrolysis and subsequent acid accumulation under thermophilic incubation lead to inhibited methanogenesis at the early stage than in mesophilic systems. It is concluded that buffer addition is therefore required for any mixing ratio of food waste to CEPT sludge for improved CH4 recovery for both mesophilic and thermophilic operations.

  19. Characterization of gtf, a Glucosyltransferase Gene in the Genomes of Pediococcus parvulus and Oenococcus oeni, Two Bacterial Species Commonly Found in Wine▿

    PubMed Central

    Dols-Lafargue, Marguerite; Lee, Hyo Young; Le Marrec, Claire; Heyraud, Alain; Chambat, Gérard; Lonvaud-Funel, Aline

    2008-01-01

    “Ropiness” is a bacterial alteration in wines, beers, and ciders, caused by β-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the corresponding gtf gene is also present on the chromosomes of several strains of Oenococcus oeni isolated from nonropy wines. gtf is surrounded by mobile elements that may be implicated in its integration into the chromosome of O. oeni. gtf is expressed in all the gtf+ strains, and β-glucan is detected in the majority of these strains. Part of this β-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functional gtf gene (gtf+) are more resistant to several stresses occurring in wine (alcohol, pH, and SO2) and exhibit increased adhesion capacities compared to their gtf mutant variants. PMID:18469121

  20. Characterization of gtf, a glucosyltransferase gene in the genomes of Pediococcus parvulus and Oenococcus oeni, two bacterial species commonly found in wine.

    PubMed

    Dols-Lafargue, Marguerite; Lee, Hyo Young; Le Marrec, Claire; Heyraud, Alain; Chambat, Gérard; Lonvaud-Funel, Aline

    2008-07-01

    "Ropiness" is a bacterial alteration in wines, beers, and ciders, caused by beta-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the corresponding gtf gene is also present on the chromosomes of several strains of Oenococcus oeni isolated from nonropy wines. gtf is surrounded by mobile elements that may be implicated in its integration into the chromosome of O. oeni. gtf is expressed in all the gtf(+) strains, and beta-glucan is detected in the majority of these strains. Part of this beta-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functional gtf gene (gtf(+)) are more resistant to several stresses occurring in wine (alcohol, pH, and SO(2)) and exhibit increased adhesion capacities compared to their gtf mutant variants. PMID:18469121

  1. Improved model systems for bacterial membranes from differing species: the importance of varying composition in PE/PG/cardiolipin ternary mixtures.

    PubMed

    Lopes, Silvia C; Neves, Cristina S; Eaton, Peter; Gameiro, Paula

    2012-09-01

    Steady-state fluorescence anisotropy and dynamic light scattering (DLS) were used to determine the thermotropic properties of lipid systems that act as models for bacterial membranes of Yersinia kristensenii and Proteus mirabilis. Lipid proportions of PE:PG:CL of 0.60:0.20:0.20 and 0.80:0.15:0.05, were used in order to mimic these two membranes respectively. We observed that the introduction of cardiolipin (CL) as a third lipid component of any PE:PG mixture, changes the system's properties considerably. The results obtained by these two techniques show that the main transition temperatures obtained are undoubtedly CL-dependent. Additionally AFM experiments were performed and these results show that even at small concentration CL produces important changes not only in the membrane thermotropic properties, but also in the bilayer structure. In summary, we were able to compare how low and high CL concentration affect bacterial membrane model system properties which can provide a further explanation for the different antibiotic susceptibilities reported for Y. kristensenii and P. mirabilis.

  2. Bioflocculant production and biosorption of zinc and lead by a novel bacterial species, Achromobacter sp. TERI-IASST N, isolated from oil refinery waste.

    PubMed

    Subudhi, Sanjukta; Batta, Neha; Pathak, Mihirjyoti; Bisht, Varsha; Devi, Arundhuti; Lal, Banwari; Al khulifah, Bader

    2014-10-01

    A bioflocculant-producing bacterial isolate designated as 'TERI-IASST N' was isolated from activated sludge samples collected from an oil refinery. This isolate demonstrated maximum bioflocculation activity (74%) from glucose among 15 different bioflocculant-producing bacterial strains isolated from the sludge samples and identified as Achromobacter sp. based on 16S rRNA gene sequence. Optimization of pH and supplementation of urea as nitrogen source in the production medium enhanced the flocculation activity of strain TERI-IASST N to 84% (at pH 6). This strain revealed maximum flocculation activity (90%) from sucrose compared to the flocculation activity observed from other carbon sources as investigated (glucose, lactose, fructose, maltose and starch). Ca(2+) served as the suitable divalent cation for maximum bioflocculation activity of TERI-IASST strain N. Maximum flocculation activity was observed at optimum C/N ratio of 1. Flocculation activity of this strain decreased to 75% in the presence of heavy metals; Zn, Pb, Ni, Cu and Cd. In addition strain N revealed considerable biosorption of Zn (430mgL(-1)) and Pb (30mgL(-1)). Bioflocculant yield of strain N was 10.5gL(-1). Fourier transform infrared spectrum indicated the presence of carboxyl, hydroxyl, and amino groups, typical of glycoprotein. Spectroscopic analysis of bioflocculant by nuclear magnetic resonance revealed that it is a glycoprotein, consisting of 57% total sugar and 13% protein.

  3. Inhibitory effects on bacterial growth and beta-ketoacyl-ACP reductase by different species of maple leaf extracts and tannic acid.

    PubMed

    Wu, Dan; Wu, Xiao-Dong; You, Xue-Fu; Ma, Xiao-Feng; Tian, Wei-Xi

    2010-01-01

    It is important to develop new antibiotics aimed at novel targets. The investigation found that the leaf extracts from five maples (Acer platanoides, Acer campestre, Acer rubrum, Acer saccharum and Acer truncatum Bunge collected in Denmark, Canada and China) and their component tannic acid displayed antibacterial ability against 24 standard bacteria strains with the minimum inhibitory concentration of 0.3-8.0 mg/mL. Unlike the standard antibiotic levofloxacin (LFX), these samples inhibited Gram-positive bacteria more effectively than they inhibited Gram-negative bacteria. These samples effectively inhibited two antidrug bacterial strains. The results show that these samples inhibit bacteria by a different mechanism from LFX. These samples potently inhibited b-ketoacyl-ACP reductase (FabG), which is an important enzyme in bacterial fatty acid synthesis. Tannic acid showed the strongest inhibition on FabG with a half inhibition concentration of 0.78 microM (0.81 microg/mL). Furthermore, tannic acid and two maple leaf extracts showed time-dependent irreversible inhibition of FabG. These three samples also exhibited better inhibition on bacteria. It is suggested that FabG is the antibacteria target of maple leaf extracts and tannic acid, and both reversible and irreversible inhibitions of FabG are important for the antibacterial effect.

  4. Preferential Use of Carbon Sources in Culturable Aerobic Mesophilic Bacteria of Coptotermes curvignathus's (Isoptera: Rhinotermitidae) Gut and Its Foraging Area.

    PubMed

    Wong, W Z; H'ng, P S; Chin, K L; Sajap, Ahmad Said; Tan, G H; Paridah, M T; Othman, Soni; Chai, E W; Go, W Z

    2015-10-01

    The lower termite, Coptotermes curvignathus, is one of the most prominent plantation pests that feed upon, digest, and receive nourishment from exclusive lignocellulose diets. The objective of this study was to examine the utilization of sole carbon sources by isolated culturable aerobic bacteria among communities from the gut and foraging pathway of C. curvignathus. We study the bacteria occurrence from the gut of C. curvignathus and its surrounding feeding area by comparing the obtained phenotypic fingerprint with Biolog's extensive species library. A total of 24 bacteria have been identified mainly from the family Enterobacteriaceae from the identification of Biolog Gen III. Overall, the bacteria species in the termite gut differ from those of foraging pathway within a location, except Acintobacter baumannii, which was the only bacteria species found in both habitats. Although termites from a different study area do not have the same species of bacteria in the gut, they do have a bacterial community with similar role in degrading certain carbon sources. Sugars were preferential in termite gut isolates, while nitrogen carbon sources were preferential in foraging pathway isolates. The preferential use of specific carbon sources by these two bacterial communities reflects the role of bacteria for regulation of carbon metabolism in the termite gut and foraging pathway. PMID:26314017

  5. Preferential Use of Carbon Sources in Culturable Aerobic