Genomic Insights into the Biomineralization and Environmental Function of Magnetotactic Bacteria

NASA Astrophysics Data System (ADS)

Lin, W.; Pan, Y.

2015-12-01

Microorganisms have populated the Earth for billions of years and their activities are important biologic forces shaping our planetary environments. Microbial biomineralization that selectively take up environmental elements (e.g., C, S, P, Fe) and synthesize minerals either intracellularly or extracellularly is of great interest. One of the most interesting examples of these types of organisms are magnetotactic bacteria (MTB), a polyphyletic group of prokaryotes that uptake iron from aquatic habitats and biomineralize intracellular nano-sized iron minerals of magnetite (Fe3O4) and/or greigite (Fe3S4), known as magnetosomes, and orientate and swim along the Earth's magnetic field. However, our knowledge on the biomineralization mechanisms of MTB and their environmental function remains very limited because the genomic information of most MTB is still not fully understood. By using metagenomic approaches, we have acquired genomic sequences of environmental MTB communities and discovered several conserved genomic fragments containing gene operons for magnetite or greigite biomineralization from Proteobacteria and Nitrospirae MTB. The comparison of these gene clusters has provided valuable insights into the origin and evolution of magnetosome biomineralization. We further obtained several draft genomes of uncultivated MTB belonging to the phylum Nitrospirae, which reveals a metabolic flexibility of this poorly understood magnetotactic group and indicates their considerable roles in the biogeochemical cycles of iron and sulfur.

Selection of Surrogate Bacteria for Use in Food Safety Challenge Studies: A Review.

PubMed

Hu, Mengyi; Gurtler, Joshua B

2017-09-01

Nonpathogenic surrogate bacteria are prevalently used in a variety of food challenge studies in place of foodborne pathogens such as Listeria monocytogenes, Salmonella, Escherichia coli O157:H7, and Clostridium botulinum because of safety and sanitary concerns. Surrogate bacteria should have growth characteristics and/or inactivation kinetics similar to those of target pathogens under given conditions in challenge studies. It is of great importance to carefully select and validate potential surrogate bacteria when verifying microbial inactivation processes. A validated surrogate responds similar to the targeted pathogen when tested for inactivation kinetics, growth parameters, or survivability under given conditions in agreement with appropriate statistical analyses. However, a considerable number of food studies involving putative surrogate bacteria lack convincing validation sources or adequate validation processes. Most of the validation information for surrogates in these studies is anecdotal and has been collected from previous publications but may not be sufficient for given conditions in the study at hand. This review is limited to an overview of select studies and discussion of the general criteria and approaches for selecting potential surrogate bacteria under given conditions. The review also includes a list of documented bacterial pathogen surrogates and their corresponding food products and treatments to provide guidance for future studies.

Antibiotic profiles of bacteria isolated on selective campylobacter media

USDA-ARS?s Scientific Manuscript database

The objective of this study was to determine antibiotic profiles of non-Campylobacter bacteria recovered on selective Campylobacter media. Broiler carcasses were obtained from a processing facility, and whole-carcass rinses were performed by shaking carcasses in plastic bags with 200 mL of distilled...

A bivalent cationic dye enabling selective photo-inactivation against Gram-negative bacteria.

PubMed

Li, Ke; Zhang, Yang-Yang; Jiang, Guo-Yu; Hou, Yuan-Jun; Zhang, Bao-Wen; Zhou, Qian-Xiong; Wang, Xue-Song

2015-05-07

A piperazine-modified Crystal Violet was found to be able to selectively inactivate Gram-negative bacteria upon visible light irradiation but left Gram-positive bacteria less damaged, which can serve as a blueprint for the development of novel narrow-spectrum agents to replenish the current arsenal of photodynamic antimicrobial chemotherapy (PACT).

Resistance of bioparticles formed of phosphate-accumulating bacteria and zeolite to harsh environmental conditions.

PubMed

Ivankovic, Tomislav; Hrenovic, Jasna; Matonickin-Kepcija, Renata

2013-01-01

Extreme environmental conditions, such as pH fluctuations, high concentrations of toxicants or grazing of protozoa, can potentially be found in wastewater treatment systems. This study was carried out to provide specific evidence on how 'bioparticles' can resist these conditions. The term 'bioparticle' is used to describe a particle comprising natural zeolitized tuff with a developed biofilm of the phosphate-accumulating bacterial species, Acinetobacter junii, on the surface. The bacteria in the biofilm were protected from the negative influence of extremely low pH, high concentrations of benzalkonium-chloride and grazing by Paramecium caudatum and Euplotes affinis, even under conditions that caused complete eradication of planktonic bacteria. During an incubation of 24 h, the biofilms were maintained and bacteria detached from the bioparticles, thus bioaugmenting the wastewater. The bioparticles provided a safe environment for the survival of bacteria in harsh environmental conditions and could be used for successful bioaugmentation in wastewater treatment plants.

Fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers and selected tributaries, Allegheny County, Pennsylvania, 2001-2005

USGS Publications Warehouse

Buckwalter, Theodore F.; Zimmerman, Tammy M.; Fulton, John W.

2006-01-01

Concentrations of fecal-indicator bacteria were determined in 1,027 water-quality samples collected from July 2001 through August 2005 during dry- (72-hour dry antecedent period) and wet-weather (48-hour dry antecedent period and at least 0.3 inch of rain in a 24-hour period) conditions in the Allegheny, Monongahela, and Ohio Rivers (locally referred to as the Three Rivers) and selected tributaries in Allegheny County. Samples were collected at five sampling sites on the Three Rivers and at eight sites on four tributaries to the Three Rivers having combined sewer overflows. Water samples were analyzed for three fecal-indicator organisms fecal coliform, Escherichia coli (E. coli), and enterococci bacteria. Left-bank and right-bank surface-water samples were collected in addition to a cross-section composite sample at each site. Concentrations of fecal coliform, E. coli, and enterococci were detected in 98.6, 98.5, and 87.7 percent of all samples, respectively. The maximum fecal-indicator bacteria concentrations were collected from Sawmill Run, a tributary to the Ohio River; Sawmill Run at Duquesne Heights had concentrations of fecal coliform, E. coli, and enterococci of 410,000, 510,000, and 180,000 col/100 mL, respectively, following a large storm. The samples collected in the Three Rivers and selected tributaries frequently exceeded established recreational standards and criteria for bacteria. Concentrations of fecal coliform exceeded the Pennsylvania water-quality standard (200 col/100 mL) in approximately 63 percent of the samples. Sample concentrations of E. coli and enterococci exceeded the U.S. Environmental Protection Agency (USEPA) water-quality criteria (235 and 61 col/100 mL, respectively) in about 53 and 47 percent, respectively, of the samples. Fecal-indicator bacteria were most strongly correlated with streamflow, specific conductance, and turbidity. These correlations most frequently were observed in samples collected from tributary sites. Fecal

Selection and Characterization of Biofuel-Producing Environmental Bacteria Isolated from Vegetable Oil-Rich Wastes

PubMed Central

Escobar-Niño, Almudena; Luna, Carlos; Luna, Diego; Marcos, Ana T.; Cánovas, David; Mellado, Encarnación

2014-01-01

Fossil fuels are consumed so rapidly that it is expected that the planet resources will be soon exhausted. Therefore, it is imperative to develop alternative and inexpensive new technologies to produce sustainable fuels, for example biodiesel. In addition to hydrolytic and esterification reactions, lipases are capable of performing transesterification reactions useful for the production of biodiesel. However selection of the lipases capable of performing transesterification reactions is not easy and consequently very few biodiesel producing lipases are currently available. In this work we first isolated 1,016 lipolytic microorganisms by a qualitative plate assay. In a second step, lipolytic bacteria were analyzed using a colorimetric assay to detect the transesterification activity. Thirty of the initial lipolytic strains were selected for further characterization. Phylogenetic analysis revealed that 23 of the bacterial isolates were Gram negative and 7 were Gram positive, belonging to different clades. Biofuel production was analyzed and quantified by gas chromatography and revealed that 5 of the isolates produced biofuel with yields higher than 80% at benchtop scale. Chemical and viscosity analysis of the produced biofuel revealed that it differed from biodiesel. This bacterial-derived biofuel does not require any further downstream processing and it can be used directly in engines. The freeze-dried bacterial culture supernatants could be used at least five times for biofuel production without diminishing their activity. Therefore, these 5 isolates represent excellent candidates for testing biofuel production at industrial scale. PMID:25099150

Acetic acid bacteria in traditional balsamic vinegar: phenotypic traits relevant for starter cultures selection.

PubMed

Gullo, Maria; Giudici, Paolo

2008-06-30

This review focuses on acetic acid bacteria in traditional balsamic vinegar process. Although several studies are available on acetic acid bacteria ecology, metabolism and nutritional requirements, their activity as well as their technological traits in homemade vinegars as traditional balsamic vinegar is not well known. The basic technology to oxidise cooked grape must to produce traditional balsamic vinegar is performed by the so called "seed-vinegar" that is a microbiologically undefined starter culture obtained from spontaneous acetification of previous raw material. Selected starter cultures are the main technological improvement in order to innovate traditional balsamic vinegar production but until now they are rarely applied. To develop acetic acid bacteria starter cultures, selection criteria have to take in account composition of raw material, acetic acid bacteria metabolic activities, applied technology and desired characteristics of the final product. For traditional balsamic vinegar, significative phenotypical traits of acetic acid bacteria have been highlighted. Basic traits are: ethanol preferred and efficient oxidation, fast rate of acetic acid production, tolerance to high concentration of acetic acid, no overoxidation and low pH resistance. Specific traits are tolerance to high sugar concentration and to a wide temperature range. Gluconacetobacter europaeus and Acetobacter malorum strains can be evaluated to develop selected starter cultures since they show one or more suitable characters.

Host Immune Selection of Rumen Bacteria through Salivary Secretory IgA

PubMed Central

Fouhse, Janelle M.; Smiegielski, Luke; Tuplin, Melanie; Guan, Le Luo; Willing, Benjamin P.

2017-01-01

The rumen microbiome is integral to efficient production in cattle and shows strong host specificity, yet little is known about what host factors shape rumen microbial composition. Secretory immunoglobulin A (SIgA) is produced in large amounts in the saliva, can coat both commensal and pathogenic microbes within the gut, and presents a plausible mechanism of host specificity. However, the role salivary SIgA plays in commensal bacteria selection in ruminants remains elusive. The main objectives of this study were to develop an immuno-affinity benchtop method to isolate SIgA-tagged microbiota and to determine if salivary SIgA preferentially binds selected bacteria. We hypothesized that SIgA-tagged bacteria would differ from total bacteria, thus supporting a potential host-derived mechanism in commensal bacterial selection. Whole rumen (n = 9) and oral secretion samples (n = 10) were incubated with magnetic beads conjugated with anti-secretory IgA antibodies to enrich SIgA-tagged microbiota. Microbial DNA from the oral secretion, whole rumen, SIgA-tagged oral secretion, and SIgA-tagged rumen was isolated for amplicon sequencing of V1–V3 region of 16S rDNA genes. Whole rumen and oral secretion had distinctive (P < 0.05) bacterial compositions indicated by the non-parametric multidimensional scaling plot using Euclidean distance metrics. The SIgA-tagged microbiota from rumen and oral secretion had similar abundance of Bacteroidetes, Actinobacteria, Fibrobacter, candidate phyla TM7, and Tenericutes and are clustered tightly. Composition of SIgA-tagged oral secretion microbiota was more similar to whole rumen microbiota than whole oral secretion due to enrichment of rumen bacteria (Lachnospiraceae) and depletion of oral taxa (Streptococcus, Rothia, Neisseriaceae, and Lactobacillales). In conclusion, SIgA-tagged oral secretion microbiota had an increased resemblance to whole rumen microbiota, suggesting salivary SIgA-coating may be one host-derived mechanism impacting

Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

PubMed Central

Ferrari, Belinda C.; Binnerup, Svend J.; Gillings, Michael

2005-01-01

Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used. PMID:16332866

Presence of archaea and selected bacteria in infected root canal systems.

PubMed

Brzezińska-Błaszczyk, Ewa; Pawłowska, Elżbieta; Płoszaj, Tomasz; Witas, Henryk; Godzik, Urszula; Agier, Justyna

2018-05-01

Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson's χ 2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student's t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.

RNA-Based Methods Increase the Detection of Fecal Bacteria and Fecal Identifiers in Environmental Waters

EPA Science Inventory

We evaluated the use of qPCR RNA-based methods in the detection of fecal bacteria in environmental waters. We showed that RNA methods can increase the detection of fecal bacteria in multiple water matrices. The data suggest that this is a viable alternative for the detection of a...

Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells

PubMed Central

Hepworth, Matthew R.; Fung, Thomas C.; Masur, Samuel H.; Kelsen, Judith R.; McConnell, Fiona M.; Dubrot, Juan; Withers, David R.; Hugues, Stephanie; Farrar, Michael A.; Reith, Walter; Eberl, Gerard; Baldassano, Robert N.; Laufer, Terri M.; Elson, Charles O.; Sonnenberg, Gregory F.

2015-01-01

Inflammatory CD4+ T cell responses to self or commensal bacteria underlie the pathogenesis of autoimmunity and inflammatory bowel disease (IBD), respectively. While selection of self-specific T cells in the thymus limits responses to tissue antigens, the mechanisms that control selection of commensal bacteria-specific T cells remain poorly understood. Here we demonstrate that group 3 innate lymphoid cell (ILC3)-intrinsic expression of major histocompatibility complex class II (MHCII) is regulated similarly to thymic epithelial cells, and that MHCII+ ILC3s directly induce cell death of activated commensal bacteria-specific T cells. Further, MHCII on human colonic ILC3s was reduced in pediatric IBD patients. Collectively, these results define a selection pathway for commensal bacteria-specific CD4+ T cells in the intestine, and suggest that this process is dysregulated in human IBD. PMID:25908663

[Selective-differential nutrient medium "Shewanella IRHLS agar" for isolation of Shewanella genus bacteria].

PubMed

Sivolodsky, E P

2015-01-01

Development of a selective-differential nutrient medium for isolation of Shewanella genus bacteria. 73 strains of Shewanella bacteria (S. algae--3, S. baltica--26, S. putrefaciens--44) and 80 strains of 22 other bacteria genera were used. Shewanella species were identified by methods and criteria proposed by Nozue H. et al., 1992; Khashe S. et al., 1998. Nutrient media "Shewanella IRHLS Agar" for shewanella isolation was developed. Medium selective factors: irgazan DP-300 (I). 0.14-0.2 g/l and rifampicin (R) 0.0005-0.001 g/l. Shevanella colonies were detected by the production of hydrogen sulfide (H), lipase presence (L), lack of sorbitol fermentation (S). The medium suppressed the growth of hydrogen sulfide producers (Salmonella, Proteus) and blocked hydrogen sulfide production by Citrobacter. Growth of Escherichia, Enterobacter, Klebsiella, Shigella, Staphylococcus, Bacillus was also suppressed, Analytical sensitivity of the medium was 1-2 CFU/ml for Shewanella and Stenotrophomonas, Aerombnas, Serratia genera bacteria. 72 strains of Shewanella were isolated from water of Neva river in this medium, 91.7 ± 3.2% of those produced H2S. 1 strain of S. algae was isolated from clinical material. The developed media allows to use it in a complex for Stenotrophomo- nas sp., Aeromonas sp., Serratia sp., Citrobactersp. and Shewanella bacteria isolation.

A study on identification of bacteria in environmental samples using single-cell Raman spectroscopy: feasibility and reference libraries.

PubMed

Baritaux, Jean-Charles; Simon, Anne-Catherine; Schultz, Emmanuelle; Emain, C; Laurent, P; Dinten, Jean-Marc

2016-05-01

We report on our recent efforts towards identifying bacteria in environmental samples by means of Raman spectroscopy. We established a database of Raman spectra from bacteria submitted to various environmental conditions. This dataset was used to verify that Raman typing is possible from measurements performed in non-ideal conditions. Starting from the same dataset, we then varied the phenotype and matrix diversity content included in the reference library used to train the statistical model. The results show that it is possible to obtain models with an extended coverage of spectral variabilities, compared to environment-specific models trained on spectra from a restricted set of conditions. Broad coverage models are desirable for environmental samples since the exact conditions of the bacteria cannot be controlled.

Desiccation: An environmental and food industry stress that bacteria commonly face.

PubMed

Esbelin, Julia; Santos, Tiago; Hébraud, Michel

2018-02-01

Water is essential for all living organisms, for animals as well as for plants and micro-organisms. For these latter, the presence of water or a humid environment with a high air relative humidity (RH) is necessary for their survival and growth. Thus, variations in the availability of water or in the air relative humidity constitute widespread environmental stresses which challenge microorganisms, and especially bacteria. Indeed, in their direct environment, bacteria are often faced with conditions that remove cell-bound water through air-drying of the atmosphere. Bacterial cells are subject to daily or seasonal environmental variations, sometimes going through periods of severe desiccation. This is also the case in the food industry, where air dehumidification treatments are applied after the daily cleaning-disinfection procedures. In plants producing low-water activity products, it is also usual to significantly reduce or eliminate water usage. Periodic desiccation exposure affects bacteria viability and so they require strategies to persist. Negative effects of desiccation are wide ranging and include direct cellular damage but also changes in the biochemical and biophysical properties of cells for which planktonic cells are more exposed than cells in biofilm. Understanding the mechanisms of desiccation adaptation and tolerance has a biological and biotechnological interest. This review gives an overview of the factors influencing desiccation tolerance and the biological mechanisms involved in this stress response. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Correlation of bacteria in the contaminated drug and the environmental microbes in the clean room for pharmaceutical microbial test investigated by FTIR].

PubMed

Pei, Lin; Hu, Chang-qin; Ma, Shi-hong; Dai, Hui; Hang, Tai-jun

2007-11-01

The FTIR method was used to investigate the correlation of bacteria in the contaminated drug and the environmental microbes in the clean room for pharmaceutical microbial test. The similarity of bacteria in the contaminated drug and environmental microbes was compared by critical hit value method and cluster analysis method. This constructed the FTIR spectra library of clean room environmental microbe, and determined the criterion to promptly judge if the bacteria isolated from pharmaceuticals were contaminated by environment or not, hence the exactness of "one-off report" of sterile test result can be guaranteed, and can be used for the dynamic monitoring of environmental bacteria of clean room. The method is proven to be simple, accurate and rapid, and can be easily spread to the pharmaceutical microbial control.

Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria.

PubMed

Silveira, Melise Chaves; Catanho, Marcos; Miranda, Antônio Basílio de

2018-01-01

β-lactamases, which are found in several bacterial species and environments, are the main cause of resistance to β-lactams in Gram-negative bacteria. In 2009, a protein (LRA-13) with two β-lactamase domains (one class C domain and one class D domain) was experimentally characterised, and an extended action spectrum against β-lactams consistent with two functional domains was found. Here, we present the results of searches in the non-redundant NCBI protein database that revealed the existence of a group of homologous bifunctional β-lactamases in the genomes of environmental bacteria. These findings suggest that bifunctional β-lactamases are widespread in nature; these findings also raise concern that bifunctional β-lactamases may be transferred to bacteria of clinical importance through lateral gene transfer mechanisms.

Concentration and detection of bacteria in virtual environmental samples based on non-immunomagnetic separation and quantum dots by using a laboratory-made system

NASA Astrophysics Data System (ADS)

Cheng, Zhi; Wu, Taihu; Chen, Feng; Du, Yaohua; Gu, Biao; Li, Chao; Yang, Zijian

2012-03-01

This study investigated a method that simultaneously detects three bacteria, Salmonella typhimurium, Escherichia coli, and Staphylococcus aureus via an approach that combines un-immunized magnetic nanoparticles for the enrichment and antibody-conjugated quantum dots (QDs) as fluorescence markers, by using a laboratory-made system. In the enrichment procedure, the un-immunized superparamagnetic polymer nanoparticles and the three bacteria formed "beadcell" complex. Magnetic nanoparticles with different size were used and some interferents were added into the bacteria suspension respectively to check the influence on concentration efficiency. In the immuno-fluorescence labeling procedure, QDs with different emission wavelenghs were immobilized with antibody. Antibody conjugated QDs capture the bacteria selectively and specifically so that "sandwich" complex were formed. The suspension of the labeled bacteria was trickled onto a microporous membrane. A 450nm semiconductor laser was used as a part of the laboratory-made system to excite the QDs. Three PMT detectors were utilized to detect the fluorescence intensity. These un-immunized magnetic nanoparticles can be applied in nonspecific separation and enrichment of bacteria from environmental samples, and this method, of which the detection procedures are completed within 2 h, can be applied to the cost-effective and rapid detecting of bacterial contamination.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.

PubMed

Hannigan, Geoffrey D; Duhaime, Melissa B; Koutra, Danai; Schloss, Patrick D

2018-04-01

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

PubMed Central

Hannigan, Geoffrey D.; Duhaime, Melissa B.; Koutra, Danai

2018-01-01

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. PMID:29668682

Assessment of airborne bacteria in selected occupational environments in Quezon City, Philippines.

PubMed

Rendon, Rhoshela Vi C; Garcia, Bea Clarise B; Vital, Pierangeli G

2017-05-04

Exposure to bioaerosols has been associated with health deterioration among workers in several occupational environments. This highlights the need to study the microbiological quality of air of workplaces as no such study has been conducted yet in the Philippines. To detect and characterize the culturable mesophilic airborne bacteria in selected occupational environments we used passive sedimentation technique. It was observed that the number of colony-forming units was highest in junk shop, followed by the light railway transit station and last the office. By contrast, the bacterial composition was similar in all sites: Gram-positive cocci > Gram-positive bacilli > Gram-negative bacteria. Staphylococcus aureus and Bacillus spp. were also detected in all sites. These findings suggest that the presence of airborne bacteria may be a potential health hazard in urban occupational environments in the Philippines.

Purple non-sulfur photosynthetic bacteria monitor environmental stresses.

PubMed

Kis, Mariann; Sipka, Gábor; Asztalos, Emese; Rázga, Zsolt; Maróti, Péter

2015-10-01

Heavy metal ion pollution and oxygen deficiency are major environmental risks for microorganisms in aqueous habitat. The potential of purple non-sulfur photosynthetic bacteria for biomonitoring and bioremediation was assessed by investigating the photosynthetic capacity in heavy metal contaminated environments. Cultures of bacterial strains Rhodobacter sphaeroides, Rhodospirillum rubrum and Rubrivivax gelatinosus were treated with heavy metal ions in micromolar (Hg(2+)), submillimolar (Cr(6+)) and millimolar (Pb(2+)) concentration ranges. Functional assays (flash-induced absorption changes and bacteriochlorophyll fluorescence induction) and electron micrographs were taken to specify the harmful effects of pollution and to correlate to morphological changes of the membrane. The bacterial strains and functional tests showed differentiated responses to environmental stresses, revealing that diverse mechanisms of tolerance and/or resistance are involved. The microorganisms were vulnerable to the prompt effect of Pb(2+), showed weak tolerance to Hg(2+) and proved to be tolerant to Cr(6+). The reaction center controlled electron transfer in Rvx. gelatinosus demonstrated the highest degree of resistance against heavy metal exposure. Copyright © 2015 Elsevier B.V. All rights reserved.

Selection of electrogenic bacteria for microbial fuel cell in removing Victoria blue R from wastewater.

PubMed

Chen, Chih-Yu; Tsai, Teh-Hua; Wu, Pei-Ssu; Tsao, Shuo-En; Huang, Yu-Shan; Chung, Ying-Chien

2018-01-28

This study was conducted to select electrogenic bacteria from wastewater sludge. Phylogenetic analysis revealed that Proteobacteria was the dominant phylum in the microbial fuel cell (MFC) during the decomposition process of organic pollutants. Five culturable bacteria strains - namely, Bacillus subtilis, Flavobacterium sp., Aeromonas hydrophila, Citrobacter freundii, and Stenotrophomonas sp. - have a double potential in dye removal and electricity generation. We inoculated the mixed electrogenic bacteria at a specific ratio and treated them with a triphenylmethane dye, Victoria blue R (VBR), to evaluate their electricity generation ability for the artificial and real wastewater. The results of the VBR shock-loading experiment indicated that the inoculated MFC could adapt to shock loading in 1-2 days and exhibited high removal efficiency (95-100%) for 100-800 mg L -1 VBR with a power density of 8.62 ± 0.10 to 34.81 ± 0.25 mW m -2 . The selected electrogenic bacteria in the MFC could use VBR as only electron donor for power generation. The matrix effects of the real wastewater on VBR removal and electricity generation of MFC were insignificant. VBR degradation by the electrogenic bacteria involves a stepwise demethylation process to yield partially dealkylated VBR species. In addition, these results demonstrate the feasibility of inoculating culturable bacteria strains to develop an efficient MFC for purifying wastewater.

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

PubMed Central

Magennis, E. Peter; Fernandez-Trillo, Francisco; Sui, Cheng; Spain, Sebastian G.; Bradshaw, David; Churchley, David; Mantovani, Giuseppe; Winzer, Klaus; Alexander, Cameron

2014-01-01

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms, for diagnostic or anti-infective applications, but which can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerisation of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms which produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualisation of pathogens. PMID:24813421

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

NASA Astrophysics Data System (ADS)

Magennis, E. Peter; Fernandez-Trillo, Francisco; Sui, Cheng; Spain, Sebastian G.; Bradshaw, David J.; Churchley, David; Mantovani, Giuseppe; Winzer, Klaus; Alexander, Cameron

2014-07-01

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms for diagnostic or anti-infective applications, but that can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerization of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms that produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualization of pathogens.

A scanning electron microscopic evaluation of in vitro dentinal tubules penetration by selected anaerobic bacteria.

PubMed

Siqueira, J F; De Uzeda, M; Fonseca, M E

1996-06-01

In vitro root canal dentinal tubule invasion by selected anaerobic bacteria commonly isolated from endodontic infections was evaluated. Dentinal cylinders obtained from bovine incisors were inoculated with bacteria, and microbial penetration into tubules was demonstrated by scanning electron microscopy. The results indicated that all bacterial strains tested were able to penetrate into dentinal tubules, but to different extents.

Influences of Media Compositions on Characteristics of Isolated Bacteria Exhibiting Lignocellulolytic Activities from Various Environmental Sites.

PubMed

Gong, Gyeongtaek; Lee, Sun-Mi; Woo, Han Min; Park, Tai Hyun; Um, Youngsoon

2017-11-01

Efficient isolation of lignocellulolytic bacteria is essential for the utilization of lignocellulosic biomass. In this study, bacteria with cellulolytic, xylanolytic, and lignolytic activities were isolated from environmental sites such as mountain, wetland, and mudflat using isolation media containing the combination of lignocellulose components (cellulose, xylan, and lignin). Eighty-nine isolates from the isolation media were characterized by analyzing taxonomic ranks and cellulolytic, xylanolytic, and lignolytic activities. Most of the cellulolytic bacteria showed multienzymatic activities including xylanolytic activity. The isolation media without lignin were efficient in isolating bacteria exhibiting multienzymatic activities even including lignolytic activity, whereas a lignin-containing medium was effective to isolate bacteria exhibiting lignolytic activity only. Multienzymatic activities were mainly observed in Bacillus and Streptomyces, while Burkholderia was the most abundant genus with lignolytic activity only. This study provides insight into isolation medium for efficient isolation of lignocellulose-degrading microorganisms.

Microbial selectivity of UV treatment on antibiotic-resistant heterotrophic bacteria in secondary effluents of a municipal wastewater treatment plant.

PubMed

Guo, Mei-Ting; Yuan, Qing-Bin; Yang, Jian

2013-10-15

Little is known about the microbial selectivity of UV treatment for antibiotic resistant bacteria, and the results of limited studies are conflicting. To understand the effect of UV disinfection on antibiotic resistant bacteria, both total heterotrophic bacteria and antibiotic resistant bacteria (including cephalexin-, ciprofloxacin-, erythromycin-, gentamicin-, vancomycin-, sulfadiazine-, rifampicin-, tetracycline- and chloramphenicol-resistant bacteria) were examined in secondary effluent samples from a municipal wastewater treatment plant. Bacteria resistant to both erythromycin and tetracycline were chosen as the representative of multiple-antibiotic-resistant bacteria and their characteristics after UV treatment were also investigated. UV disinfection results in effective inactivation for total heterotrophic bacteria, as well as all antibiotic resistant bacteria. After UV treatment at a fluence of 5 mJ/cm(2), the log reductions of nine types of antibiotic resistant bacteria varied from 1.0 ± 0.1 to 2.4 ± 0.1. Bacteria resistant to both erythromycin and tetracycline had a similar fluence response as did total heterotrophic bacteria. The findings suggest that UV disinfection could eliminate antibiotic resistance in wastewater treatment effluents and thus ensure public health security. Our experimental results indicated that UV disinfection led to enrichment of bacteria with resistance to sulfadiazine, vancomycin, rifampicin, tetracycline and chloramphenicol, while the proportions of cephalexin-, erythromycin-, gentamicin- and ciprofloxacin-resistant bacteria in the wastewater decreased. This reveals the microbial selectivity of UV disinfection for antibiotic resistant bacteria. Copyright © 2013 Elsevier Ltd. All rights reserved.

Chemotactic selection of pollutant degrading soil bacteria

DOEpatents

Hazen, Terry C.

1994-01-01

A method for identifying soil microbial strains which may be bacterial degraders of pollutants comprising the steps of placing a concentration of a pollutant in a substantially closed container, placing the container in a sample of soil for a period of time ranging from one minute to several hours, retrieving the container, collecting the contents of the container, and microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to inoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

Chemotactic selection of pollutant degrading soil bacteria

DOEpatents

Hazen, T.C.

1991-03-04

A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

[Effect of tigecycline on selected multiresistant bacteria].

PubMed

Kolár, Milan; Hanulík, Vojtech; Chromá, Magdalena

2009-02-01

Currently, one of the most serious problems in medicine is the increasing resistance of pathogenic bacteria to antimicrobial drugs. Bacterial resistance may potentially be solved in particular by decreasing the consumption of antibiotics and increasing the quality of their use. Equally important, however, is the development of new antimicrobial drugs and their use in clinical practice. One of the new antibiotic agents is tigecycline of the glycylcycline group. The presented work aimed at assessing its in vitro effect on selected multiresistant bacteria. Clinical samples were collected from patients hospitalized in the University Hospital Olomouc to isolate ESBL- and AmpC beta-lactamase-producing enterobacteria, methicillin-resistant Staphylococcus aureus (MRSA) strains and vancomycin-resistant enterococci (VRE). In the isolates, susceptibility to tigecycline was determined by the standard microdilution method. A total of 350 isolates were tested (100 MRSA, 10 0 VRE, 100 ESBL-positive and 50 AmpC-positive enterobacteria). In the cases of VRE and MRSA, no resistance to tigecycline was detected and the minimum inhibitory concentrations (MIC) did not exceed 0.25 mg/l and 0.5 mg/l, respectively. In ESBL-positive enterobacteria, 97% susceptibility (MIC range = or <0.06 to 4 mg/l) was detected; in AmpC-positive enterobacteria, the MIC range was = or <0.03-2 mg/l and susceptibility reached 98 %. Tigecycline may be considered a suitable alternative in the treatment of infections caused by the above-mentioned multiresistant strains.

Performing Analyses for Waterborne Bacteria. Module 13. Vocational Education Training in Environmental Health Sciences.

ERIC Educational Resources Information Center

Consumer Dynamics Inc., Rockville, MD.

This module, one of 25 on vocational education training for careers in environmental health occupations, contains self-instructional materials on performing analyses for waterborne bacteria. Following guidelines for students and instructors and an introduction that explains what the student will learn are three lessons: (1) naming, sterilizing and…

Selection of bacteriocin producer strains of lactic acid bacteria from a dairy environment.

PubMed

Lasagno, M; Beoleito, V; Sesma, F; Raya, R; Font de Valdez, G; Eraso, A

2002-01-01

Two strains showing bacteriocin production were selected from a total of 206 lactic acid bacteria isolated from samples of milk, milk serum, whey and homemade cheeses in Southern Cordoba, Argentina. This property was detected by means of well diffusion assays. The strains were identified as Enterococcus hirae and Enterococcus durans. The protein nature of those substances was proved by showing their sensitivity to type IV and XXV proteases, papaine, trypsin, pepsin and K proteinase. The bacteriocins inhibited the growth of Listeria monocytogenes, Bacillus cereus, Clostridium perfringes and two strains of Staphylococcus aureus, an A-enterotoxin and a B-enterotoxin producers. All of these bacteria are common pathogens usually associated with food borne diseases (ETA). These lactic acid bacteria or their bacteriocins could be suitable candidates for food preservation and specially useful in the our regional dairy industry.

Rationalizing and advancing the 3-MPBA SERS sandwich assay for rapid detection of bacteria in environmental and food matrices.

PubMed

Pearson, Brooke; Mills, Alexander; Tucker, Madeline; Gao, Siyue; McLandsborough, Lynne; He, Lili

2018-06-01

Bacterial foodborne illness continues to be a pressing issue in our food supply. Rapid detection methods are needed for perishable foods due to their short shelf lives and significant contribution to foodborne illness. Previously, a sensitive and reliable surface-enhanced Raman spectroscopy (SERS) sandwich assay based on 3-mercaptophenylboronic acid (3-MBPA) as a capturer and indicator molecule was developed for rapid bacteria detection. In this study, we explored the advantages and constraints of this assay over the conventional aerobic plate count (APC) method and further developed methods for detection in real environmental and food matrices. The SERS sandwich assay was able to detect environmental bacteria in pond water and on spinach leaves at higher levels than the APC method. In addition, the SERS assay appeared to have higher sensitivity to quantify bacteria in the stationary phase. On the other hand, the APC method was more sensitive to cell viability. Finally, a method to detect bacteria in a challenging high-sugar juice matrix was developed to enhance bacteria capture. This study advanced the SERS technique for real applications in environment and food matrices. Copyright © 2017 Elsevier Ltd. All rights reserved.

Scanning electron microscopy coupled with energy-dispersive X-ray spectrometry for quick detection of sulfur-oxidizing bacteria in environmental water samples

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing

2017-01-01

Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages.

PubMed

Örmälä-Odegrip, Anni-Maria; Ojala, Ville; Hiltunen, Teppo; Zhang, Ji; Bamford, Jaana K H; Laakso, Jouni

2015-05-07

Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our results could have larger scale

Photothermal Nanotherapeutics and Nanodiagnostics for Selective Killing of Bacteria Targeted with Gold Nanoparticles

PubMed Central

Zharov, Vladimir P.; Mercer, Kelly E.; Galitovskaya, Elena N.; Smeltzer, Mark S.

2006-01-01

We describe a new method for selective laser killing of bacteria targeted with light-absorbing gold nanoparticles conjugated with specific antibodies. The multifunctional photothermal (PT) microscope/spectrometer provides a real-time assessment of this new therapeutic intervention. In this integrated system, strong laser-induced overheating effects accompanied by the bubble-formation phenomena around clustered gold nanoparticles are the main cause of bacterial damage. PT imaging and time-resolved monitoring of the integrated PT responses assessed these effects. Specifically, we used this technology for selective killing of the Gram-positive bacterium Staphylococcus aureus by targeting the bacterial surface using 10-, 20-, and 40-nm gold particles conjugated with anti-protein A antibodies. Labeled bacteria were irradiated with focused laser pulses (420–570 nm, 12 ns, 0.1–5 J/cm2, 100 pulses), and laser-induced bacterial damage observed at different laser fluences and nanoparticle sizes was verified by optical transmission, electron microscopy, and conventional viability testing. PMID:16239330

The fecal bacteria

USGS Publications Warehouse

Sadowsky, Michael J.; Whitman, Richard L.

2011-01-01

The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

In vitro screening of probiotic lactic acid bacteria and prebiotic glucooligosaccharides to select effective synbiotics.

PubMed

Grimoud, Julien; Durand, Henri; Courtin, Céline; Monsan, Pierre; Ouarné, Françoise; Theodorou, Vassilia; Roques, Christine

2010-10-01

Probiotics and prebiotics have been demonstrated to positively modulate the intestinal microflora and could promote host health. Although some studies have been performed on combinations of probiotics and prebiotics, constituting synbiotics, results on the synergistic effects tend to be discordant in the published works. The first aim of our study was to screen some lactic acid bacteria on the basis of probiotic characteristics (resistance to intestinal conditions, inhibition of pathogenic strains). Bifidobacterium was the most resistant genus whereas Lactobacillus farciminis was strongly inhibited. The inhibitory effect on pathogen growth was strain dependent but lactobacilli were the most effective, especially L. farciminis. The second aim of the work was to select glucooligosaccharides for their ability to support the growth of the probiotics tested. We demonstrated the selective fermentability of oligodextran and oligoalternan by probiotic bacteria, especially the bifidobacteria, for shorter degrees of polymerisation and absence of metabolism by pathogenic bacteria. Thus, the observed characteristics confer potential prebiotic properties on these glucooligosaccharides, to be further confirmed in vivo, and suggest some possible applications in synbiotic combinations with the selected probiotics. Furthermore, the distinctive patterns of the different genera suggest a combination of lactobacilli and bifidobacteria with complementary probiotic effects in addition to the prebiotic ones. These associations should be further evaluated for their synbiotic effects through in vitro and in vivo models. Copyright © 2010 Elsevier Ltd. All rights reserved.

Impact of micro-environmental changes on respiratory tract infections with intracellular bacteria.

PubMed

Shima, Kensuke; Coopmeiners, Jonas; Graspeuntner, Simon; Dalhoff, Klaus; Rupp, Jan

2016-11-01

Community-acquired pneumonia is caused by intra- and extracellular bacteria, with some of these bacteria also being linked to the pathogenesis of chronic lung diseases, including asthma and chronic obstructive pulmonary disease. Chlamydia pneumoniae is an obligate intracellular pathogen that is highly sensitive to micro-environmental conditions controlling both pathogen growth and host immune responses. The availability of nutrients, as well as changes in oxygen, pH and interferon-γ levels, have been shown to directly influence the chlamydial life cycle and clearance. Although the lung has been traditionally regarded as a sterile environment, sequencing approaches have enabled the identification of a large number of bacteria in healthy and diseased lungs. The influence of the lung microbiota on respiratory infections has not been extensively studied so far and data on chlamydial infections are currently unavailable. In the present study, we speculate on how lung microbiota might interfere with acute and chronic infections by focusing exemplarily on the obligate intracellular C. pneumoniae. Furthermore, we consider changes in the gut microbiota as an additional player in the control of lung infections, especially in view the increasing evidence suggesting the involvement of the gut microbiota in various immunological processes throughout the human body. © 2016 Federation of European Biochemical Societies.

Isolating "Unknown" Bacteria in the Introductory Microbiology Laboratory: A New Selective Medium for Gram-Positives.

ERIC Educational Resources Information Center

McKillip, John L.; Drake, MaryAnne

1999-01-01

Describes the development, preparation, and use of a medium that can select against a wide variety of Gram-negative bacteria while still allowing growth and differentiation of a wide range of Gram-positives. (WRM)

Effect of phenolic compounds on the growth of selected probiotic and pathogenic bacteria.

PubMed

Pacheco-Ordaz, R; Wall-Medrano, A; Goñi, M G; Ramos-Clamont-Montfort, G; Ayala-Zavala, J F; González-Aguilar, G A

2018-01-01

Fruit extracts from different tissues (pulp, seed and peel) have shown antimicrobial and prebiotic activities related to their phenolic profile, although structure-specific evaluations have not been reported yet. The effect of five phenolic compounds (catechin and gallic, vanillic, ferulic and protocatechuic acids) identified in different fruits, particularly in mango, was evaluated on the growth of two probiotic (Lactobacillus rhamnosusGG ATCC 53103 and Lactobacillus acidophilusNRRLB 4495) and two pathogenic (Escherichia coli 0157:H7 ATCC 43890 and Salmonella enterica serovar Typhimurium ATCC 14028) bacteria. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of phenolic acids ranged from 15-20 mmol l -1 and 20-30 mmol l -1 against E. coli and S. Typhimurium, respectively. For catechin, the MIC and MBC were 35 mmol l -1 and >35 mmol l -1 against E. coli and S. Typhimurium, respectively. The presence of catechin and gallic, protocatechuic and vanillic acids in MRS broth without dextrose allowed the growth of lactobacilli. Catechin combined with protocatechuic or vanillic acid mildly allowed the growth of both probiotics. In conclusion, phenolic compounds can selectively inhibit the growth of pathogenic bacteria without affecting the viability of probiotics. This study provides relevant information about the effects of phenolic compounds commonly present in fruit and vegetables on the growth of probiotic and pathogenic bacteria. The compounds selectively allowed the growth of probiotic lactobacilli (Lactobacillus rhamnosus GG and Lactobacillus acidophilus) and inhibited pathogenic bacteria (Escherichia coli and Salmonella Typhimurium) at the same concentration (20 mmol l -1 ). These findings can contribute to the formulation of nutraceutical products, such as synbiotics, that can restore or maintain an optimal composition of human microbiota, potentially improving the overall health of the consumer. © 2017 The

Environmental assessment of three egg production systems - Part III: Airborne bacteria concentrations and emissions.

PubMed

Zhao, Y; Zhao, D; Ma, H; Liu, K; Atilgan, A; Xin, H

2016-07-01

Airborne microorganism level is an important indoor air quality indicator, yet it has not been well documented for laying-hen houses in the United States. As a part of the Coalition for Sustainable Egg Supply (CSES) environmental monitoring project, this study comparatively monitored the concentrations and emissions of airborne total and Gram-negative (Gram(-)) bacteria in three types of commercial laying-hen houses, i.e., conventional cage (CC), aviary (AV), and enriched colony (EC) houses, over a period of eight months covering the mid and late stages of the flock cycle. It also delineated the relationship between airborne total bacteria and particulate matter smaller than 10 μm in aerodynamic diameter (PM10). The results showed airborne total bacteria concentrations (log CFU/m(3)) of 4.7 ± 0.3 in CC, 6.0 ± 0.8 in AV, and 4.8 ± 0.3 in EC, all being higher than the level recommended for human environment (3.0 log CFU/m(3)). The much higher concentrations in AV arose from the presence of floor litter and hen activities on it, as evidenced by the higher concentrations in the afternoon (with litter access) than in the morning (without litter access). The overall means and standard deviation of airborne total bacteria emission rates, in log CFU/[h-hen] (or log CFU/[h-AU], AU = animal unit or 500 kg live weight) were 4.8 ± 0.4 (or 7.3 ± 0.4) for CC, 6.1 ± 0.7 (or 8.6 ± 0.7) for AV, and 4.8 ± 0.5 (or 7.3 ± 0.5) for EC. Both concentration and emission rate of airborne total bacteria were positively related to PM10 Gram(-) bacteria were present at low concentrations in all houses; and only 2 samples (6%) in CC, 7 (22%) samples in AV, and 2 (6%) samples in EC out of 32 air samples collected in each house were found positive with Gram(-) bacteria. The concentration of airborne Gram(-) bacteria was estimated to be <2% of the total bacteria. Total bacteria counts in manure on belt (in all houses) and floor litter (only in AV) were similar; however, the manure had

The Selective Value of Bacterial Shape

PubMed Central

Young, Kevin D.

2006-01-01

Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so. PMID:16959965

Functional metagenomic selection of RubisCOs from uncultivated bacteria

USGS Publications Warehouse

Varaljay, Vanessa A; Satagopan, Sriram; North, Justin A.; Witteveen, Briana; Dourado, Manuella N.; Anantharaman, Karthik; Arbing, Mark A.; McCann, Shelley; Oremland, Ronald S.; Banfield, Jillian F.; Wrighton, Kelly C.; Tabita, F. Robert

2016-01-01

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO2-dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of theGallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possessCO2/O2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO2-fixing enzymes not previously characterized.

Commensal bacteria-dependent select expression of CXCL2 contributes to periodontal tissue homeostasis.

PubMed

Zenobia, Camille; Luo, Xiao Long; Hashim, Ahmed; Abe, Toshiharu; Jin, Lijian; Chang, Yucheng; Jin, Zhi Chao; Sun, Jian Xun; Hajishengallis, George; Curtis, Mike A; Darveau, Richard P

2013-08-01

The oral and intestinal host tissues both carry a heavy microbial burden. Although commensal bacteria contribute to healthy intestinal tissue structure and function, their contribution to oral health is poorly understood. A crucial component of periodontal health is the recruitment of neutrophils to periodontal tissue. To elucidate this process, gingival tissues of specific-pathogen-free and germ-free wild-type mice and CXCR2KO and MyD88KO mice were examined for quantitative analysis of neutrophils and CXCR2 chemoattractants (CXCL1, CXCL2). We show that the recruitment of neutrophils to the gingival tissue does not require commensal bacterial colonization but is entirely dependent on CXCR2 expression. Strikingly, however, commensal bacteria selectively upregulate the expression of CXCL2, but not CXCL1, in a MyD88-dependent way that correlates with increased neutrophil recruitment as compared with germ-free conditions. This is the first evidence that the selective use of chemokine receptor ligands contributes to neutrophil homing to healthy periodontal tissue. © 2013 John Wiley & Sons Ltd.

Ability of organic and inorganic bedding materials to promote growth of environmental bacteria.

PubMed

Godden, S; Bey, R; Lorch, K; Farnsworth, R; Rapnicki, P

2008-01-01

The major objective of this study was to contrast the ability of 4 commonly utilized bedding materials to promote growth of environmental bacteria under controlled conditions. A second objective was to describe the relationship between bacterial growth and specific biochemical or nutritional properties of these bedding materials. Unused samples of clean sand (CS; n = 20), recycled sand (RS; n = 21), digested manure solids (DS; n = 15), and shavings (SH; n = 15) were collected from bedding storage areas on 49 commercial Minnesota and Wisconsin dairy farms. Sterilized bedding samples were inoculated with Klebsiella pneumoniae and Enterococcus faecium then incubated, in triplicate, for 72 h at 37 degrees C. Subsamples were collected after 0, 24, 48, and 72 h of incubation for culture and enumeration of bacteria. Subsamples of bedding were also tested for pH, total C content (%), and total N content (%). If bacterial growth occurred, peak levels were typically achieved within 24 h. Digested manure solids promoted the greatest amounts of growth of K. pneumoniae, followed by RS and then SH, whereas CS promoted the least. There would seem to be a tradeoff in selecting SH as a bedding material, because it supported moderate growth of K. pneumoniae but caused a rapid decline in the numbers of E. faecium. However, RS, CS, and DS each only supported relatively small amounts of growth of E. faecium, so the benefit of SH relative to other bedding materials is limited. High bedding pH may partially explain why some bedding materials supported growth of E. faecium (e.g., DS and RS). Both high bedding pH (e.g., as for DS or RS) and high total C (%) content (e.g., as for DS and SH) may partially explain why some bedding materials supported growth of K. pneumoniae.

Screening and characterization of phosphate solubilizing bacteria from isolate of thermophilic bacteria

NASA Astrophysics Data System (ADS)

Yulianti, Evy; Rakhmawati, Anna

2017-08-01

The aims of this study were to select bacteria that has the ability to dissolve phosphate from thermophilic bacteria isolates after the Merapi eruption. Five isolates of selected bacteria was characterized and continued with identification. Selection was done by using a pikovskaya selective medium. Bacterial isolates were grown in selective medium and incubated for 48 hours at temperature of 55 ° C. Characterization was done by looking at the cell and colony morphology, physiological and biochemical properties. Identification was done with the Profile Matching method based on the reference genus Oscillospira traced through Bergey's Manual of Determinative Bacteriology. Dendogram was created based on similarity index SSM. The results showed there were 14 isolates of bacteria that were able to dissolve phosphate indicated by a clear zone surrounding the bacterial colony on selective media. Five isolates were selected with the largest clear zone. Isolates D79, D92, D110a, D135 and D75 have different characters. The result of phenotypic characters identification with Genus Oscillospira profile has a percentage of 100% similarity to isolate D92 and D110a; 92.31% for isolates D79, and 84.6% for isolates D75 and D135. Dendogram generated from average linkage algorithm / UPGMA using the Simple Matching Coefficient (SSM) algorithms showed, isolate thermophilic bacteria D75 and D135 are combined together to form cluster 1. D110a and D92 form a sub cluster A. Sub cluster A and D79 form cluster 2

Environmental Pollution, A Selective Bibliography.

ERIC Educational Resources Information Center

Clearinghouse for Federal Scientific and Technical Information, Springfield, VA.

This bibliography on environmental pollution is comprised primarily of reports of federally sponsored research by such departments and agencies as HEW, Interior, AEC, NASA, Defense, Transportation, and others. The reports were selected from Clearinghouse announcement journals during the period 1968 through April 1970. The bibliography contains…

Bioremediation of diesel fuel contaminated soil: effect of non ionic surfactants and selected bacteria addition.

PubMed

Collina, Elena; Lasagni, Marina; Pitea, Demetrio; Franzetti, Andrea; Di Gennaro, Patrizia; Bestetti, Giuseppina

2007-09-01

Aim of this work was to evaluate influence of two commercial surfactants and inoculum of selected bacteria on biodegradation of diesel fuel in different systems. Among alkyl polyethossilates (Brij family) and sorbitan derivates (Tween family) a first selection of surfactants was performed by estimation of Koc and Dafnia magna EC50 with molecular descriptor and QSAR model. Further experiments were conducted to evaluate soil sorption, biodegradability and toxicity. In the second part of the research, the effect of Brij 56, Tween 80 and selected bacteria addition on biodegradation of diesel fuel was studied in liquid cultures and in slurry and solid phase systems. The latter experiments were performed with diesel contaminated soil in bench scale slurry phase bioreactor and solid phase columns. Tween 80 addition increased the biodegradation rate of hydrocarbons both in liquid and in slurry phase systems. Regarding the effect of inoculum, no enhancement of biodegradation rate was observed neither in surfactant added nor in experiments without addition. On the contrary, in solid phase experiments, inoculum addition resulted in enhanced biodegradation compared to surfactant addition.

Distinction of Gram-positive and -negative bacteria using a colorimetric microbial viability assay based on the reduction of water-soluble tetrazolium salts with a selection medium.

PubMed

Tsukatani, Tadayuki; Suenaga, Hikaru; Higuchi, Tomoko; Shiga, Masanobu; Noguchi, Katsuya; Matsumoto, Kiyoshi

2011-01-01

Bacteria are fundamentally divided into two groups: Gram-positive and Gram-negative. Although the Gram stain and other techniques can be used to differentiate these groups, some issues exist with traditional approaches. In this study, we developed a method for differentiating Gram-positive and -negative bacteria using a colorimetric microbial viability assay based on the reduction of the tetrazolium salt {2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt} (WST-8) via 2-methyl-1,4-napthoquinone with a selection medium. We optimized the composition of the selection medium to allow the growth of Gram-negative bacteria while inhibiting the growth of Gram-positive bacteria. When the colorimetric viability assay was carried out in a selection medium containing 0.5µg/ml crystal violet, 5.0 µg/ml daptomycin, and 5.0µg/ml vancomycin, the reduction in WST-8 by Gram-positive bacteria was inhibited. On the other hand, Gram-negative bacteria produced WST-8-formazan in the selection medium. The proposed method was also applied to determine the Gram staining characteristics of bacteria isolated from various foodstuffs. There was good agreement between the results obtained using the present method and those obtained using a conventional staining method. These results suggest that the WST-8 colorimetric assay with selection medium is a useful technique for accurately differentiating Gram-positive and -negative bacteria.

Effectiveness of disinfectant wipes for decontamination of bacteria on patients' environmental and medical equipment surfaces at Siriraj Hospital.

PubMed

Seenama, Chakkraphong; Tachasirinugune, Peenithi; Jintanothaitavorn, Duangporn; Kachintorn, Kanchana; Thamlikitkul, Visanu

2013-02-01

To determine the effectiveness of Virusolve+ disinfectant wipes and PAL disinfectant wipes for decontamination of inoculated bacteria on patients' environmental and medical equipment surfaces at Siriraj Hospital. Tryptic soy broths containing MRSA and XDR A. baumannii were painted onto the surfaces of patient's stainless steel bed rail, patient's fiber footboard, control panel of infusion pump machine and control panel of respirator. The contaminated surfaces were cleaned by either tap water, tap water containing detergent, Virusolve+ disinfectant wipes or PAL disinfectant wipes. The surfaces without any cleaning procedures served as the control surface. The contaminated surfaces cleaned with the aforementioned procedures and control surfaces were swabbed with cotton swabs. The swabs were streaked on agar plates to determine the presence of MRSA and XDR A. baumannii. MRSA and XDR A. baumannii were recovered from all control surfaces. All surfaces cleaned with tap water or tap water containing detergent revealed presence of both MRSA and XDR A. baumannii. However the amounts of bacteria on the surfaces cleaned with tap water containing detergent were less than those cleaned with tap water alone. All surfaces cleaned with PAL disinfectant wipes also revealed presence of both MRSA and XDR A. baumannii. However the amounts of bacteria on the surfaces cleaned with PAL disinfectant wipes were less than those cleaned with tap water containing detergent. No bacteria were recovered from all surfaces cleaned with Virusolve+ disinfectant wipes. Virusolve+ disinfectant wipes were more effective than tap water; tap water containing detergent and PAL disinfectant wipes for decontamination of bacteria inoculated on patients environmental and medical equipment surfaces at Siriraj Hospital.

Selected Analytical Methods for Environmental Remediation ...

EPA Pesticide Factsheets

The US Environmental Protection Agency’s Office of Research and Development (ORD) conducts cutting-edge research that provides the underpinning of science and technology for public health and environmental policies and decisions made by federal, state and other governmental organizations. ORD’s six research programs identify the pressing research needs with input from EPA offices and stakeholders. Research is conducted by ORD’s 3 labs, 4 centers, and 2 offices located in 14 facilities. The EPA booth at APHL will have several resources available to attendees, mostly in the form of print materials, that showcase our research labs, case studies of research activities, and descriptions of specific research projects. The Selected Analytical Methods for Environmental Remediation and Recovery (SAM), a library of selected methods that are helping to increase the nation's laboratory capacity to support large-scale emergency response operations, will be demoed by EPA scientists at the APHL Experience booth in the Exhibit Hall on Tuesday during the morning break. Please come to the EPA booth #309 for more information! To be on a loop at our ORD booth demo during APHL.

Selected environmental risk factors and congenital heart defects.

PubMed

Kuciene, Renata; Dulskiene, Virginija

2008-01-01

The aim of the article is to review the published scientific literature and epidemiological studies about the effect of selected environmental risk factors on congenital heart defects in infants. According to recent reports, the prevalence of congenital heart defects is around 1% of live births. Congenital heart malformations are the leading cause of infant mortality. Unfortunately, the majority of the causes of heart defects remain unknown. These malformations are caused by interaction of genetic and environmental factors. The article reviews selected environmental risk factors: maternal illnesses and conditions associated with metabolic disorder (maternal diabetes, obesity, phenylketonuria), maternal lifestyle factors (alcohol use, smoking), which may increase the risk of congenital heart defects.

Microbial Resistance to Triclosan: A Case Study in Natural Selection

ERIC Educational Resources Information Center

Serafini, Amanda; Matthews, Dorothy M.

2009-01-01

Natural selection is the mechanism of evolution caused by the environmental selection of organisms most fit to reproduce, sometimes explained as "survival of the fittest." An example of evolution by natural selection is the development of bacteria that are resistant to antimicrobial agents as a result of exposure to these agents. Triclosan, which…

Environmental factors influencing landfill gas biofiltration: Lab scale study on methanotrophic bacteria growth.

PubMed

Amodeo, Corrado; Sofo, Adriano; Tito, Maria Teresa; Scopa, Antonio; Masi, Salvatore; Pascale, Raffaella; Mancini, Ignazio M; Caniani, Donatella

2018-03-29

The post-management of landfills represents an important challenge for landfill gas treatment. Traditional systems (energy recovery, flares, etc.) present technical problems in treating flow with low methane (CH 4 ) concentrations. The objective of this study was to isolate methanotrophic bacteria from a field-scale biofilter in order to study the bacteria in laboratories and evaluate the environmental factors that mostly influence Microbial Aerobic Methane Oxidation (MAMO). The soil considered was sampled from the biofilter located in the landfill of Venosa (Basilicata Region, Italy) and it was mainly composed of wood chips and compost. The results showed that methanotrophic microorganisms are mainly characterized by a slow growth and a significant sensitivity to CH 4 levels. Temperature and nitrogen (N) also have a very important role on their development. On the basis of the results, biofilters for biological CH 4 oxidation can be considered a viable alternative to mitigate CH 4 emissions from landfills.

Quantity-activity relationship of denitrifying bacteria and environmental scaling in streams of a forested watershed

USGS Publications Warehouse

O'Connor, B.L.; Hondzo, Miki; Dobraca, D.; LaPara, T.M.; Finlay, J.A.; Brezonik, P.L.

2006-01-01

The spatial variability of subreach denitrification rates in streams was evaluated with respect to controlling environmental conditions, molecular examination of denitrifying bacteria, and dimensional analysis. Denitrification activities ranged from 0 and 800 ng-N gsed-1 d-1 with large variations observed within short distances (<50 m) along stream reaches. A log-normal probability distribution described the range in denitrification activities and was used to define low (16% of the probability distributibn), medium (68%), and high (16%) denitrification potential groups. Denitrifying bacteria were quantified using a competitive polymerase chain reaction (cPCR) technique that amplified the nirK gene that encodes for nitrite reductase. Results showed a range of nirK quantities from 103 to 107 gene-copy-number gsed.-1 A nonparametric statistical test showed no significant difference in nirK quantifies among stream reaches, but revealed that samples with a high denitrification potential had significantly higher nirK quantities. Denitrification activity was positively correlated with nirK quantities with scatter in the data that can be attributed to varying environmental conditions along stream reaches. Dimensional analysis was used to evaluate denitrification activities according to environmental variables that describe fluid-flow properties, nitrate and organic material quantities, and dissolved oxygen flux. Buckingham's pi theorem was used to generate dimensionless groupings and field data were used to determine scaling parameters. The resulting expressions between dimensionless NO3- flux and dimensionless groupings of environmental variables showed consistent scaling, which indicates that the subreach variability in denitrification rates can be predicted by the controlling physical, chemical, and microbiological conditions. Copyright 2006 by the American Geophysical Union.

Simultaneous hydrocarbon biodegradation and biosurfactant production by oilfield-selected bacteria.

PubMed

Mnif, S; Chamkha, M; Labat, M; Sayadi, S

2011-09-01

To study the bacterial diversity associated with hydrocarbon biodegradation potentiality and biosurfactant production of Tunisian oilfields bacteria. Eight Tunisian hydrocarbonoclastic oilfields bacteria have been isolated and selected for further characterization studies. Phylogenetic analysis revealed that three thermophilic strains belonged to the genera Geobacillus, Bacillus and Brevibacillus, and that five mesophilic strains belonged to the genera Pseudomonas, Lysinibacillus, Achromobacter and Halomonas. The bacterial strains were cultivated on crude oil as sole carbon and energy sources, in the presence of different NaCl concentrations (1, 5 and 10%, w/v), and at 37 or 55°C. The hydrocarbon biodegradation potential of each strain was quantified by GC-MS. Strain C450R, phylogenetically related to the species Pseudomonas aeruginosa, showed the maximum crude oil degradation potentiality. During the growth of strain C450R on crude oil (2%, v/v), the emulsifying activity (E24) and glycoside content increased and reached values of 77 and 1.33 g l(-1), respectively. In addition, the surface tension (ST) decreased from 68 to 35.1 mN m(-1), suggesting the production of a rhamnolipid biosurfactant. Crude biosurfactant had been partially purified and characterized. It showed interest stability against temperature and salinity increasing and important emulsifying activity against oils and hydrocarbons. The results of this study showed the presence of diverse aerobic bacteria in Tunisian oilfields including mesophilic, thermophilic and halotolerant strains with interesting aliphatic hydrocarbon degradation potentiality, mainly for the most biosurfactant produced strains. It may be suggested that the bacterial isolates are suitable candidates for practical field application for effective in situ bioremediation of hydrocarbon-contaminated sites. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Human pigmentation genes under environmental selection

PubMed Central

2012-01-01

Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe. PMID:23110848

Longevity enhances selection of environmental sex determination.

PubMed

Bull, J J; Bulmer, M G

1989-12-01

Environmental sex determination (ESD) is a mechanism in which an individual develops as male or female largely in response to some environmental effect experienced early in life. Its forms range from sex determination by egg incubation temperature in reptiles to sex determination of photoperiod in amphipods. Previous theoretical work as suggested that ESD is favored by natural selection if the fitness consequences of the early environmental experience differ for males and females, so that an individual benefits by being male under some conditions and female under others. A drawback of ESD is that it enables climatic changes to influence the population sex ratio, and such fluctuations select against ESD. This study employed numerical analyses to investigate the balance between these two opposing forces. The negative impact of climatic fluctuations appears to depend greatly on species longevity: substantial between-year fluctuations are of little consequence in selecting against ESD in long-lived species because annual sex ratio fluctuations tend to cancel and thus alter the total population sex ratio only slightly. Thus, if a species is sufficiently long-lived, extreme ESD can be maintained despite only a weak advantage. This result offers one explanation for the failure to demonstrate an advantage for the extreme forms of ESD observed in reptiles.

Biosurfactant-assisted bioremediation of crude oil by indigenous bacteria isolated from Taean beach sediment.

PubMed

Lee, Dong Wan; Lee, Hanbyul; Kwon, Bong-Oh; Khim, Jong Seong; Yim, Un Hyuk; Kim, Beom Seok; Kim, Jae-Jin

2018-05-25

Crude oil and its derivatives are considered as one group of the most pervasive environmental pollutants in marine environments. Bioremediation using oil-degrading bacteria has emerged as a promising green cleanup alternative in more recent years. The employment of biosurfactant-producing and hydrocarbon-utilizing indigenous bacteria enhances the effectiveness of bioremediation by making hydrocarbons bioavailable for degradation. In this study, the best candidates of biosurfactant-producing indigenous bacteria were selected by screening of biochemical tests. The selected bacteria include Bacillus algicola (003-Phe1), Rhodococcus soli (102-Na5), Isoptericola chiayiensis (103-Na4), and Pseudoalteromonas agarivorans (SDRB-Py1). In general, these isolated species caused low surface tension values (33.9-41.3 mN m -1 ), high oil spreading (1.2-2.4 cm), and hydrocarbon emulsification (up to 65%) warranting active degradation of hydrocarbons. FT-IR and LC-MS analyses indicated that the monorhamnolipid (Rha-C 16:1 ) and dirhamnolipid (Rha-Rha-C 6 -C 6:1 ) were commonly produced by the bacteria as potent biosurfactants. The residual crude oil after the biodegradation test was quantitated using GC-MS analysis. The bacteria utilized crude oil as their sole carbon source while the amount of residual crude oil significantly decreased. In addition the cell-free broth containing biosurfactants produced by bacterial strains significantly desorbed crude oil in oil-polluted marine sediment. The selected bacteria might hold additional capacity in crude oil degradation. Biosurfactant-producing indigenous bacteria therefore degrade crude oil hydrocarbon compounds, produce biosurfactants that can increase the emulsification of crude oil and are thus more conducive to the degradation of crude oil. Copyright © 2018 Elsevier Ltd. All rights reserved.

Isolation and Characterisation of 1-Alkyl-3-Methylimidazolium Chloride Ionic Liquid-Tolerant and Biodegrading Marine Bacteria

PubMed Central

Megaw, Julianne; Busetti, Alessandro; Gilmore, Brendan F.

2013-01-01

The aim of this study was to isolate and identify marine-derived bacteria which exhibited high tolerance to, and an ability to biodegrade, 1-alkyl-3-methylimidazolium chloride ionic liquids. The salinity and hydrocarbon load of some marine environments may induce selective pressures which enhance the ability of microbes to grow in the presence of these liquid salts. The isolates obtained in this study generally showed a greater ability to grow in the presence of the selected ionic liquids compared to microorganisms described previously, with two marine-derived bacteria, Rhodococcus erythropolis and Brevibacterium sanguinis growing in concentrations exceeding 1 M 1-ethyl-3-methylimidazolium chloride. The ability of these bacteria to degrade the selected ionic liquids was assessed using High Performance Liquid Chromatography (HPLC), and three were shown to degrade the selected ionic liquids by up to 59% over a 63-day test period. These bacterial isolates represent excellent candidates for further potential applications in the bioremediation of ionic liquid-containing waste or following accidental environmental exposure. PMID:23560109

Identification of pink-pigmented bacteria isolated from environmental water samples and their biofilm formation abilities.

PubMed

Furuhata, Katsunori; Kato, Yuko; Goto, Keiichi; Saitou, Keiko; Sugiyama, Jun-Ichi; Hara, Motonobu; Fukuyama, Masahumi

2008-06-01

Sixty-seven strains of pink-pigmented bacteria, which were isolated from environmental water samples collected nationwide, were identified by partial 16S rDNA sequence analysis. In addition, the biofilm formation ability of the isolates was experimentally investigated. We could identify only 2 strains at the species level: Pedobacter roseus HS-38 and Runella slithyformis HS-77. The results showed that of the strains tested, 22 strains (32.8%) were Pedobacter spp., which was most frequently identified, followed by 19 strains (28.4%) of Arcicella spp., 16 strains (23.9%) of Deinococcus spp., 5 strains (7.5%) of Roseomonas spp., 4 strains (6.0%) of Flectobacillus spp. and 1 strain (1.5%) of Runella sp. Most isolates showed low similarity values to previously known species, and they were found to be novel species. At a result, it was difficult to identify environmental water-derived pink-pigmented bacteria at the species level. On the other hand, when we measured the absorbance by the crystal violet staining to examine the quantities of biofilm formation of these strains, fifty-five (82.0%) of the 67 isolates formed biofilm. The absorbance of Deinococcus sp. HS-75 was the highest (3.56). When comparing the absorbance values among the genera, Roseomonas spp. showed the highest absorbance (mean:1.62), followed by Deinococcus spp. (mean: 1.03), and Arcicella spp. (mean: 1.01). Strains of Flectobacillus spp. (mean: 0.48) and Pedobacter spp. (mean: 0.42) showed lower absorbance values. As above, it was shown that, at the species level, the pink-pigmented bacteria in the water in the Japanese environment had various levels of ability to form biofilm.

Relatively high antibiotic resistance among heterotrophic bacteria from arctic fjord sediments than water - Evidence towards better selection pressure in the fjord sediments

NASA Astrophysics Data System (ADS)

Hatha, A. A. Mohamed; Neethu, C. S.; Nikhil, S. M.; Rahiman, K. M. Mujeeb; Krishnan, K. P.; Saramma, A. V.

2015-12-01

The objective of this study was to determine the prevalence of antibiotic resistance among aerobic heterotrophic bacteria and coliform bacteria from water and sediment of Kongsfjord. The study was based on the assumption that arctic fjord environments are relatively pristine and offer very little selection pressure for drug resistant mutants. In order to test the hypothesis, 200 isolates belonging to aerobic heterotrophic bacteria and 114 isolates belonging to coliforms were tested against 15 antibiotics belonging to 5 different classes such as beta lactams, aminoglycosides, quinolones, sulpha drugs and tetracyclines. Resistance to beta lactam and extended spectrum beta lactam (ESBL) antibiotics was considerably high and they found to vary significantly (p < 0.05) between heterotrophic and coliform bacteria. Though the coliforms showed significantly high level of antibiotic resistance against ESBL's extent and diversity of antibiotic resistance (as revealed by multiple antibiotic resistance index and resistance patterns), was high in the aerobic heterotrophic bacteria. Most striking observation was that isolates from fjord sediments (both heterotrophic bacteria and coliforms) in general showed relatively high prevalence of antibiotic resistance against most of the antibiotics tested, indicating to better selection pressure for drug resistance mutants in the fjord sediments.

Inactivation of Escherichia coli and coliform bacteria in traditional brass and earthernware water storage vessels.

PubMed

Tandon, Puja; Chhibber, Sanjay; Reed, Robert H

2005-07-01

The detection and enumeration of indicator bacteria such as Escherichia coli is used to assess the extent of faecal contamination of drinking water. On the basis of this approach, the effectiveness of storing water contaminated with faecal indicator bacteria in brass or earthern vessels (mutkas) of the type used in rural India have been investigated. Suspensions of bacteria in sterile distilled water were maintained for up to 48 h in each vessel and enumerated by surface plate counts on nutrient agar (non-selective) and several selective coliform media at 37 degrees C either under standard aerobic conditions, or under conditions designed to neutralise reactive oxygen species (ROS), e.g. using an anaerobic cabinet to prepare plates of pre-reduced growth medium or by inclusion of sodium pyruvate in the growth medium, with incubation of aerobically-prepared plates in an anaerobic jar. The counts obtained for E. coli decreased on short-term storage in a brass mutka; counts for selective media were lower than for equivalent counts for non-selective medium, with ROS-neutralised conditions giving consistently higher counts than aerobic incubation. However, after 48 h, no bacteria were cultivable under any conditions. Similar results were obtained using water from environmental sources in the Panjab, and from rural households where brass and earthern mutkas are used for storage of drinking water, with enumeration on selective coliform media (presumptive total coliforms). In all cases results indicated that, while storage of water in a brass mutka can inactivate E. coli and coliforms over a 48 h period, standard aerobic plate counting using selective media may not be fully effective in enumerating sub-lethally damaged bacteria.

Comparison and continuous estimates of fecal coliform and Escherichia coli bacteria in selected Kansas streams, May 1999 through April 2002

USGS Publications Warehouse

Rasmussen, Patrick P.; Ziegler, Andrew C.

2003-01-01

The sanitary quality of water and its use as a public-water supply and for recreational activities, such as swimming, wading, boating, and fishing, can be evaluated on the basis of fecal coliform and Escherichia coli (E. coli) bacteria densities. This report describes the overall sanitary quality of surface water in selected Kansas streams, the relation between fecal coliform and E. coli, the relation between turbidity and bacteria densities, and how continuous bacteria estimates can be used to evaluate the water-quality conditions in selected Kansas streams. Samples for fecal coliform and E. coli were collected at 28 surface-water sites in Kansas. Of the 318 samples collected, 18 percent exceeded the current Kansas Department of Health and Environment (KDHE) secondary contact recreational, single-sample criterion for fecal coliform (2,000 colonies per 100 milliliters of water). Of the 219 samples collected during the recreation months (April 1 through October 31), 21 percent exceeded the current (2003) KDHE single-sample fecal coliform criterion for secondary contact rec-reation (2,000 colonies per 100 milliliters of water) and 36 percent exceeded the U.S. Environmental Protection Agency (USEPA) recommended single-sample primary contact recreational criterion for E. coli (576 colonies per 100 milliliters of water). Comparisons of fecal coliform and E. coli criteria indicated that more than one-half of the streams sampled could exceed USEPA recommended E. coli criteria more frequently than the current KDHE fecal coliform criteria. In addition, the ratios of E. coli to fecal coliform (EC/FC) were smallest for sites with slightly saline water (specific conductance greater than 1,000 microsiemens per centimeter at 25 degrees Celsius), indicating that E. coli may not be a good indicator of sanitary quality for those streams. Enterococci bacteria may provide a more accurate assessment of the potential for swimming-related illnesses in these streams. Ratios of EC/FC and

Occurrence of bacteria in Blue Marsh Lake and selected tributaries, Berks County, Pennsylvania; September-October 2001

USGS Publications Warehouse

Zimmerman, Michele L.

2002-01-01

The Commonwealth of Pennsylvania has water-quality standards that limit the number of specific bacteria in water that is considered safe for recreational use. Bacteria such as fecal streptococci, fecal coliforms, and Escherichia coli (E. coli) are used to assess recreational water quality because they usually live in the intestines of warm-blooded animals. Fecal indicator bacteria commonly are associated with waterborne disease-causing organisms (pathogens). These indicator bacteria are used routinely as a measure of the quality of water for recreational activities such as swimming, boating, and water skiing. If the indicator bacteria are present, effective measures could be taken to prevent the transmission or epidemic outbreak of waterborne diseases as a result of contamination of these waters from human or animal waste.Blue Marsh Lake is on Tulpehocken Creek in Berks County, Pa., and drains a largely agricultural basin. Land use in the basin is approximately 60 percent cropland, and 85 percent of the farms are livestock and poultry farms.The potential sources of fecal bacteria are:geese that inhabit the recreational areas of the lake,humans that visit the Dry Brooks Day Use Area (swimming area), andfarm animals, wastewater facilities, and household septic systems in the basin (bacteria from these sources could enter the lake through tributaries).To meet the recreational water-quality standard, lake water may not have more than 200 colony-forming units (CFU) of fecal coliforms per 100 milliliters (mL). During the week of July 23, 2001, data collected by the U.S. Army Corps of Engineers (USACE) at the swimming area at Blue Marsh Lake showed concentrations of fecal coliforms in the water exceeding the standard. To determine the extent of elevated concentrations of fecal indicator bacteria, further study of the lake and selected tributaries was needed.

Viewing marine bacteria, their activity and response to environmental drivers from orbit: satellite remote sensing of bacteria.

PubMed

Grimes, D Jay; Ford, Tim E; Colwell, Rita R; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G

2014-04-01

Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.

[Immobilization of introduced bacteria and degradation of pyrene and benzo(alpha) pyrene in soil by immobilized bacteria].

PubMed

Wang, Xin; Li, Peijun; Song, Shouzhi; Zhong, Yong; Zhang, Hui; Verkhozina, E V

2006-11-01

In this study, introduced bacteria were applied in the bioremediation of pyrene and benzo (alpha) pyrene in organic pollutants-contaminated soils, aimed to test whether it was feasible to introduce bacteria to environmental engineering. Three introduced bacteria were immobilized separately or together to degrade the pyrene and benzo (alpha) pyrene in soil, taking dissociated bacteria as the control, and comparing with three indigenous bacteria. The results showed that immobilized introduced bacteria, either single or mixed, had higher degradation efficiency than dissociated bacteria. Compared with indigenous bacteria, some introduced bacteria had predominance to some degree. The introduced bacteria-mixture had better degradation efficiency after being immobilized. The degradation rate of pyrene and benzo(alpha) pyrene after treated with immobilized bacteria-( B61-B67)-mixture for 96 hours was 43.49% and 38.55%, respectively.

Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs

PubMed Central

Græsbøll, Kaare; Damborg, Peter; Mellerup, Anders; Herrero-Fresno, Ana; Larsen, Inge; Holm, Anders; Nielsen, Jens Peter; Christiansen, Lasse Engbo; Angen, Øystein; Ahmed, Shahana

2017-01-01

ABSTRACT This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis-induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested. IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in

Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs.

PubMed

Græsbøll, Kaare; Damborg, Peter; Mellerup, Anders; Herrero-Fresno, Ana; Larsen, Inge; Holm, Anders; Nielsen, Jens Peter; Christiansen, Lasse Engbo; Angen, Øystein; Ahmed, Shahana; Folkesson, Anders; Olsen, John Elmerdahl

2017-06-15

This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis -induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested. IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in livestock

Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria.

PubMed

Repar, Jelena; Supek, Fran; Klanjscek, Tin; Warnecke, Tobias; Zahradka, Ksenija; Zahradka, Davor

2017-04-01

A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species. However, here we show that rates of genome rearrangements, measured as loss of gene order conservation with time, are higher in radiation-resistant species in multiple, phylogenetically independent groups of bacteria. Comparison of indicators of selection for genome organization between radiation-resistant and phylogenetically matched, nonresistant species argues against tolerance to disruption of genome structure as a strategy for radiation resistance. Interestingly, an important mechanism affecting genome rearrangements in prokaryotes, the symmetrical inversions around the origin of DNA replication, shapes genome structure of both radiation-resistant and nonresistant species. In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria. Copyright © 2017 Repar et al.

Detection of Extended Spectrum Beta-Lactamases Resistance Genes among Bacteria Isolated from Selected Drinking Water Distribution Channels in Southwestern Nigeria.

PubMed

Adesoji, Ayodele T; Ogunjobi, Adeniyi A

2016-01-01

Extended Spectrum Beta-Lactamases (ESBL) provide high level resistance to beta-lactam antibiotics among bacteria. In this study, previously described multidrug resistant bacteria from raw, treated, and municipal taps of DWDS from selected dams in southwestern Nigeria were assessed for the presence of ESBL resistance genes which include bla TEM, bla SHV, and bla CTX by PCR amplification. A total of 164 bacteria spread across treated (33), raw (66), and municipal taps (68), belonging to α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Flavobacteriia, Bacilli, and Actinobacteria group, were selected for this study. Among these bacteria, the most commonly observed resistance was for ampicillin and amoxicillin/clavulanic acid (61 isolates). Sixty-one isolates carried at least one of the targeted ESBL genes with bla TEM being the most abundant (50/61) and bla CTX being detected least (3/61). Klebsiella was the most frequently identified genus (18.03%) to harbour ESBL gene followed by Proteus (14.75%). Moreover, combinations of two ESBL genes, bla SHV + bla TEM or bla CTX + bla TEM, were observed in 11 and 1 isolate, respectively. In conclusion, classic bla TEM ESBL gene was present in multiple bacterial strains that were isolated from DWDS sources in Nigeria. These environments may serve as foci exchange of genetic traits in a diversity of Gram-negative bacteria.

Isolation of bacteria-containing phagosomes by magnetic selection

PubMed Central

Lönnbro, Per; Nordenfelt, Pontus; Tapper, Hans

2008-01-01

Background There is a growing awareness of the importance of intracellular events in determining the outcome of infectious disease. To improve the understanding of such events, like phagosome maturation, we set out to develop a versatile technique for phagosome isolation that is rapid and widely applicable to different pathogens. Results We developed two different protocols to isolate phagosomes containing dead or live bacteria modified with small magnetic particles, in conjunction with a synchronized phagocytosis protocol and nitrogen cavitation. For dead bacteria, we performed analysis of the phagosome samples by microscopy and immunoblot, and demonstrated the appearance of maturation markers on isolated phagosomes. Conclusion We have presented detailed protocols for phagosome isolation, which can be adapted for use with different cell types and prey. The versatility and simplicity of the approach allow better control of phagosome isolation, the parameters of which are critical in studies of host-bacteria interaction and phagosome maturation. PMID:18588680

Rapid, highly sensitive detection of Gram-negative bacteria with lipopolysaccharide based disposable aptasensor.

PubMed

Zhang, Jian; Oueslati, Rania; Cheng, Cheng; Zhao, Ling; Chen, Jiangang; Almeida, Raul; Wu, Jayne

2018-07-30

Gram-negative bacteria are one of the most common microorganisms in the environment. Their differential detection and recognition from Gram-positive bacteria has been attracting much attention over the years. Using Escherichia coli (E. coli) as a model, we demonstrated on-site detection of Gram-negative bacteria by an AC electrokinetics-based capacitive sensing method using commercial microelectrodes functionalized with an aptamer specific to lipopolysaccharides. Dielectrophoresis effect was utilized to enrich viable bacteria to the microelectrodes rapidly, achieving a detection limit of 10 2 cells/mL within a 30 s' response time. The sensor showed a negligible response to Staphylococcus aureus (S. aureus), a Gram-positive species. The developed sensor showed significant advantages in sensitivity, selectivity, cost, operation simplicity, and response time. Therefore, this sensing method has shown great application potential for environmental monitoring, food safety, and real-time diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Balancing Bacteria-Osteoblast Competition through Selective Physical Puncture and Biofunctionalization of ZnO/Polydopamine/Arginine-Glycine-Aspartic Acid-Cysteine Nanorods.

PubMed

Li, Jun; Tan, Lei; Liu, Xiangmei; Cui, Zhenduo; Yang, Xianjin; Yeung, Kelvin Wai Kwok; Chu, Paul K; Wu, Shuilin

2017-11-28

Bacterial infection and lack of bone tissue integration are two major concerns of orthopedic implants. In addition, osteoinductivity often decreases and toxicity may arise when antibacterial agents are introduced to increase the antibacterial ability. Here hybrid ZnO/polydopamine (PDA)/arginine-glycine-aspartic acid-cysteine (RGDC) nanorod (NR) arrays are designed and prepared on titanium (Ti) implants to not only enhance the osteoinductivity but also effectively kill bacteria simultaneously, which are ascribed to the selective physical puncture and the biofunctionalization of ZnO/PDA/RGDC nanorods during the competition between bacteria and osteoblasts. That is, owing to the much larger size of osteoblasts than bacteria, the hybrid NRs can puncture bacteria but not damage osteoblasts. Meanwhile, the cytocompatibility can be enhanced through the suppression of both reactive oxygen species and higher Zn 2+ concentration by the covering of PDA and RGDC. The in vitro results confirm the selective puncture of the bacterial membrane and the better osteoinductivity. In vivo tests also show much higher antibacterial efficacy of the hybrid NRs with far less amounts of lobulated neutrophils and adherent bacteria in the surrounding tissues. In addition, the hybrid NRs also accelerate formation of new bone tissues (20.1% higher than pure Ti) and osteointegration between implants and newly formed tissues (32.0% higher than pure Ti) even in the presence of injected bacteria. This work provides a surface strategy for designing implants with desirable ability of osseointegration and infection prevention simultaneously, which will exhibit tremendous clinical potential in orthopedic and dental applications.

Rapid classification of heavy metal-exposed freshwater bacteria by infrared spectroscopy coupled with chemometrics using supervised method

NASA Astrophysics Data System (ADS)

Gurbanov, Rafig; Gozen, Ayse Gul; Severcan, Feride

2018-01-01

Rapid, cost-effective, sensitive and accurate methodologies to classify bacteria are still in the process of development. The major drawbacks of standard microbiological, molecular and immunological techniques call for the possible usage of infrared (IR) spectroscopy based supervised chemometric techniques. Previous applications of IR based chemometric methods have demonstrated outstanding findings in the classification of bacteria. Therefore, we have exploited an IR spectroscopy based chemometrics using supervised method namely Soft Independent Modeling of Class Analogy (SIMCA) technique for the first time to classify heavy metal-exposed bacteria to be used in the selection of suitable bacteria to evaluate their potential for environmental cleanup applications. Herein, we present the powerful differentiation and classification of laboratory strains (Escherichia coli and Staphylococcus aureus) and environmental isolates (Gordonia sp. and Microbacterium oxydans) of bacteria exposed to growth inhibitory concentrations of silver (Ag), cadmium (Cd) and lead (Pb). Our results demonstrated that SIMCA was able to differentiate all heavy metal-exposed and control groups from each other with 95% confidence level. Correct identification of randomly chosen test samples in their corresponding groups and high model distances between the classes were also achieved. We report, for the first time, the success of IR spectroscopy coupled with supervised chemometric technique SIMCA in classification of different bacteria under a given treatment.

Highly Effective Polyphosphate Synthesis, Phosphate Removal, and Concentration Using Engineered Environmental Bacteria Based on a Simple Solo Medium-Copy Plasmid Strategy.

PubMed

Wang, Xin; Wang, Xiaomeng; Hui, Kaimin; Wei, Wei; Zhang, Wen; Miao, Aijun; Xiao, Lin; Yang, Liuyan

2018-01-02

Microbial polyphosphate (polyP) production is vital to the removal of phosphate from wastewater. However, to date, engineered polyP synthesis using genetically accessible environmental bacteria remains a challenge. This study develops a simple solo medium-copy plasmid-based polyphosphate kinase (PPK1) overexpression strategy for achieving maximum intracellular polyphosphate accumulation by environmental bacteria. The polyP content of the subsequently engineered Citrobacter freundii (CPP) could reach as high as 12.7% of its dry weight. The biomass yield of CPP was also guaranteed because of negligible metabolic burden effects resulting from the medium plasmid copy number. Consequently, substantial removal of phosphate (P i ) from the ambient environment was achieved simultaneously. Because of the need for exogenous P i for in vivo ATP regeneration, CPP could thoroughly remove P i from synthetic municipal wastewater when it was applied for the "one-step" removal of P i with a bench-scale sequence batch membrane reactor. Almost all the phosphorus except for that assimilated by CPP for cellular growth could be recovered in the form of more concentrated P i . Overall, engineering environmental bacteria to overexpress PPK1 via a solo medium-copy plasmid strategy may represent a valuable general option for not only biotechnological research based on sufficient intracellular polyP production but also removal of P i from wastewater and P i enrichment.

A Theoretical Approach for Selecting Elementary School Environmental Variables.

ERIC Educational Resources Information Center

Sinclair, Robert L.

To determine specific environmental variables of the elementary school is the purpose of this study. Stable characteristics of intelligence and achievement were selected because they were considered useful for generating salient environmental counterparts likely to exist in elementary institutions. Achievement motivation, language development, and…

Weather and environmental factors associated with F+ coliphages and fecal indicator bacteria in beach sand at two recreational marine beaches

EPA Science Inventory

Studies have demonstrated that fecal indicator bacteria (FIB) and pathogens may be present in beach sand and suggest an increased risk of enteric illness among beachgoers contacting sand. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR...

Environmental risk assessment of selected pharmaceuticals in Turkey.

PubMed

Oğuz, Merve; Mihçiokur, Hamdi

2014-07-01

In this study, environmental risks of selected pharmaceuticals were investigated to assess potential hazards. Ciprofloxacin, Clarithromycin, Cefuroxime axetil, antibiotics, Benzalkoniuman antiseptic, Paracetamol, an analgesic, and Naproxen, an anti-inflammatory, were selected due to their high rate of usage in Turkey. Ciprofloxacin was found to have the highest risk due to its high PEC/PNEC ratio (28.636). Benzalkonium, Paracetamol and Clarithromycin have a potential to cause environmental hazards. The biodegradation and biological concentration factors (BCF) of the drugs were also determined using EPA/STWIN and EPA/BCFWIN programs. The results illustrated that these pharmaceuticals are nonbiodegradable in wastewater treatment plants. The BCFs of Benzalkonium and Clarithromycin were found to be very high, 70.790 L/kg and 56.490 L/kg, respectively. It was suggested that alternative treatment methods other than biological ones should be investigated for these pharmaceuticals because of their low biodegradability. Also, unnecessary use of antibiotics is supposed to be discouraged to reduce environmental hazards. Copyright © 2014 Elsevier B.V. All rights reserved.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth.

PubMed

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

2016-01-01

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Bactericidal efficacy of elevated pH on fish pathogenic and environmental bacteria

USGS Publications Warehouse

Starliper, Clifford E.; Watten, Barnaby J.

2013-01-01

Ship ballast water is a recognized medium for transfer and introductions of nonindigenous species. There is a need for new ballast water treatment methods that effectively and safely eliminate or greatly minimize movements of these species. The present study employed laboratory methods to evaluate the bactericidal efficacy of increased pH (pH 10.0–12.0) for exposure durations of up to 72 h to kill a variety of Gram-negative and Gram-positive bacteria including fish pathogens (Aeromonas spp., Yersinia ruckeri, Edwardsiella ictaluri, Serratia liquefaciens, Carnobacterium sp.), other common aquatic-inhabitant bacteria (Serratia marcescens, Pseudomonas fluorescens, Staphylococcus sp., Bacillus sp.) and indicators listed in International Maritime Organization D2 Standards; namely, Vibrio cholera (an environmental isolate from fish), Escherichia coli and Enterococcus faecalis. Volumes of 5 N NaOH were added to tryptic soy broth to obtain desired pH adjustments. Viable cells were determined after 0, 4, 12, 24, 48, and 72 h. Initial (0 h) cell numbers ranged from 3.40 × 104 cfu/mL for Bacillus sp. to 2.44 × 107 cfu/mL for E. faecalis. The effective endpoints of pH and treatment duration necessary to realize 100% bactericidal effect varied; however, all bacteria tested were killed within 72 h at pH 12.0 or lower. The lowest parameters examined, 4 h at pH 10.0, were bactericidal to V. cholera, E. ictaluri, three of four isolates of E. coli, and (three of four) Aeromonas salmonicida subsp. salmonicida. Bactericidal effect was attained at pH 10.0 within 12 h for the other A. salmonicida subsp. salmonicida, and within 24 h for P. fluorescens, and the remaining E. coli.

Highly selective colorimetric bacteria sensing based on protein-capped nanoparticles.

PubMed

Qiu, Suyan; Lin, Zhenyu; Zhou, Yaomin; Wang, Donggen; Yuan, Lijuan; Wei, Yihua; Dai, Tingcan; Luo, Linguang; Chen, Guonan

2015-02-21

A rapid and cost-effective colorimetric sensor has been developed for the detection of bacteria (Bacillus subtilis was selected as an example). The sensor was designed to rely on lysozyme-capped AuNPs with the advantages of effective amplification and high specificity. In the sensing system, lysozyme was able to bind strongly to Bacillus subtilis, which effectively induced a color change of the solution from light purple to purplish red. The lowest concentration of Bacillus subtilis detectable by the naked eye was 4.5 × 10(3) colony-forming units (CFU) mL(-1). Similar results were discernable from UV-Vis absorption measurements. A good specificity was observed through a statistical analysis method using the SPSS software (version 17.0). This simple colorimetric sensor may therefore be a rapid and specific method for a bacterial detection assay in complex samples.

Contributions of Environmental Clubs toward Improved Environmental Programs in Selected Secondary Schools in Ibadan, Nigeria

ERIC Educational Resources Information Center

Ana, G. R. E. E.; Oloruntoba, E. O.; Sridhar, M. K. C.

2009-01-01

The descriptive cross-sectional study assessed contributions of Youth Environmental Scout (YES) clubs toward sustainable environmental programs in selected schools in Ibadan, southwest Nigeria. It involved administration of questionnaires, in-depth interviews and observation checklists and results were analyzed using SPSS 10 software package.…

Selection of lactic acid bacteria isolated from Tunisian cereals and exploitation of the use as starters for sourdough fermentation.

PubMed

Mamhoud, Asma; Nionelli, Luana; Bouzaine, Taroub; Hamdi, Moktar; Gobbetti, Marco; Rizzello, Carlo Giuseppe

2016-05-16

Wheat bread is the most popular staple food consumed in Tunisia and, despite the niche production of some typical breads (e.g. Tabouna, Mlawi, Mtabga), the major part is currently produced with baker's yeast at industrial or, mainly, at artisanal level, while the use of sourdough fermentation is rarely reported. Considering the growing national demand for cereal baked goods, it can be hypothesized that sourdough fermentation through the use of selected lactic acid bacteria as starters could improve the overall quality and the diversification of local products. Different cereal grains were collected from the regions of Ariana, Bizerta, Beja Nabeul, and Seliana, and the autochthonous lactic acid bacteria were isolated, identified, characterized and selected on the basis of the kinetics of acidification, the proteolytic activity, and the quotient of fermentation. Lactobacillus curvatus MA2, Pediococcus pentosaceus OA2, and Pediococcus acidilactici O1A1 were used together as mixed starter to obtain a selected sourdough. According to the backslopping procedure, a type I sourdough was made from a Tunisian flour (spontaneous sourdough). Compared to the use of the spontaneous sourdough, the one obtained with selected and mixed starters by a unique fermentation step, favored the increase of the concentrations of organic acids, phenols, and total free amino acids, the most suitable quotient of fermentation, and the most intense phytase and antioxidant activities, that increased ca. 20% compared to the control. Moreover, the selected starters improved the in vitro protein digestibility (ca. 82% when selected sourdough was used), textural and sensory features of the breads, as determined by textural profile analysis and panel test, respectively. This study aimed at exploiting the potential of selected autochthonous lactic acid bacteria and extending the use of a sourdough (type II), thanks to the set-up of a two-step fermentation protocol designed for application at the

Occurrence of fecal coliform bacteria in selected streams in Wyoming, 1990-99

USGS Publications Warehouse

Clark, Melanie L.; Norris, Jodi R.

2000-01-01

The U.S. Geological Survey (USGS), in cooperation with the Wyoming Department of Environmental Quality (WDEQ), is collecting water samples for analysis of fecal coliform bacteria at 18 stream sites as part of a statewide network. Contamination by bacteria of fecal origin in streams where contact recreation is a designated water use is a concern because of potential public-health risk from the presence of enteric pathogens. Fecal coliform concentrations are temporally and spatially variable in Wyoming streams-concentrations ranged from less than 1 to 45,000 colonies per 100 milliliters of water during 1990-99. Fecal coliform concentrations were less than the water-quality criterion of 400 colonies per 100 milliliters in 83 percent of the samples, indicating fecal coliform contamination is not a widespread problem in these Wyoming streams. However, 14 of the 18 monitoring sites had at least one sample in which the fecal coliform concentration exceeded 400 colonies per 100 milliliters at some time during the 10-year period. Fecal coliform concentrations generally are higher during April through September than during October through March. The higher concentrations coincide with the time period when the public-health risk is higher because summer months are when contact recreation use is more likely occurring. Fecal coliform concentrations were positively correlated with discharge and stream temperature and generally were negatively correlated with pH, specific conductance, and dissolved oxygen.

International Environmental Education: General Perspectives, Communications, and Program Status in Selected Countries.

ERIC Educational Resources Information Center

Shaffer, Barry E.

To enlighten the reader on the status of environmental education internationally, this paper discusses current environmental concerns, trends, and problems; reviews environmental-related communications between countries since 1965; and describes environmental education programs in selected countries. Environmental education is interpreted to…

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes.

PubMed

Logares, Ramiro; Tesson, Sylvie V M; Canbäck, Björn; Pontarp, Mikael; Hedlund, Katarina; Rengefors, Karin

2018-05-04

Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6,000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining ∼72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (∼72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Selection of enhanced antimicrobial activity posing lactic acid bacteria characterised by (GTG)5-PCR fingerprinting.

PubMed

Šalomskienė, Joana; Abraitienė, Asta; Jonkuvienė, Dovilė; Mačionienė, Irena; Repečkienė, Jūratė

2015-07-01

The aim of the study was a detail evaluation of genetic diversity among the lactic acid bacteria (LAB) strains having an advantage of a starter culture in order to select genotypically diverse strains with enhanced antimicrobial effect on some harmfull and pathogenic microorganisms. Antimicrobial activity of LAB was performed by the agar well diffusion method and was examined against the reference strains and foodborne isolates of Bacillus cereus, Listeria monocytogenes, Escherichia coli, Staphylococcus aureus and Salmonella Typhimurium. Antifungal activity was tested against the foodborne isolates of Candida parapsilosis, Debaromyces hansenii, Kluyveromyces marxianus, Pichia guilliermondii, Yarowia lipolytica, Aspergillus brasiliensis, Aspergillus versicolor, Cladosporium herbarum, Penicillium chrysogenum and Scopulariopsis brevicaulis. A total 40 LAB strains representing Lactobacillus (23 strains), Lactococcus (13 strains) and Streptococcus spp. (4 strains) were characterised by repetitive sequence based polymerase chain reaction fingerprinting which generated highly discriminatory profiles, confirmed the identity and revealed high genotypic heterogeneity among the strains. Many of tested LAB demonstrated strong antimicrobial activity specialised against one or few indicator strains. Twelve LAB strains were superior in suppressing growth of the whole complex of pathogenic bacteria and fungi. These results demonstrated that separate taxonomic units offered different possibilities of selection for novel LAB strains could be used as starter cultures enhancing food preservation.

Integrated optical biosensor for rapid detection of bacteria

NASA Astrophysics Data System (ADS)

Mathesz, Anna; Valkai, Sándor; Újvárosy, Attila; Aekbote, Badri; Sipos, Orsolya; Stercz, Balázs; Kocsis, Béla; Szabó, Dóra; Dér, András

2016-02-01

In medical diagnostics, rapid detection of pathogenic bacteria from body fluids is one of the basic issues. Most state-of-the-art methods require optical labeling, increasing the complexity, duration and cost of the analysis. Therefore, there is a strong need for developing selective sensory devices based on label-free techniques, in order to increase the speed, and reduce the cost of detection. In a recent paper, we have shown that an integrated optical Mach-Zehnder interferometer, a highly sensitive all-optical device made of a cheap photopolymer, can be used as a powerful lab-on-a-chip tool for specific, labelfree detection of proteins. By proper modifications of this technique, our interferometric biosensor was combined with a microfluidic system allowing the rapid and specific detection of bacteria from solutions, having the surface of the sensor functionalized by bacterium-specific antibodies. The experiments proved that the biosensor was able to detect Escherichia coli bacteria at concentrations of 106 cfu/ml within a few minutes, that makes our device an appropriate tool for fast, label-free detection of bacteria from body fluids such as urine or sputum. On the other hand, possible applications of the device may not be restricted to medical microbiology, since bacterial identification is an important task in microbial forensics, criminal investigations, bio-terrorism threats and in environmental studies, as well.

Integrated optical biosensor for rapid detection of bacteria

NASA Astrophysics Data System (ADS)

Mathesz, Anna; Valkai, Sándor; Újvárosy, Attila; Aekbote, Badri; Sipos, Orsolya; Stercz, Balázs; Kocsis, Béla; Szabó, Dóra; Dér, András

2015-12-01

In medical diagnostics, rapid detection of pathogenic bacteria from body fluids is one of the basic issues. Most state-of-the-art methods require optical labeling, increasing the complexity, duration and cost of the analysis. Therefore, there is a strong need for developing selective sensory devices based on label-free techniques, in order to increase the speed, and reduce the cost of detection. In a recent paper, we have shown that an integrated optical Mach-Zehnder interferometer, a highly sensitive all-optical device made of a cheap photopolymer, can be used as a powerful lab-on-a-chip tool for specific, labelfree detection of proteins. By proper modifications of this technique, our interferometric biosensor was combined with a microfluidic system allowing the rapid and specific detection of bacteria from solutions, having the surface of the sensor functionalized by bacterium-specific antibodies. The experiments proved that the biosensor was able to detect Escherichia coli bacteria at concentrations of 106 cfu/ml within a few minutes, that makes our device an appropriate tool for fast, label-free detection of bacteria from body fluids such as urine or sputum. On the other hand, possible applications of the device may not be restricted to medical microbiology, since bacterial identification is an important task in microbial forensics, criminal investigations, bio-terrorism threats and in environmental studies, as well.

Isolation, selection and characterization of root-associated growth promoting bacteria in Brazil Pine (Araucaria angustifolia).

PubMed

Ribeiro, Carlos Marcelo; Cardoso, Elke Jurandy Bran Nogueira

2012-01-20

Araucaria angustifolia, a unique species of this genus that occurs naturally in Brazil, has a high socio-economic and environmental value and is critically endangered of extinction, since it has been submitted to intense predatory exploitation during the last century. Root-associated bacteria from A. angustifolia were isolated, selected and characterized for their biotechnological potential of growth promotion and biocontrol of plant pathogenic fungi. Ninety-seven strains were isolated and subjected to chemical tests. All isolates presented at least one positive feature, characterizing them as potential PGPR. Eighteen isolates produced indole-3-acetic acid (IAA), 27 were able to solubilize inorganic phosphate, 21 isolates were presumable diazotrophs, with pellicle formation in nitrogen-free culture medium, 83 were phosphatases producers, 37 were positive for siderophores and 45 endospore-forming isolates were antagonistic to Fusarium oxysporum, a pathogen of conifers. We also observed the presence of bacterial strains with multiple beneficial mechanisms of action. Analyzing the fatty acid methyl ester (FAME) and partial sequencing of the 16S rRNA gene of these isolates, it was possible to characterize the most effective isolates as belonging to Bacillaceae (9 isolates), Enterobacteriaceae (11) and Pseudomonadaceae (1). As far as we know, this is the first study to include the species Ewingella americana as a PGPR. Copyright © 2011 Elsevier GmbH. All rights reserved.

Characterisation and biochemical properties of predominant lactic acid bacteria from fermenting cassava for selection as starter cultures.

PubMed

Kostinek, M; Specht, I; Edward, V A; Pinto, C; Egounlety, M; Sossa, C; Mbugua, S; Dortu, C; Thonart, P; Taljaard, L; Mengu, M; Franz, C M A P; Holzapfel, W H

2007-03-20

A total of 375 lactic acid bacteria were isolated from fermenting cassava in South Africa, Benin, Kenya and Germany, and were characterised by phenotypic and genotypic tests. These could be divided into five main groups comprising strains of facultatively heterofermentative rods, obligately heterofermentative rods, heterofermentative cocci, homofermentative cocci and obligately homofermentative rods, in decreasing order of predominance. Most of the facultatively heterofermentative rods were identified by phenotypic tests as presumptive Lactobacillus plantarum-group strains, which also comprised the most predominant bacteria (54.4% of strains) isolated in the study. The next predominant group of lactic acid bacteria (14.1% of total isolates) consisted of obligately heterofermentative rods belonging either to the genus Lactobacillus or Weissella, followed by the heterofermentative cocci (13.9% of isolates) belonging to the genera Weissella or Leuconostoc. Homofermentative cocci were also isolated (13.3% of isolates). Biochemical properties such as production of alpha-amylase, beta-glucosidase, tannase, antimicrobials (presumptive bacteriocin and H(2)O(2)-production), acidification and fermentation of the indigestible sugars raffinose and stachyose, were evaluated in vitro for selection of potential starter strains. A total of 32 strains with one or more desirable biochemical properties were pre-selected and identified using rep-PCR fingerprinting in combination with 16S rRNA sequencing of representative rep-PCR cluster isolates. Of these strains, 18 were identified as L. plantarum, four as Lactobacillus pentosus, two each as Leuconostoc fallax, Weissella paramesenteroides and Lactobacillus fermentum, one each as Leuconostoc mesenteroides subsp. mesenteroides and Weissella cibaria, while two remained unidentified but could be assigned to the L. plantarum-group. These strains were further investigated for clonal relationships, using RAPD-PCR with three primers, and of

A selective medium for recovery and enumeration of endolithic bacteria.

PubMed

Bhattacharjee, Kaushik; Joshi, S R

2016-10-01

The study of lithic microbial communities, inhabiting rock substrates has been gathering momentum due to a growing attention of their wide importance as model systems in ecological studies and for their community structure. It is generally accepted that the success of cultivation-based technique is primarily based on suitable culture medium for isolation. The media available for enumeration and recovery of endolithic bacteria are mainly specific to particular type of rock which may not be suitable to isolate endolithic bacterial community from diverse lithobiontic niches. In this study, a new unoptimized medium was formulated, designated LM10 (unoptimized) for enumeration and recovery of endolithic bacteria by addition and/or omission of media components to the basal medium R2G, which was selected after experimental evaluation of five different existing media. The endolithic bacterial count in LM10 medium (unoptimized) was significantly higher than the R2G medium (t=-12.57, p<0.0001). The culture and nutritional parameters associated with unoptimized LM10 medium were optimized using statistical approach to maximize the recovery and enumeration of endolithic bacteria. The first phase of the study comprised of a Plackett-Burman (PB) design experiment conducted to screen thirteen medium components and two culture parameters as variables with effect on bacterial enumeration and recovery. Out of these, Yeast extract, Casein hydrolysate, Glucose, Starch and Sodium thiosulphate were found to be significantly affecting the bacterial count (p<0.05) based on PB design. On keeping rest of the media components and culture conditions at fixed value as per the PB design analyses (p>0.05 and coefficients), further optimization was carried out for significant factors using Box-Behnken design (BBD) of response surface methodology (RSM). Optimized media components obtained by BBD were Yeast extract, Casein hydrolysate, Glucose and Starch in 0.05g/l each and Sodium thiosulphate in 0

Increasing selection response by Bayesian modeling of heterogeneous environmental variances

USDA-ARS?s Scientific Manuscript database

Heterogeneity of environmental variance among genotypes reduces selection response because genotypes with higher variance are more likely to be selected than low-variance genotypes. Modeling heterogeneous variances to obtain weighted means corrected for heterogeneous variances is difficult in likel...

Social behavior of bacteria: from physics to complex organization

NASA Astrophysics Data System (ADS)

Ben-Jacob, E.

2008-10-01

I describe how bacteria develop complex colonial patterns by utilizing intricate communication capabilities, such as quorum sensing, chemotactic signaling and exchange of genetic information (plasmids) Bacteria do not store genetically all the information required for generating the patterns for all possible environments. Instead, additional information is cooperatively generated as required for the colonial organization to proceed. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessments of information). These afford the cell certain plasticity to select its response to biochemical messages it receives, including self-alteration and broadcasting messages to initiate alterations in other bacteria. Hence, new features can collectively emerge during self-organization from the intra-cellular level to the whole colony. Collectively bacteria store information, perform decision make decisions (e.g. to sporulate) and even learn from past experience (e.g. exposure to antibiotics)-features we begin to associate with bacterial social behavior and even rudimentary intelligence. I also take Schrdinger’s’ “feeding on negative entropy” criteria further and propose that, in addition organisms have to extract latent information embedded in the environment. By latent information we refer to the non-arbitrary spatio-temporal patterns of regularities and variations that characterize the environmental dynamics. In other words, bacteria must be able to sense the environment and perform internal information processing for thriving on latent information embedded in the complexity of their environment. I then propose that by acting together, bacteria can perform this most elementary cognitive function more efficiently as can be illustrated by their cooperative behavior.

Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter.

PubMed

Liu, Huan; Zhang, Xu; Zhang, Hao; Yao, Xiangwu; Zhou, Meng; Wang, Jiaqi; He, Zhanfei; Zhang, Huihui; Lou, Liping; Mao, Weihua; Zheng, Ping; Hu, Baolan

2018-02-01

In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers. Copyright © 2017 Elsevier Ltd

Deployable micro-traps to sequester motile bacteria

NASA Astrophysics Data System (ADS)

di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-04-01

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria.

Deployable micro-traps to sequester motile bacteria

PubMed Central

Di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-01-01

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria. PMID:28378786

Deployable micro-traps to sequester motile bacteria.

PubMed

Di Giacomo, Raffaele; Krödel, Sebastian; Maresca, Bruno; Benzoni, Patrizia; Rusconi, Roberto; Stocker, Roman; Daraio, Chiara

2017-04-05

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria.

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae.

PubMed

Gross, Roy; Guzman, Carlos A; Sebaihia, Mohammed; dos Santos, Vítor A P Martins; Pieper, Dietmar H; Koebnik, Ralf; Lechner, Melanie; Bartels, Daniela; Buhrmester, Jens; Choudhuri, Jomuna V; Ebensen, Thomas; Gaigalat, Lars; Herrmann, Stefanie; Khachane, Amit N; Larisch, Christof; Link, Stefanie; Linke, Burkhard; Meyer, Folker; Mormann, Sascha; Nakunst, Diana; Rückert, Christian; Schneiker-Bekel, Susanne; Schulze, Kai; Vorhölter, Frank-Jörg; Yevsa, Tetyana; Engle, Jacquelyn T; Goldman, William E; Pühler, Alfred; Göbel, Ulf B; Goesmann, Alexander; Blöcker, Helmut; Kaiser, Olaf; Martinez-Arias, Rosa

2008-09-30

Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

PubMed Central

Gross, Roy; Guzman, Carlos A; Sebaihia, Mohammed; Martins dos Santos, Vítor AP; Pieper, Dietmar H; Koebnik, Ralf; Lechner, Melanie; Bartels, Daniela; Buhrmester, Jens; Choudhuri, Jomuna V; Ebensen, Thomas; Gaigalat, Lars; Herrmann, Stefanie; Khachane, Amit N; Larisch, Christof; Link, Stefanie; Linke, Burkhard; Meyer, Folker; Mormann, Sascha; Nakunst, Diana; Rückert, Christian; Schneiker-Bekel, Susanne; Schulze, Kai; Vorhölter, Frank-Jörg; Yevsa, Tetyana; Engle, Jacquelyn T; Goldman, William E; Pühler, Alfred; Göbel, Ulf B; Goesmann, Alexander; Blöcker, Helmut; Kaiser, Olaf; Martinez-Arias, Rosa

2008-01-01

Background Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. Results In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. Conclusion The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches. PMID:18826580

Methanotrophic bacteria.

PubMed Central

Hanson, R S; Hanson, T E

1996-01-01

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

What Are the Environmental Determinants of Phenotypic Selection? A Meta-analysis of Experimental Studies.

PubMed

Caruso, Christina M; Martin, Ryan A; Sletvold, Nina; Morrissey, Michael B; Wade, Michael J; Augustine, Kate E; Carlson, Stephanie M; MacColl, Andrew D C; Siepielski, Adam M; Kingsolver, Joel G

2017-09-01

Although many selection estimates have been published, the environmental factors that cause selection to vary in space and time have rarely been identified. One way to identify these factors is by experimentally manipulating the environment and measuring selection in each treatment. We compiled and analyzed selection estimates from experimental studies. First, we tested whether the effect of manipulating the environment on selection gradients depends on taxon, trait type, or fitness component. We found that the effect of manipulating the environment was larger when selection was measured on life-history traits or via survival. Second, we tested two predictions about the environmental factors that cause variation in selection. We found support for the prediction that variation in selection is more likely to be caused by environmental factors that have a large effect on mean fitness but not for the prediction that variation is more likely to be caused by biotic factors. Third, we compared selection gradients from experimental and observational studies. We found that selection varied more among treatments in experimental studies than among spatial and temporal replicates in observational studies, suggesting that experimental studies can detect relationships between environmental factors and selection that would not be apparent in observational studies.

Isolation and Characterization of Bacteria Capable of Tolerating the Extreme Conditions of Clean Room Environments▿

PubMed Central

La Duc, Myron T.; Dekas, Anne; Osman, Shariff; Moissl, Christine; Newcombe, David; Venkateswaran, Kasthuri

2007-01-01

In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4°C to 65°C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 106 cells/m2. However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (α- and β-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of

Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments.

PubMed

La Duc, Myron T; Dekas, Anne; Osman, Shariff; Moissl, Christine; Newcombe, David; Venkateswaran, Kasthuri

2007-04-01

In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4 degrees C to 65 degrees C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 10(6) cells/m(2). However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (alpha- and beta-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means

Evaluating Bacteriocin Production by Environmental Enterococci: An Inquiry-Based Activity in Bacterial Antgonism

ERIC Educational Resources Information Center

Middleton, June

2007-01-01

Bacteriocins, bacteriocidal proteins produced by bacteria, have a very restricted killing range. In this exercise each student isolates an environmental "Enterococcus spp." culture using selective media and then evaluates it for bacteriocin activity against "Enterococcus" strains isolated by classmates.

Stalking Antibiotic-Resistant Bacteria in Common Vegetables

ERIC Educational Resources Information Center

Brock, David; Boeke, Caroline; Josowitz, Rebecca; Loya, Katherine

2004-01-01

The study developed a simple experimental protocol for studying antibiotic resistant bacteria that will allow students to determine the proportion of such bacteria found on common fruit and vegetable crops. This protocol can open up the world of environmental science and show how human behavior can dramatically alter ecosystems.

Killer Pigments in Bacteria: An Ecological Nightmare.

ERIC Educational Resources Information Center

Benathen, Isaiah A.; Saccardi, Marion

2000-01-01

Describes an alternative to teaching ecology by using bacteria to test competitor survival. Students observe a time-dependent selective killing of other unrelated bacteria by Pseudomonas aeruginosa. (SAH)

Methods for dispersing hydrocarbons using autoclaved bacteria

DOEpatents

Tyndall, Richard L.

1996-01-01

A method of dispersing a hydrocarbon includes the steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; autoclaving the bacterium to derive a dispersant solution therefrom; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; and autoclaving the bacterium to derive a dispersant solution therefrom.

Methods for dispersing hydrocarbons using autoclaved bacteria

DOEpatents

Tyndall, R.L.

1996-11-26

A method of dispersing a hydrocarbon includes the following steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; autoclaving the bacterium to derive a dispersant solution; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; and autoclaving the bacterium to derive a dispersant solution.

Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

PubMed Central

Stiefel, Philipp; Zambelli, Tomaso

2013-01-01

In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources. PMID:23770907

Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes.

PubMed

Cottrell, Matthew T; Kirchman, David L

2016-10-01

Bacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as "Candidatus Pelagibacter ubique," a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control in Pelagibacter and in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophs Polaribacter sp. strain MED152 and Ruegeria pomeroyi When growth levels changed, transcript levels remained steady in Pelagibacter and SAR92 but shifted in MED152 and R. pomeroyi Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success of Pelagibacter and possibly other oligotrophic microbes that dominate microbial communities in the oceans. Diverse heterotrophic bacteria drive biogeochemical cycling in the ocean. The most abundant types of marine bacteria are oligotrophs with small, streamlined genomes. The metabolic controls that regulate the response of oligotrophic bacteria to environmental conditions remain unclear. Our results reveal that transcriptional control is lower in marine oligotrophic bacteria than in marine copiotrophic bacteria. Although responses of bacteria to environmental conditions are commonly regulated at the level of transcription, metabolism in the most abundant bacteria in the

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery.

PubMed

Jiang, Jie; Pan, Chaohu; Xiao, Aiping; Yang, Xiai; Zhang, Guimin

2017-05-01

Six bacteria strains from heavy-metal-polluted ramie rhizosphere soil were isolated through Cd 2+ stress, which were numbered as JJ1, JJ2, JJ10, JJ11, JJ15, and JJ18. Sequence alignment and phylogenic analysis showed that strain JJ1 belonged to Pseudomonas, strain JJ2 belonged to Cupriavidus, strains JJ11 and JJ15 belonged to Bacillus, and strains JJ10 and JJ18 belonged to Acinetobacter. The tolerance capability of all the strains was the trend of Pb 2+  > Zn 2+  > Cu 2+  > Cd 2+ , the maximum tolerance concentration to Cd 2+ was 200 mg/L, to Pb 2+ was 1600 mg/L, to Zn 2+ was 600 mg/L, and to Cu 2+ was 265 mg/L. Strains JJ1, JJ11, JJ15, and JJ18 could grow well under pH 9.0, and strains JJ2, JJ11, and JJ18 could grow well under 7% of NaCl. The results showed that as a whole these strains had high environmental adaptability. This is the first report that heavy-metal-tolerant bacteria were found from ramie rhizosphere soil, which could be as a foundation to discover the relationship between ramie, rhizosphere bacteria and heavy metals.

Sex-specific selection under environmental stress in seed beetles.

PubMed

Martinossi-Allibert, I; Arnqvist, G; Berger, D

2017-01-01

Sexual selection can increase rates of adaptation by imposing strong selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex-specific reductions in fitness components, genotype-by-environment interactions and the strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all levels of stress. Although genetic variance in fitness increased in magnitude under severe stress, heritability decreased and particularly so in males. Moreover, genotype-by-environment interactions for fitness were common but specific to the type of stress, sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation.

PubMed

De Filippis, Francesca; Troise, Antonio Dario; Vitaglione, Paola; Ercolini, Danilo

2018-08-01

Kombucha is a traditional beverage produced by tea fermentation, carried out by a symbiotic consortium of bacteria and yeasts. Acetic Acid Bacteria (AAB) usually dominate the bacterial community of Kombucha, driving the fermentative process. The consumption of this beverage was often associated to beneficial effects for the health, due to its antioxidant and detoxifying properties. We characterized bacterial populations of Kombucha tea fermented at 20 or 30 °C by using culture-dependent and -independent methods and monitored the concentration of gluconic and glucuronic acids, as well as of total polyphenols. We found significant differences in the microbiota at the two temperatures. Moreover, different species of Gluconacetobacter were selected, leading to a differential abundance of gluconic and glucuronic acids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit

PubMed Central

Grimes, D. Jay; Ford, Tim E.; Colwell, Rita R.; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G.

2014-01-01

Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions. PMID:24477922

The mechanical life of magnetotactic bacteria inside sediments: implications for paleo- and environmental magnetism

NASA Astrophysics Data System (ADS)

Egli, Ramon; Mao, Xuegang

2015-04-01

Magnetotactic bacteria (MTB) are responsible for up to almost 100% of the magnetic signature of certain sediments through fossil reminders called magnetofossils. Besides being stable carriers of useful paleomagnetic signals, magnetofossils provide interesting environmental proxies that reflect MTB abundance variations due to nutrient supply and/or dilution by detrital/aeolian inputs. Unfortunately factors affecting MTB abundances in sediment are poorly known and based at best on extrapolations of observations on pure cultures. For example, MTB displacement models have been always based on the assumption that full alignment with the Earth magnetic field is possible, as observed in water. However, we recently found that the alignment of living MTB does not exceed few % inside sediments. This observation raises questions on the true nature of the biologic advantage of such bacteria over other motile organisms, and, ultimatively, on what is controlling their abundance in sediment. Here we report experiments that demonstrate the role of the Earth magnetic field in directing MTB to optimal living depths with the observed poor magnetic alignment. These exerments explain the apparent useless abundance of magnetosomes in certain MTB strains (e.g. M. Bavaricum) and reveal unexpected differences between strains with respect to their ability to cope with chemical signals and absent or reversed magnetic fields.

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria

PubMed Central

Zgadzaj, Rafal; James, Euan K.; Kelly, Simon; Kawaharada, Yasuyuki; de Jonge, Nadieh; Jensen, Dorthe B.; Madsen, Lene H.; Radutoiu, Simona

2015-01-01

Legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules. For the symbionts, a complex genetic mechanism that allows mutual recognition and plant infection has emerged from genetic studies under axenic conditions. In contrast, little is known about the mechanisms controlling the endophytic infection. Here we investigate the contribution of both the host and the symbiotic microbe to endophyte infection and development of mixed colonised nodules in Lotus japonicus. We found that infection threads initiated by Mesorhizobium loti, the natural symbiont of Lotus, can selectively guide endophytic bacteria towards nodule primordia, where competent strains multiply and colonise the nodule together with the nitrogen-fixing symbiotic partner. Further co-inoculation studies with the competent coloniser, Rhizobium mesosinicum strain KAW12, show that endophytic nodule infection depends on functional and efficient M. loti-driven Nod factor signalling. KAW12 exopolysaccharide (EPS) enabled endophyte nodule infection whilst compatible M. loti EPS restricted it. Analysis of plant mutants that control different stages of the symbiotic infection showed that both symbiont and endophyte accommodation within nodules is under host genetic control. This demonstrates that when legume plants are exposed to complex communities they selectively regulate access and accommodation of bacteria occupying this specialized environmental niche, the root nodule. PMID:26042417

[Species diversity and ecological distribution of anaerobic ammonium-oxidizing bacteria].

PubMed

Chen, Ting-Ting; Zheng, Ping; Hu, Bao-Lan

2009-05-01

Anaerobic ammonium oxidation (anammox) is an important discovery in microbiology and environmental sciences, which can simultaneously remove NH4(+) -N and NO3(-) -N, being valuable in environmental engineering. However, anaerobic ammonium oxidizers are extremely slow-growing, and their population's doubling time is longer than 11 days, which seriously restricts the application of anammox process. Therefore, the study of anammox bacteria is of significance. It has been proved that besides planctomycetes, the first recognized anammox bacteria, both nitrifying bacteria and denitrifying bacteria are also capable of anaerobic ammonium oxidation. These anammox bacteria have wide-spread habitats, which offered a chance to exploit new bacterial resources for anammox. Nitrifying bacteria and denitrifying bacteria have the function of anammox, and their metabolic diversity provides a basis to speed up the start-up of anammox reactor. It was revealed that anaerobic digestion sludge can present anammox activity, with sulphate as electron acceptor. The new bioreaction lays a foundation for the development of novel N-removal biotechnology, being conducive to the development and application of anammox to get more bacterial resources for anammox and to make clear the ecological distribution of anammox bacteria.

A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria.

PubMed

Marathe, Nachiket P; Regina, Viduthalai R; Walujkar, Sandeep A; Charan, Shakti Singh; Moore, Edward R B; Larsson, D G Joakim; Shouche, Yogesh S

2013-01-01

The arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. Selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. We hypothesize that waste-water treatment plants (WWTPs) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there together with exceptionally strong and persistent selection pressures from the antibiotic-contaminated waste. Previous analyses of effluent from an Indian industrial WWTP that processes waste from bulk drug production revealed the presence of a range of drugs, including broad spectrum antibiotics at extremely high concentrations (mg/L range). In this study, we have characterized the antibiotic resistance profiles of 93 bacterial strains sampled at different stages of the treatment process from the WWTP against 39 antibiotics belonging to 12 different classes. A large majority (86%) of the strains were resistant to 20 or more antibiotics. Although there were no classically-recognized human pathogens among the 93 isolated strains, opportunistic pathogens such as Ochrobactrum intermedium, Providencia rettgeri, vancomycin resistant Enterococci (VRE), Aerococcus sp. and Citrobacter freundii were found to be highly resistant. One of the O. intermedium strains (ER1) was resistant to 36 antibiotics, while P. rettgeri (OSR3) was resistant to 35 antibiotics. Class 1 and 2 integrons were detected in 74/93 (80%) strains each, and 88/93 (95%) strains harbored at least one type of integron. The qPCR analysis of community DNA also showed an unprecedented high prevalence of integrons, suggesting that the bacteria living under such high selective pressure have an appreciable potential for genetic exchange of resistance genes via mobile gene cassettes. The present study provides insight into

Environmental and Public Health Implications of Water Reuse: Antibiotics, Antibiotic Resistant Bacteria, and Antibiotic Resistance Genes

PubMed Central

Hong, Pei-Ying; Al-Jassim, Nada; Ansari, Mohd Ikram; Mackie, Roderick I.

2013-01-01

Water scarcity is a global problem, and is particularly acute in certain regions like Africa, the Middle East, as well as the western states of America. A breakdown on water usage revealed that 70% of freshwater supplies are used for agricultural irrigation. The use of reclaimed water as an alternative water source for agricultural irrigation would greatly alleviate the demand on freshwater sources. This paradigm shift is gaining momentum in several water scarce countries like Saudi Arabia. However, microbial problems associated with reclaimed water may hinder the use of reclaimed water for agricultural irrigation. Of particular concern is that the occurrence of antibiotic residues in the reclaimed water can select for antibiotic resistance genes among the microbial community. Antibiotic resistance genes can be associated with mobile genetic elements, which in turn allow a promiscuous transfer of resistance traits from one bacterium to another. Together with the pathogens that are present in the reclaimed water, antibiotic resistant bacteria can potentially exchange mobile genetic elements to create the “perfect microbial storm”. Given the significance of this issue, a deeper understanding of the occurrence of antibiotics in reclaimed water, and their potential influence on the selection of resistant microorganisms would be essential. In this review paper, we collated literature over the past two decades to determine the occurrence of antibiotics in municipal wastewater and livestock manure. We then discuss how these antibiotic resistant bacteria may impose a potential microbial risk to the environment and public health, and the knowledge gaps that would have to be addressed in future studies. Overall, the collation of the literature in wastewater treatment and agriculture serves to frame and identify potential concerns with respect to antibiotics, antibiotic resistant bacteria, and antibiotic resistance genes in reclaimed water. PMID:27029309

Coupling of radiofrequency with magnetic nanoparticles treatment as an alternative physical antibacterial strategy against multiple drug resistant bacteria

NASA Astrophysics Data System (ADS)

Chaurasia, Akhilesh K.; Thorat, Nanasaheb D.; Tandon, Anshula; Kim, Jin-Hahn; Park, Sung Ha; Kim, Kyeong Kyu

2016-09-01

Antibiotic resistant bacteria not only affect human health and but also threatens the safety in hospitals and among communities. However, the emergence of drug resistant bacteria is inevitable due to evolutionary selection as a consequence of indiscriminate antibiotic usage. Therefore, it is necessary to develop a novel strategy by which pathogenic bacteria can be eliminated without triggering resistance. We propose a novel magnetic nanoparticle-based physical treatment against pathogenic bacteria, which blocks biofilm formation and kills bacteria. In this approach, multiple drug resistant Staphylococcus aureus USA300 and uropathogenic Escherichia coli CFT073 are trapped to the positively charged magnetic core-shell nanoparticles (MCSNPs) by electrostatic interaction. All the trapped bacteria can be completely killed within 30 min owing to the loss of membrane potential and dysfunction of membrane-associated complexes when exposed to the radiofrequency current. These results indicate that MCSNP-based physical treatment can be an alternative antibacterial strategy without leading to antibiotic resistance, and can be used for many purposes including environmental and therapeutic applications.

Coupling of radiofrequency with magnetic nanoparticles treatment as an alternative physical antibacterial strategy against multiple drug resistant bacteria

PubMed Central

Chaurasia, Akhilesh K.; Thorat, Nanasaheb D.; Tandon, Anshula; Kim, Jin-Hahn; Park, Sung Ha; Kim, Kyeong Kyu

2016-01-01

Antibiotic resistant bacteria not only affect human health and but also threatens the safety in hospitals and among communities. However, the emergence of drug resistant bacteria is inevitable due to evolutionary selection as a consequence of indiscriminate antibiotic usage. Therefore, it is necessary to develop a novel strategy by which pathogenic bacteria can be eliminated without triggering resistance. We propose a novel magnetic nanoparticle-based physical treatment against pathogenic bacteria, which blocks biofilm formation and kills bacteria. In this approach, multiple drug resistant Staphylococcus aureus USA300 and uropathogenic Escherichia coli CFT073 are trapped to the positively charged magnetic core-shell nanoparticles (MCSNPs) by electrostatic interaction. All the trapped bacteria can be completely killed within 30 min owing to the loss of membrane potential and dysfunction of membrane-associated complexes when exposed to the radiofrequency current. These results indicate that MCSNP-based physical treatment can be an alternative antibacterial strategy without leading to antibiotic resistance, and can be used for many purposes including environmental and therapeutic applications. PMID:27670157

Revealing potential functions of VBNC bacteria in polycyclic aromatic hydrocarbons biodegradation.

PubMed

Su, X M; Bamba, A M; Zhang, S; Zhang, Y G; Hashmi, M Z; Lin, H J; Ding, L X

2018-04-01

The bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites is not running smoothly, because of the lower activity of PAH-degrading bacteria in actual bioremediation applications. The phenomenon of "viable but nonculturable" (VBNC) state may be a main limiting factor for their poor biodegradation capabilities of PAHs. Due to their abilities of entering into the VBNC state, most of bacterial populations with PAH-degradation potential remain unculturable. Resuscitation of VBNC bacteria will enhance the degradation capability of indigenous bacteria which will eventually obtain their better capabilities in environmental bioremediation. Although evidences have been presented indicating that resuscitation of VBNC bacteria in polychlorinated biphenyl (PCB)-contaminated environments not only significantly enhanced PCB degradation, but also obtained novel highly efficient PCB-degrading bacteria, scanty information is available on the VBNC bacteria in PAH-contaminated sites. VBNC bacteria, as a vast majority of potential microbial resource could be the repository of novel highly efficient PAH-biodegraders. Therefore, studies need to be done on resuscitation of VBNC bacteria to overcome key bottlenecks in bioremediation of PAH-contaminated sites. This mini-review provides a new insight into the potential functions of VBNC bacteria in PAHs biodegradation. As the vast majority microbial resource, viable but nonculturable (VBNC) bacteria, which showed their potential functions in polycyclic aromatic hydrocarbons (PAHs) biodegradation, can be of great significance in environmental bioremediation. It is therefore important to resuscitate VBNC bacteria for their better capabilities. Meanwhile, preventing the indigenous functional community from entering into the VBNC state will also maintain the high activity of PAH-degrading bacteria in actual bioremediation applications. Undoubtedly, much more work needs to be done to reveal indigenous micro-organisms in the

Seasonal abundance and diversity of culturable heterotrophic bacteria in relation to environmental factors in the Gulf of Antalya, Eastern Mediterranean, Turkey.

PubMed

Çardak, Mine; Özgür Özbek, Elif; Kebapçioğlu, Turhan

2015-04-01

The abundance of culturable heterotropic bacteria studied on and according to depth levels and seasons in the Gulf of Antalya. Environmental factors were compared regarding culturable heterotrophic bacteria abundance and diversities of bacteria. During the study period (between August 2009 and April 2010, seasonally in the Gulf of Antalya, at six stations and six depth levels (0-20 cm, 10, 25, 50, 100, 200 m). The bacterial isolates were identified in the automated micro identification system VITEK 2 Compact 30 (Biomereux, France). The mean abundance was higher in Sts. D, E and F than Sts. A, B and C, located in the eastern part of the gulf. The mean abundance decreased as the depth level increased. The mean abundance of CHB ranged between 8.15 × 10(6) and 2.54 × 10(8) CFU ml(-1) throughout the year. Abundance of CHB differed according to the variations of biotic and abiotic factors. A total of 27 taxa of bacteria including six bacterial classes were reported in this study as the first records for the Gulf of Antalya. Six bacterial classes: Gamma Proteobacteria (46.81 %), Bacilli (27.66 %), Beta Proteobacteria (12.77 %), Alfa Proteobacteria (6.38 %), Actinobacteria (4.26 %) and Flavobacteria (2.13 %) were determined. The study resulted in increased knowledge on the composition and biochemical response of bacteria isolated from eutrophic and oligotrophic areas. 23 bacteria species belonging to 16 families were reported.

The effect of conventional wastewater treatment on the levels of antimicrobial-resistant bacteria in effluent: a meta-analysis of current studies.

PubMed

Harris, Suvi; Cormican, Martin; Cummins, Enda

2012-12-01

Antimicrobial agents in the environment are a cause for concern. Antimicrobial drug residues and their metabolites reach the aquatic and terrestrial environment primarily through wastewater treatment plants (WWTP). In addition to the potential direct negative health and environmental effects, there is potential for the development of antimicrobial-resistant bacteria. Residue levels below the minimum inhibitory concentration for a bacterial species can be important in selection of resistance. There is uncertainty associated with resistance formation during WWTP processing. A meta-analysis study was carried out to analyse the effect of WWTP processing on the levels of antimicrobial-resistant bacteria within bacterial populations. An analysis of publications relating to multiple antimicrobial-resistant (MAR) bacteria (n = 61), single antimicrobial-resistant (SAR) E. coli (n = 81) and quinolone/fluoroquinolone-resistant (FR) bacteria (n = 19) was carried out. The odds-ratio (OR) of MAR (OR = 1.60, p < 0.01), SAR (OR = 1.33, p < 0.01) and FR (OR = 1.19, p < 0.01) bacteria was determined. The results infer that WWTP processing results in an increase in the proportion of resistant bacteria in effluent, even though the overall bacterial population may have reduced (i.e. a reduction in total bacterial numbers but an increase in the percentage of resistant bacteria). The results support the need for further research into the development of antimicrobial-resistant strains and possible selective pressures operating in WWTPs.

Structurally altered capsular polysaccharides produced by mutant bacteria

NASA Technical Reports Server (NTRS)

Petersen, Gene R. (Inventor); Kern, Roger G. (Inventor); Richards, Gil F. (Inventor)

1995-01-01

Structurally altered capsular polysaccharides are produced by mutant bacteria. These polysaccharides are isolated by selecting a wild type bacterial strain and a phage producing degradative enzymes that have substrate specificity for the capsular polysaccharides produced by the wild type bacteria. Phage-resistant mutants producing capsular polysaccharides are selected and the structurally altered capsular polysaccharide is isolated therefrom.

Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria.

PubMed

Maphosa, Farai; de Vos, Willem M; Smidt, Hauke

2010-06-01

Various 'omics' methods have enabled environmental probing at the molecular level and have created an important new paradigm in bioremediation design and management. Ecogenomics - the application of genomics to ecological and environmental sciences - defines phylogenetic and functional biodiversity at the DNA, RNA and protein levels. It capitalizes on this knowledge to elucidate functions and interactions of organisms at the ecosystem level in relation to ecological and evolutionary processes. Effective bioremediation of widespread halo-organic pollutants in anaerobic environments requires knowledge of catabolic potential and in situ dynamics of organohalide-respiring and co-metabolizing microorganisms. Here, we discuss the potential of ecogenomics approaches in developing high-throughput methods for detecting and monitoring organohalide respirers, and for providing improvements to selection, specificity and sensitivity of target biomarkers and their application to evaluate bioremediation strategies.

Relation between selected well-construction characteristics and occurrence of bacteria in private household-supply wells, south-central and southeastern Pennsylvania

USGS Publications Warehouse

Zimmerman, Tammy M.; Zimmerman, Michele L.; Lindsey, Bruce D.

2001-01-01

Total coliform and Escherichia coli (E. coli) bacteria were analyzed in ground water sampled from 78 private household-supply wells as part of a study by the U.S. Geological Survey in cooperation with the Pennsylvania Department of Environmental Protection to evaluate the relation between well construction characteristics and the occurrence of bacteria in ground water. Sampling was done in eight counties in south-central and southeastern Pennsylvania from September 2000 to March 2001. All samples were collected from wells in close proximity to agricultural land-use areas.Total coliform bacteria were found in water from 62 percent (48 of 78) of the wells, and bacteria were just as likely to be found in sanitary wells (grouted/loose-fitting well cap or grouted/sanitary sealed well cap) as in nonsanitary wells (nongrouted/ loose-fitting well cap). The areas underlain by carbonate bedrock had the highest percentages of total coliform detected (about 75 percent). Nearly half of the samples collected in the areas underlain by noncarbonate bedrock also were found to have total coliform present. E. coli bacteria were found in water from 10 percent of the wells. Seventeen percent of the samples that were positive for total coliform also were positive for E. coli. The presence of E. coli bacteria was more likely in water from nonsanitary wells. Additionally, the presence of E. coli bacteria was more likely in ground water from wells underlain by carbonate bedrock. A further breakdown of the data into four groups on the basis of sanitary construction and bedrock type indicated the presence of E. coli was more likely in water from nonsanitary wells in areas underlain by carbonate bedrock.Statistical analysis of other well-construction characteristics that might relate to occurrence of bacteria showed that the presence of total coliform bacteria was related to the depth to water-bearing zone in both sanitary and nonsanitary wells in areas underlain by carbonate bedrock

Selectivity of natural, synthetic and environmental estrogens for zebrafish estrogen receptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinto, Caroline; Grimaldi, Marina; Boulahtouf, Abdelhay

2014-10-01

Zebrafish, Danio rerio, is increasingly used as an animal model to study the effects of pharmaceuticals and environmental estrogens. As most of these estrogens have only been tested on human estrogen receptors (ERs), it is necessary to measure their effects on zebrafish ERs. In humans there are two distinct nuclear ERs (hERα and hERβ), whereas the zebrafish genome encodes three ERs, zfERα and two zfERβs (zfERβ1 and zfERβ2). In this study, we established HeLa-based reporter cell lines stably expressing each of the three zfERs. We first reported that estrogens more efficiently activate the zfERs at 28 °C as compared tomore » 37 °C, thus reflecting the physiological temperature of zebrafish in wildlife. We then showed significant differences in the ability of agonist and antagonist estrogens to modulate activation of the three zfER isotypes in comparison to hERs. Environmental compounds (bisphenol A, alkylphenols, mycoestrogens) which are hER panagonists and hERβ selective agonists displayed greater potency for zfERα as compared to zfERβs. Among hERα selective synthetic agonists, PPT did not activate zfERα while 16α-LE2 was the most zfERα selective compound. Altogether, these results confirm that all hER ligands control in a similar manner the transcriptional activity of zfERs although significant differences in selectivity were observed among subtypes. The zfER subtype selective ligands that we identified thus represent new valuable tools to dissect the physiological roles of the different zfERs. Finally, our work also points out that care has to be taken in transposing the results obtained using the zebrafish as a model for human physiopathology. - Highlights: • Zebrafish is increasingly used to study the effects of estrogens. • We assessed the activity of pharmaceutical and environmental estrogens on zfERs. • Environmental estrogens displayed greater potency for zfERα compared to zfERβs. • hERβ selective agonists displayed greater

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

USGS Publications Warehouse

Cinotto, Peter J.

2005-01-01

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag

Dynamics of Dark-Fly Genome Under Environmental Selections

PubMed Central

Izutsu, Minako; Toyoda, Atsushi; Fujiyama, Asao; Agata, Kiyokazu; Fuse, Naoyuki

2015-01-01

Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize “Dark-fly”, a Drosophila melanogaster line maintained in constant dark conditions for more than 60 years. Our previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. We found here that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination we designed an experiment for genome reselection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. We thereby detected condition-dependent selections toward approximately 6% of the genome. In addition, we observed the time-course trajectory of SNP frequency in the mixed populations through generations 0, 22, and 49, which resulted in notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly. PMID:26637434

Partial least squares for efficient models of fecal indicator bacteria on Great Lakes beaches

USGS Publications Warehouse

Brooks, Wesley R.; Fienen, Michael N.; Corsi, Steven R.

2013-01-01

At public beaches, it is now common to mitigate the impact of water-borne pathogens by posting a swimmer's advisory when the concentration of fecal indicator bacteria (FIB) exceeds an action threshold. Since culturing the bacteria delays public notification when dangerous conditions exist, regression models are sometimes used to predict the FIB concentration based on readily-available environmental measurements. It is hard to know which environmental parameters are relevant to predicting FIB concentration, and the parameters are usually correlated, which can hurt the predictive power of a regression model. Here the method of partial least squares (PLS) is introduced to automate the regression modeling process. Model selection is reduced to the process of setting a tuning parameter to control the decision threshold that separates predicted exceedances of the standard from predicted non-exceedances. The method is validated by application to four Great Lakes beaches during the summer of 2010. Performance of the PLS models compares favorably to that of the existing state-of-the-art regression models at these four sites.

Enhanced bacterial affinity of PVDF membrane: its application as improved sea water sampling tool for environmental monitoring.

PubMed

Kumar, Sweta Binod; Sharnagat, Preeti; Manna, Paramita; Bhattacharya, Amit; Haldar, Soumya

2017-02-01

Isolation of diversified bacteria from seawater is a major challenge in the field of environmental microbiology. In the present study, an attempt has been made to select specific membrane with improved property of attaching diversified bacteria. Initially, different concentrations (15, 18, and 20% W/W) of polysulfone (PSF) were used to check their affinity for the attachment of selected gram-positive (Bacillus subtilis) and gram-negative (Escherichia coli) bacteria. Among these, 20% W/W PSF showed maximum attachment. Therefore, membrane prepared with other materials such as polyvinylidene fluoride (PVDF) and polyether sulfone (PES) were used with the same concentration (20% W/W) to check their improved bacterial attachment property. Comparative study of bacterial attachment on three different membranes revealed that PVDF possessed the highest affinity towards both the groups of bacteria. This property was confirmed by different analytical methods viz. contact angle, atomic force microscopy, zeta potential, and flux study and further validated with seawater samples collected from seven sites of western coast and Lakshadweep island of India, using Biolog EcoPlate™. All the samples showed that bacterial richness and diversity was high in PVDF membrane in comparison to surrounding seawater samples. Interestingly, affinity for more diversified bacteria was reported to be higher in water sample with less turbidity and low bacteria load. This finding can facilitate the development of PVDF (20% W/W) membrane as a simple, cheap, and less labor intensive environmental sampling tool for the isolation of diversified bacteria from seawater sample wih different physiochemical properties. Graphical abstract ᅟ.

Lipopolysaccharides in diazotrophic bacteria.

PubMed

Serrato, Rodrigo V

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

Lipopolysaccharides in diazotrophic bacteria

PubMed Central

Serrato, Rodrigo V.

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure. PMID:25232535

Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

ERIC Educational Resources Information Center

Delpech, Roger

2009-01-01

This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

Antibiotic resistant bacteria in urban sewage: Role of full-scale wastewater treatment plants on environmental spreading.

PubMed

Turolla, A; Cattaneo, M; Marazzi, F; Mezzanotte, V; Antonelli, M

2018-01-01

The presence of antibiotic resistant bacteria (ARB) in wastewater was investigated and the role of wastewater treatment plants (WWTPs) in promoting or limiting antibiotic resistance was assessed. Escherichia coli (E. coli) and total heterotrophic bacteria (THB) resistance to ampicillin, chloramphenicol and tetracycline was monitored in three WWTPs located in Milan urban area (Italy), differing among them for the operating parameters of biological process, for the disinfection processes (based on sodium hypochlorite, UV radiation, peracetic acid) and for the discharge limits to be met. Wastewater was collected from three sampling points along the treatment sequence (WWTP influent, effluent from sand filtration, WWTP effluent). Antibiotic resistance to ampicillin was observed both for E. coli and for THB. Ampicillin resistant bacteria in the WWTP influents were 20-47% of E. coli and 16-25% of THB counts. A limited resistance to chloramphenicol was observed only for E. coli, while neither for E. coli nor for THB tetracycline resistance was observed. The biological treatment and sand filtration led to a decrease in the maximum percentage of ampicillin-resistant bacteria (20-29% for E. coli, 11-21% for THB). However, the conventionally adopted parameters did not seem adequate to support an interpretation of WWTP role in ARB spread. Peracetic acid was effective in selectively acting on antibiotic resistant THB, unlike UV radiation and sodium hypochlorite. The low counts of E. coli in WWTP final effluents in case of agricultural reuse did not allow to compare the effect of the different disinfection processes on antibiotic resistance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biomass measurement of methane forming bacteria in environmental samples

NASA Technical Reports Server (NTRS)

Martz, R. F.; Sebacher, D. I.; White, D. C.

1983-01-01

Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 x 10(-14) moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid 'signature'. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.

Recent Developments for Remediating Acidic Mine Waters Using Sulfidogenic Bacteria

PubMed Central

Bitencourt, José A. P.; Sahoo, Prafulla K.; Alves, Joner Oliveira; Siqueira, José O.

2017-01-01

Acidic mine drainage (AMD) is regarded as a pollutant and considered as potential source of valuable metals. With diminishing metal resources and ever-increasing demand on industry, recovering AMD metals is a sustainable initiative, despite facing major challenges. AMD refers to effluents draining from abandoned mines and mine wastes usually highly acidic that contain a variety of dissolved metals (Fe, Mn, Cu, Ni, and Zn) in much greater concentration than what is found in natural water bodies. There are numerous remediation treatments including chemical (lime treatment) or biological methods (aerobic wetlands and compost bioreactors) used for metal precipitation and removal from AMD. However, controlled biomineralization and selective recovering of metals using sulfidogenic bacteria are advantageous, reducing costs and environmental risks of sludge disposal. The increased understanding of the microbiology of acid-tolerant sulfidogenic bacteria will lead to the development of novel approaches to AMD treatment. We present and discuss several important recent approaches using low sulfidogenic bioreactors to both remediate and selectively recover metal sulfides from AMD. This work also highlights the efficiency and drawbacks of these types of treatments for metal recovery and points to future research for enhancing the use of novel acidophilic and acid-tolerant sulfidogenic microorganisms in AMD treatment. PMID:29119111

Aptamer-based viability impedimetric sensor for bacteria.

PubMed

Labib, Mahmoud; Zamay, Anna S; Kolovskaya, Olga S; Reshetneva, Irina T; Zamay, Galina S; Kibbee, Richard J; Sattar, Syed A; Zamay, Tatiana N; Berezovski, Maxim V

2012-11-06

The development of an aptamer-based viability impedimetric sensor for bacteria (AptaVISens-B) is presented. Highly specific DNA aptamers to live Salmonella typhimurium were selected via the cell-systematic evolution of ligands by exponential enrichment (SELEX) technique. Twelve rounds of selection were performed; each comprises a positive selection step against viable S. typhimurium and a negative selection step against heat killed S. typhimurium and a mixture of related pathogens, including Salmonella enteritidis, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Citrobacter freundii to ensure the species specificity of the selected aptamers. The DNA sequence showing the highest binding affinity to the bacteria was further integrated into an impedimetric sensor via self-assembly onto a gold nanoparticle-modified screen-printed carbon electrode (GNP-SPCE). Remarkably, this aptasensor is highly selective and can successfully detect S. typhimurium down to 600 CFU mL(-1) (equivalent to 18 live cells in 30 μL of assay volume) and distinguish it from other Salmonella species, including S. enteritidis and S. choleraesuis. This report is envisaged to open a new venue for the aptamer-based viability sensing of a variety of microorganisms, particularly viable but nonculturable (VBNC) bacteria, using a rapid, economic, and label-free electrochemical platform.

Dynamics of Dark-Fly Genome Under Environmental Selections.

PubMed

Izutsu, Minako; Toyoda, Atsushi; Fujiyama, Asao; Agata, Kiyokazu; Fuse, Naoyuki

2015-12-04

Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize "Dark-fly", a Drosophila melanogaster line maintained in constant dark conditions for more than 60 years. Our previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. We found here that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination we designed an experiment for genome reselection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. We thereby detected condition-dependent selections toward approximately 6% of the genome. In addition, we observed the time-course trajectory of SNP frequency in the mixed populations through generations 0, 22, and 49, which resulted in notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly. Copyright © 2016 Izutsu et al.

Microbial oxidative stress response: Novel insights from environmental facultative anaerobic bacteria.

PubMed

Fu, Huihui; Yuan, Jie; Gao, Haichun

2015-10-15

Facultative bacteria can grow under either oxic or anoxic conditions. While oxygen provides substantial advantages in energy yield by respiration, it can become life-threatening because of reactive oxygen species that derive from the molecule naturally. Thus, to survive and thrive in a given niche, these bacteria have to constantly regulate physiological processes to make maximum benefits from oxygen respiration while restraining oxidative stress. Molecular mechanisms and physiological consequences of oxidative stress have been under extensive investigation for decades, mostly on research model Escherichia coli, from which our understanding of bacterial oxidative stress response is largely derived. Nevertheless, given that bacteria live in enormously diverse environments, to cope with oxidative stress different strategies are conceivably developed. Copyright © 2015 Elsevier Inc. All rights reserved.

Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation

PubMed Central

Chao, Lin; Rang, Camilla Ulla; Proenca, Audrey Menegaz; Chao, Jasper Ubirajara

2016-01-01

Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother’s old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother’s old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington’s genetic

Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

PubMed

Chao, Lin; Rang, Camilla Ulla; Proenca, Audrey Menegaz; Chao, Jasper Ubirajara

2016-01-01

Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation

Bacteria-mediated bisphenol A degradation.

PubMed

Zhang, Weiwei; Yin, Kun; Chen, Lingxin

2013-07-01

Bisphenol A (BPA) is an important monomer in the manufacture of polycarbonate plastics, food cans, and other daily used chemicals. Daily and worldwide usage of BPA and BPA-contained products led to its ubiquitous distribution in water, sediment/soil, and atmosphere. Moreover, BPA has been identified as an environmental endocrine disruptor for its estrogenic and genotoxic activity. Thus, BPA contamination in the environment is an increasingly worldwide concern, and methods to efficiently remove BPA from the environment are urgently recommended. Although many factors affect the fate of BPA in the environment, BPA degradation is mainly depended on the metabolism of bacteria. Many BPA-degrading bacteria have been identified from water, sediment/soil, and wastewater treatment plants. Metabolic pathways of BPA degradation in specific bacterial strains were proposed, based on the metabolic intermediates detected during the degradation process. In this review, the BPA-degrading bacteria were summarized, and the (proposed) BPA degradation pathway mediated by bacteria were referred.

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier

PubMed Central

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio

2017-01-01

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas. We used high throughput DNA sequencing to identify Operational Taxonomic Units (OTUs) present in cryoconite holes and three ice-marginal environments, the moraines, the glacier forefield, and a large (> 3 m high) ice-cored dirt cone occurring on the glacier surface. Bacterial communities of cryoconite holes were different from those of ice-marginal environments and hosted fewer OTUs. However, a network analysis revealed that the cryoconite holes shared more OTUs with the moraines and the dirt cone than with the glacier forefield. Ice-marginal environments may therefore act as sources of bacteria for cryoconite holes, but differences in environmental conditions limit the number of bacterial strains that may survive in them. At the same time, cryoconite holes host a few OTUs that were not found in any ice-marginal environment we sampled, thus suggesting that some bacterial populations are positively selected by the specific environmental conditions of the cryoconite holes. PMID:28358872

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier.

PubMed

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Ambrosini, Roberto

2017-01-01

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas. We used high throughput DNA sequencing to identify Operational Taxonomic Units (OTUs) present in cryoconite holes and three ice-marginal environments, the moraines, the glacier forefield, and a large (> 3 m high) ice-cored dirt cone occurring on the glacier surface. Bacterial communities of cryoconite holes were different from those of ice-marginal environments and hosted fewer OTUs. However, a network analysis revealed that the cryoconite holes shared more OTUs with the moraines and the dirt cone than with the glacier forefield. Ice-marginal environments may therefore act as sources of bacteria for cryoconite holes, but differences in environmental conditions limit the number of bacterial strains that may survive in them. At the same time, cryoconite holes host a few OTUs that were not found in any ice-marginal environment we sampled, thus suggesting that some bacterial populations are positively selected by the specific environmental conditions of the cryoconite holes.

Combined Dielectrophoresis and Impedance Systems for Bacteria Analysis in Microfluidic On-Chip Platforms

PubMed Central

Páez-Avilés, Cristina; Juanola-Feliu, Esteve; Punter-Villagrasa, Jaime; del Moral Zamora, Beatriz; Homs-Corbera, Antoni; Colomer-Farrarons, Jordi; Miribel-Català, Pere Lluís; Samitier, Josep

2016-01-01

Bacteria concentration and detection is time-consuming in regular microbiology procedures aimed to facilitate the detection and analysis of these cells at very low concentrations. Traditional methods are effective but often require several days to complete. This scenario results in low bioanalytical and diagnostic methodologies with associated increased costs and complexity. In recent years, the exploitation of the intrinsic electrical properties of cells has emerged as an appealing alternative approach for concentrating and detecting bacteria. The combination of dielectrophoresis (DEP) and impedance analysis (IA) in microfluidic on-chip platforms could be key to develop rapid, accurate, portable, simple-to-use and cost-effective microfluidic devices with a promising impact in medicine, public health, agricultural, food control and environmental areas. The present document reviews recent DEP and IA combined approaches and the latest relevant improvements focusing on bacteria concentration and detection, including selectivity, sensitivity, detection time, and conductivity variation enhancements. Furthermore, this review analyses future trends and challenges which need to be addressed in order to successfully commercialize these platforms resulting in an adequate social return of public-funded investments. PMID:27649201

Exploitation of Albanian wheat cultivars: characterization of the flours and lactic acid bacteria microbiota, and selection of starters for sourdough fermentation.

PubMed

Nionelli, Luana; Curri, Nertila; Curiel, José Antonio; Di Cagno, Raffaella; Pontonio, Erica; Cavoski, Ivana; Gobbetti, Marco; Rizzello, Carlo Giuseppe

2014-12-01

Six Albanian soft and durum wheat cultivars were characterized based on chemical and technological features, showing different attitudes for bread making. Gliadin and glutenin fractions were selectively extracted from flours, and subjected to two-dimensional electrophoresis. Linja 7 and LVS flours showed the best characteristics, and abundance of high molecular weight (HMW)-glutenins. Type I sourdoughs were prepared through back slopping procedure, and the lactic acid bacteria were typed and identified. Lactobacillus plantarum and Leuconostoc mesenteroides were the predominant species. Thirty-eight representative isolates were singly used for sourdough fermentation of soft and durum wheat Albanian flours and their selection was carried out based on growth and acidification, quotient of fermentation, and proteolytic activity. Two different pools of lactic acid bacteria were designed to ferment soft or durum wheat flours. Sourdough fermentation with mixed and selected starters positively affected the quotient of fermentation, concentration of free amino acids, profile of phenolic acids, and antioxidant and phytase activities. This study provided the basis to exploit the potential of wheat Albanian flours based on an integrated approach, which considered the characterization of the flours and the processing conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

A light-up probe with aggregation-induced emission characteristics (AIE) for selective imaging, naked-eye detection and photodynamic killing of Gram-positive bacteria.

PubMed

Feng, Guangxue; Yuan, Youyong; Fang, Hu; Zhang, Ruoyu; Xing, Bengang; Zhang, Guanxin; Zhang, Deqing; Liu, Bin

2015-08-11

We report the design and synthesis of a red fluorescent AIE light-up probe for selective recognition, naked-eye detection, and image-guided photodynamic killing of Gram-positive bacteria, including vancomycin-resistant Enterococcus strains.

Modified insulator semiconductor electrode with functionalized nanoparticles for Proteus mirabilis bacteria biosensor development.

PubMed

Braham, Yosra; Barhoumi, Houcine; Maaref, Abderrazak; Bakhrouf, Amina; Jaffrezic-Renault, Nicole

2013-12-01

The development of enzymatic sensors for biological purposes such as biomedicine, pharmacy, food industry, and environmental toxicity requires the purification step of the enzyme. To prevent the loss of the enzyme activity, a new strategy is held in order to immobilize the bacteria. It will constitute the biological sensing element leading to a high operational stability and multiple adaptations to various conditions such as temperature, pH and ionic strength changes. In this work we describe the development of a urea biosensor by immobilizing Proteus mirabilis bacteria onto an insulator-semiconductor electrode on functionalized Fe3O4 nanoparticles (NPs), using cationic, Poly (allylamine hydrochloride) then anionic, Poly (sodium 4-styrenesulfonate) polyelectrolytes, BSA (serum bovin albumin), and glutaraldehyde as a cross-linking agent. The response of P. mirabilis to urea addition is evaluated in homogeneous and heterogeneous phases. Before the immobilization step, the activity of urease produced from the P. mirabilis bacteria was attempted using the ion ammonium selective electrodes (ISEs). Adhesion of the bacteria cells on IS electrodes have been studied using contact angle measurements. After immobilization of the bacteria, on the (Si/SiO2/Si3N4) and (Si/SiO2) substrates, the relationship between the evolution of the flat band potential ∆VFB and the urea concentration is found to be linear for values ranging from 10(-2)M to 10(-5)M. © 2013.

Symbiotic bacteria of helminths: what role may they play in ecosystems under anthropogenic stress?

PubMed

Morley, N J

2016-11-01

Symbiotic bacteria are a common feature of many animals, particularly invertebrates, from both aquatic and terrestrial habitats. These bacteria have increasingly been recognized as performing an important role in maintaining invertebrate health. Both ecto- and endoparasitic helminths have also been found to harbour a range of bacterial species which provide a similar function. The part symbiotic bacteria play in sustaining homeostasis of free-living invertebrates exposed to anthropogenic pressure (climate change, pollution), and the consequences to invertebrate populations when their symbionts succumb to poor environmental conditions, are increasingly important areas of research. Helminths are also susceptible to environmental stress and their symbiotic bacteria may be a key aspect of their responses to deteriorating conditions. This article summarizes the ecophysiological relationship helminths have with symbiotic bacteria and the role they play in maintaining a healthy parasite and the relevance of specific changes that occur in free-living invertebrate-bacteria interactions under anthropogenic pressure to helminths and their bacterial communities. It also discusses the importance of understanding the mechanistic sensitivity of helminth-bacteria relationships to environmental stress for comprehending the responses of parasites to challenging conditions.

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins.

PubMed

Madhwani, Tejal; McBain, Andrew J

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of "self" and "non-self" origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota.

Selected Analytical Methods for Environmental Remediation and Recovery (SAM) - Home

EPA Pesticide Factsheets

The SAM Home page provides access to all information provided in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM), and includes a query function allowing users to search methods by analyte, sample type and instrumentation.

Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights.

PubMed

Masschelein, J; Jenner, M; Challis, G L

2017-07-01

Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

PubMed

Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

2016-10-01

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities

Age-related changes in select fecal bacteria in foals

USDA-ARS?s Scientific Manuscript database

Adult horses depend on the microbial community in the hindgut to produce VFAs that are utilized for energy. Microbial colonization in the gastrointestinal tract of foals is essential to develop a healthy symbiotic relationship and prevent proliferation of pathogenic bacteria. However, colonization i...

Updates to Selected Analytical Methods for Environmental Remediation and Recovery (SAM)

EPA Pesticide Factsheets

View information on the latest updates to methods included in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM), including the newest recommended methods and publications.

A Treatment Plant Receiving Waste Water from Multiple Bulk Drug Manufacturers Is a Reservoir for Highly Multi-Drug Resistant Integron-Bearing Bacteria

PubMed Central

Walujkar, Sandeep A.; Charan, Shakti Singh; Moore, Edward R. B.; Larsson, D. G. Joakim; Shouche, Yogesh S.

2013-01-01

The arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. Selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. We hypothesize that waste-water treatment plants (WWTPs) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there together with exceptionally strong and persistent selection pressures from the antibiotic-contaminated waste. Previous analyses of effluent from an Indian industrial WWTP that processes waste from bulk drug production revealed the presence of a range of drugs, including broad spectrum antibiotics at extremely high concentrations (mg/L range). In this study, we have characterized the antibiotic resistance profiles of 93 bacterial strains sampled at different stages of the treatment process from the WWTP against 39 antibiotics belonging to 12 different classes. A large majority (86%) of the strains were resistant to 20 or more antibiotics. Although there were no classically-recognized human pathogens among the 93 isolated strains, opportunistic pathogens such as Ochrobactrum intermedium, Providencia rettgeri, vancomycin resistant Enterococci (VRE), Aerococcus sp. and Citrobacter freundii were found to be highly resistant. One of the O. intermedium strains (ER1) was resistant to 36 antibiotics, while P. rettgeri (OSR3) was resistant to 35 antibiotics. Class 1 and 2 integrons were detected in 74/93 (80%) strains each, and 88/93 (95%) strains harbored at least one type of integron. The qPCR analysis of community DNA also showed an unprecedented high prevalence of integrons, suggesting that the bacteria living under such high selective pressure have an appreciable potential for genetic exchange of resistance genes via mobile gene cassettes. The present study provides insight into

Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours

PubMed Central

Guzman, Cesar E.; Bereza-Malcolm, Lara T.; De Groef, Bert; Franks, Ashley E.

2015-01-01

The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0–20 mins after birth), day 1 (24 ± 1 h after birth), day 2 (48 ± 1 h after birth), and day 3 (72 ± 1 h after birth). Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose. PMID:26186002

Environmental fluctuations and host skin bacteria shift survival advantage between frogs and their fungal pathogen.

PubMed

Longo, Ana V; Zamudio, Kelly R

2017-02-01

Fluctuating environments can modulate host-pathogen interactions by providing a temporary advantage to one of the interacting organisms. However, we know very little about how environmental conditions facilitate beneficial interactions between hosts and their microbial communities, resulting in individual persistence with a particular pathogen. Here, we experimentally infected Eleutherodactylus coqui frogs with the fungal pathogen Batrachochytrium dendrobatidis (Bd) under environmental conditions known to confer the survival advantage to the host during the warm-wet season, or alternatively to the pathogen during the cool-dry season. We used 16S rRNA amplicon sequencing to quantify changes in bacterial richness and phylogenetic diversity, and identified operational taxonomic units (OTUs) that became overrepresented or suppressed as a consequence of Bd infection. During the warm-wet season, frogs limited Bd infections, recruited putatively beneficial bacteria and returned to pre-infection levels of richness and phylogenetic diversity. In contrast, during the cool-dry season, Bd infections kept increasing through time, and bacterial diversity remained constant. Our findings confirm that infection outcome not only depends on abiotic factors, but also on biotic interactions between hosts and their associated bacterial communities.

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system.

PubMed

Zarkasi, K Z; Abell, G C J; Taylor, R S; Neuman, C; Hatje, E; Tamplin, M L; Katouli, M; Bowman, J P

2014-07-01

The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated. Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. Faecal bacterial communities were highly dynamic but largely similar between randomly selected fish. In postsmolt, the faecal bacteria population was dominated by Gram-positive fermentative bacteria; however, by midsummer, members of the family Vibrionaceae predominated. As fish progressed towards harvest, a range of different bacterial genera became more prominent corresponding to a decline in Vibrionaceae. The sampled fish were fed two different commercial diet series with slightly different protein, lipid and digestible energy level; however, the effect of these differences was minimal. The overall data demonstrated dynamic hind gut communities in salmon that were related to season and fish growth phases but were less influenced by differences in commercial diets used routinely within the farm system studied. This study provides understanding of farmed salmon GI bacterial communities and describes the relative impact of diet, environmental and farm factors. © 2014 The Society for Applied Microbiology.

Poly-γ-Glutamic Acids Contribute to Biofilm Formation and Plant Root Colonization in Selected Environmental Isolates of Bacillus subtilis

PubMed Central

Yu, Yiyang; Yan, Fang; Chen, Yun; Jin, Christopher; Guo, Jian-Hua; Chai, Yunrong

2016-01-01

Bacillus subtilis is long known to produce poly-γ-glutamic acids (γ-PGA) as one of the major secreted polymeric substances. In B. subtilis, the regulation of γ-PGA production and its physiological role are still unclear. B. subtilis is also capable of forming structurally complex multicellular communities, or biofilms, in which an extracellular matrix consisting of secreted proteins and polysaccharides holds individual cells together. Biofilms were shown to facilitate B. subtilis–plant interactions. In this study, we show that different environmental isolates of B. subtilis, all capable of forming biofilms, vary significantly in γ-PGA production. This is possibly due to differential regulation of γ-PGA biosynthesis genes. In many of those environmental isolates, γ-PGA seems to contribute to robustness and complex morphology of the colony biofilms, suggesting a role of γ-PGA in biofilm formation. Our evidence further shows that in selected B. subtilis strains, γ-PGA also plays a role in root colonization by the bacteria, pinpointing a possible function of γ-PGA in B. subtilis–plant interactions. Finally, we found that several pathways co-regulate both γ-PGA biosynthesis genes and genes for the biofilm matrix in B. subtilis, but in an opposing fashion. We discussed potential biological significance of that. PMID:27891125

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.

PubMed

Guerra, Alaine B; Oliveira, Jorge S; Silva-Portela, Rita C B; Araújo, Wydemberg; Carlos, Aline C; Vasconcelos, Ana Tereza R; Freitas, Ana Teresa; Domingos, Yldeney Silva; de Farias, Mirna Ferreira; Fernandes, Glauber José Turolla; Agnez-Lima, Lucymara F

2018-04-01

Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform. Taxonomic analysis revealed the predominance of Proteobacteria in the metagenome from the drill cuttings, while Firmicutes was enriched in consortia samples. Functional analysis using the Biosurfactants and Biodegradation Database (BioSurfDB) revealed a similar pattern among the three samples regarding hydrocarbon degradation and biosurfactants production pathways. However, some statistical differences were observed between samples. Namely, the pathways related to the degradation of fatty acids, chloroalkanes, and chloroalkanes were enriched in consortia samples. The degradation colorimetric assay using dichlorophenolindophenol as an indicator was positive for several hydrocarbon substrates. The consortia were also able to produce biosurfactants, with biosynthesis of iturin, lichnysin, and surfactin among the more abundant pathways. A microcosms assay followed by gas chromatography analysis showed the efficacy of the consortia in degrading alkanes, as we observed a reduction of around 66% and 30% for each consortium in total alkanes. These data suggest the potential use of these consortia in the bioremediation of drilling residue based on autochthonous bioaugmentation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation.

PubMed

Vergani, Lorenzo; Mapelli, Francesca; Marasco, Ramona; Crotti, Elena; Fusi, Marco; Di Guardo, Antonio; Armiraglio, Stefano; Daffonchio, Daniele; Borin, Sara

2017-01-01

The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates

Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

PubMed Central

Vergani, Lorenzo; Mapelli, Francesca; Marasco, Ramona; Crotti, Elena; Fusi, Marco; Di Guardo, Antonio; Armiraglio, Stefano; Daffonchio, Daniele; Borin, Sara

2017-01-01

The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates

Interactions among sulfide-oxidizing bacteria

NASA Technical Reports Server (NTRS)

Poplawski, R.

1985-01-01

The responses of different phototrophic bacteria in a competitive experimental system are studied, one in which primary factors such as H2S or light limited photometabolism. Two different types of bacteria shared one limited source of sulfide under specific conditions of light. The selection of a purple and a green sulfur bacteria and the cyanobacterium was based on their physiological similarity and also on the fact that they occur together in microbial mats. They all share anoxygenic photosynthesis, and are thus probably part of an evolutionary continuum of phototrophic organisms that runs from, strictly anaerobic physiology to the ability of some cyanobacteria to shift between anoxygenic bacterial style photosynthesis and the oxygenic kind typical of eukaryotes.

Genetically engineered acidophilic heterotrophic bacteria by bacteriophage transduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, T.E.; Bruhn, D.F.; Bulmer, D.F.

1989-05-10

A bacteriophage capable of infecting acidophilic heterotrophic bacteria and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phage having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element from ore or coal. 1 fig., 1 tab.

Transfer of Multidrug-Resistant Bacteria between Intermingled Ecological Niches: The Interface between Humans, Animals and the Environment

PubMed Central

da Costa, Paulo Martins; Loureiro, Luís; Matos, Augusto J. F.

2013-01-01

The use of antimicrobial agents has been claimed to be the driving force for the emergence and spread of microbial resistance. However, several studies have reported the presence of multidrug-resistant bacteria in populations exposed to low levels of antimicrobial drugs or even never exposed. For many pathogens, especially those organisms for which asymptomatic colonization typically precedes infection (e.g., Enterococcus spp. and Escherichia coli), the selective effects of antimicrobial use can only be understood if we considerer all biological and environmental pathways which enable these bacteria, and the genes they carry, to spread between different biomes. This ecological framework provides an essential perspective for formulating antimicrobial use policies, precisely because it encompasses the root causes of these problems rather than merely their consequences. PMID:23343983

Uranium Interaction with Two Multi-Resistant Environmental Bacteria: Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris

PubMed Central

Llorens, Isabelle; Untereiner, Guillaume; Jaillard, Danielle; Gouget, Barbara; Chapon, Virginie; Carriere, Marie

2012-01-01

Depending on speciation, U environmental contamination may be spread through the environment or inversely restrained to a limited area. Induction of U precipitation via biogenic or non-biogenic processes would reduce the dissemination of U contamination. To this aim U oxidation/reduction processes triggered by bacteria are presently intensively studied. Using X-ray absorption analysis, we describe in the present article the ability of Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris, highly resistant to a variety of metals and metalloids or to organic pollutants, to withstand high concentrations of U and to immobilize it either through biosorption or through reduction to non-uraninite U(IV)-phosphate or U(IV)-carboxylate compounds. These bacterial strains are thus good candidates for U bioremediation strategies, particularly in the context of multi-pollutant or mixed-waste contaminations. PMID:23251623

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins

PubMed Central

Madhwani, Tejal

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of “self” and “non-self” origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota. PMID:27483159

Molecular identification of environmental bacteria in indoor air in the domestic home: description of a new species of Exiguobacterium.

PubMed

Yuan, Ivan; Xu, Jiru; Millar, B Cherie; Dooley, James S G; Rooney, Paul J; Alexander, H Denis; Moore, John E

2007-02-01

The quality of indoor air in terms of its bioaerosol composition with microorganisms is important due to its potential aetiological role in development of conditions such as Sick Building Syndrome. Hence, laboratory identification of bacteriological components in any bioaerosol from buildings may help elucidate the role of such organisms in disease states, particularly allergy-related conditions. A molecular method was developed employing universal or "broad-range" eubacterial PCR to help identify environmental culturable bacteria from domestic household air. In a "proof of concept" experiment, 16S rDNA PCR was performed on a collection of bacterial isolates originating from indoor air in the domestic home. 16S rDNA PCR was performed using a set of universal primers to successfully generate an amplicon of approximately 1400 bp, which was sequenced to obtain each isolate's identity. Sequence analysis was able to identify 12/13 of the isolates, whereby the majority were Gram-positive (12/13). Nine different genera were identified from the 13 isolates examined, of which, 12/13 were Gram-positive, with the exception being Moraxella osloensis, which was Gram-negative, as well as a novel species of Exiguobacterium. The closest phylogenetic neighbour of the wildtype isolate to a named species within this genus was E. aestuarii (1364/1384 bases; 98.4% homology), followed by E. marinum (97.5%) and with E. acetylicum being the most distantly related of all the described species. On account of this divergence within the 16S rDNA gene operon of the unknown Exiguobacterium isolate, we believe this isolate to represent a novel species of Exiguobacterium, which we have tentatively named Exiguobacterium belfastensis. Although from this study, these organisms are usually unlikely to be clinically significant to healthy individuals with a competent immune system, we recommend that molecular identification methods are used, if considered necessary, as an adjunct to first line

Transgenic plants and associated bacteria for phytoremediation of chlorinated compounds.

PubMed

Van Aken, Benoit; Doty, Sharon Lafferty

2010-01-01

Phytoremediation is the use of plants for the treatment of environmental pollution, including chlorinated organics. Although conceptually very attractive, removal and biodegradation of chlorinated pollutants by plants is a rather slow and inefficient process resulting in incomplete treatment and potential release of toxic metabolites into the environment. In order to overcome inherent limitations of plant metabolic capabilities, plants have been genetically modified, following a strategy similar to the development of transgenic crops: genes from bacteria, fungi, and mammals involved in the metabolism of organic contaminants, such as cytochrome P-450 and glutathione S-transferase, have been introduced into higher plants, resulting in significant improvement of tolerance, removal, and degradation of pollutants. Recently, plant-associated bacteria have been recognized playing a significant role in phytoremediation, leading to the development of genetically modified rhizospheric and endophytic bacteria with improved biodegradation capabilities. Transgenic plants and associated bacteria constitute a new generation of genetically modified organisms for efficient and environmental-friendly treatment of polluted soil and water. This review focuses on recent advances in the development of transgenic plants and bacteria for the treatment of chlorinated pollutants, including chlorinated solvents, polychlorinated phenols, and chlorinated herbicides.

Two size-selective mechanisms specifically trap bacteria-sized food particles in Caenorhabditis elegans.

PubMed

Fang-Yen, Christopher; Avery, Leon; Samuel, Aravinthan D T

2009-11-24

Caenorhabditis elegans is a filter feeder: it draws bacteria suspended in liquid into its pharynx, traps the bacteria, and ejects the liquid. How pharyngeal pumping simultaneously transports and filters food particles has been poorly understood. Here, we use high-speed video microscopy to define the detailed workings of pharyngeal mechanics. The buccal cavity and metastomal flaps regulate the flow of dense bacterial suspensions and exclude excessively large particles from entering the pharynx. A complex sequence of contractions and relaxations transports food particles in two successive trap stages before passage into the terminal bulb and intestine. Filtering occurs at each trap as bacteria are concentrated in the central lumen while fluids are expelled radially through three apical channels. Experiments with microspheres show that the C. elegans pharynx, in combination with the buccal cavity, is tuned to specifically catch and transport particles of a size range corresponding to most soil bacteria.

Two size-selective mechanisms specifically trap bacteria-sized food particles in Caenorhabditis elegans

PubMed Central

Fang-Yen, Christopher; Avery, Leon; Samuel, Aravinthan D. T.

2009-01-01

Caenorhabditis elegans is a filter feeder: it draws bacteria suspended in liquid into its pharynx, traps the bacteria, and ejects the liquid. How pharyngeal pumping simultaneously transports and filters food particles has been poorly understood. Here, we use high-speed video microscopy to define the detailed workings of pharyngeal mechanics. The buccal cavity and metastomal flaps regulate the flow of dense bacterial suspensions and exclude excessively large particles from entering the pharynx. A complex sequence of contractions and relaxations transports food particles in two successive trap stages before passage into the terminal bulb and intestine. Filtering occurs at each trap as bacteria are concentrated in the central lumen while fluids are expelled radially through three apical channels. Experiments with microspheres show that the C. elegans pharynx, in combination with the buccal cavity, is tuned to specifically catch and transport particles of a size range corresponding to most soil bacteria. PMID:19903886

Environmental Controls of Shellfish-Toxigenic Vibrio Bacteria in Oregon's Coasts and Estuaries

NASA Astrophysics Data System (ADS)

Gradoville, M. R.; Häse, C.; White, A. E.

2016-02-01

Vibrio species are a known and persistent concern for economically important aquaculture efforts. In Pacific Northwest shellfish hatcheries, vibriosis, caused by toxigenic Vibrio, has been responsible for major mortality events in recent decades — events that are often irregular and unpredictable. The success of shellfish hatcheries is critically linked to the chemical and biological composition of their seawater resources; thus, it is pertinent to understand the biogeochemical drivers of toxigenic Vibrio in their planktonic state. Recent evidence suggests that vibriosis outbreaks in Netarts Bay, Oregon may be related to wind-driven coastal upwelling, either through the advection of toxigenic Vibrio residing in upwelling source water, or through the creation of favorable growth conditions within the estuary. Here, we present data tracking shellfish-toxigenic Vibrio bacteria in Oregon estuaries and coastal waters through the 2015 upwelling season. Estuarine samples were collected from Netarts Bay and Yaquina Bay in May-October 2015 over a range of upwelling intensities, tidal heights, and biogeochemical conditions. Additionally, samples were collected at multiple depths from offshore coastal Oregon stations in order to test the hypothesis that toxigenic Vibrio reside in upwelling source waters. PCR-based methods were used to quantify the known shellfish pathogen V. coralliilyticus in estuary and seawater samples. These toxigenic Vibrio abundances were correlated to local environmental conditions, including temperature, salinity, carbonate chemistry, nutrients, and chlorophyll a concentrations, as well as coastal wind stress and upwelling intensity. Our analysis aims to define the environmental controls of toxigenic Vibrio in their free-living oceanic state, information that can be used to prevent future disease outbreaks in local shellfish hatcheries.

Isolation of Environmental Bacteria from Surface and Drinking Water in Mafikeng, South Africa, and Characterization Using Their Antibiotic Resistance Profiles

PubMed Central

Mulamattathil, Suma George; Mbewe, Moses; Ateba, Collins Njie

2014-01-01

The aim of this study was to isolate and identify environmental bacteria from various raw water sources as well as the drinking water distributions system in Mafikeng, South Africa, and to determine their antibiotic resistance profiles. Water samples from five different sites (raw and drinking water) were analysed for the presence of faecal indicator bacteria as well as Aeromonas and Pseudomonas species. Faecal and total coliforms were detected in summer in the treated water samples from the Modimola dam and in the mixed water samples, with Pseudomonas spp. being the most prevalent organism. The most prevalent multiple antibiotic resistance phenotype observed was KF-AP-C-E-OT-K-TM-A. All organisms tested were resistant to erythromycin, trimethoprim, and amoxicillin. All isolates were susceptible to ciprofloxacin and faecal coliforms and Pseudomonas spp. to neomycin and streptomycin. Cluster analysis based on inhibition zone diameter data suggests that the isolates had similar chemical exposure histories. Isolates were identified using gyrB, toxA, ecfX, aerA, and hylH gene fragments and gyrB, ecfX, and hylH fragments were amplified. These results demonstrate that (i) the drinking water from Mafikeng contains various bacterial species and at times faecal and total coliforms. (ii) The various bacteria are resistant to various classes of antibiotics. PMID:25105027

GEOTHERMAL ENVIRONMENTAL ASSESSMENT: BEHAVIOR OF SELECTED GEOTHERMAL BRINE CONTAMINANTS IN PLANTS AND SOILS

EPA Science Inventory

The behavior of selected elements found in the Roosevelt Hot Springs KGRA geothermal fluids was investigated in both plant and soil systems. The kinetics of these potential environmental containments were studied by using soil columns and selected cultivated and native plant spec...

Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees

PubMed Central

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

Background To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. Methods and Findings First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 103 CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. Conclusions The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of

Oligo-DNA custom macroarray for monitoring major pathogenic and non-pathogenic fungi and bacteria in the phyllosphere of apple trees.

PubMed

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3) CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species

43 CFR 3420.3-4 - Regional tract ranking, selection, environmental analysis and scheduling.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Regional tract ranking, selection...) COMPETITIVE LEASING Competitive Leasing § 3420.3-4 Regional tract ranking, selection, environmental analysis... natural environment; and socioeconomic impacts. The subfactors the regional coal team will consider under...

Regulated Proteolysis in Bacteria.

PubMed

Mahmoud, Samar A; Chien, Peter

2018-06-20

Regulated proteolysis is a vital process that affects all living things. Bacteria use energy-dependent AAA+ proteases to power degradation of misfolded and native regulatory proteins. Given that proteolysis is an irreversible event, specificity and selectivity in degrading substrates are key. Specificity is often augmented through the use of adaptors that modify the inherent specificity of the proteolytic machinery. Regulated protein degradation is intricately linked to quality control, cell-cycle progression, and physiological transitions. In this review, we highlight recent work that has shed light on our understanding of regulated proteolysis in bacteria. We discuss the role AAA+ proteases play during balanced growth as well as how these proteases are deployed during changes in growth. We present examples of how protease selectivity can be controlled in increasingly complex ways. Finally, we describe how coupling a core recognition determinant to one or more modifying agents is a general theme for regulated protein degradation.

Use of the alr gene as a food-grade selection marker in lactic acid bacteria.

PubMed

Bron, Peter A; Benchimol, Marcos G; Lambert, Jolanda; Palumbo, Emmanuelle; Deghorain, Marie; Delcour, Jean; De Vos, Willem M; Kleerebezem, Michiel; Hols, Pascal

2002-11-01

Both Lactococcus lactis and Lactobacillus plantarum contain a single alr gene, encoding an alanine racemase (EC 5.1.1.1), which catalyzes the interconversion of D-alanine and L-alanine. The alr genes of these lactic acid bacteria were investigated for their application as food-grade selection markers in a heterologous complementation approach. Since isogenic mutants of both species carrying an alr deletion (Deltaalr) showed auxotrophy for D-alanine, plasmids carrying a heterologous alr were constructed and could be selected, since they complemented D-alanine auxotrophy in the L. plantarum Deltaalr and L. lactis Deltaalr strains. Selection was found to be highly stringent, and plasmids were stably maintained over 200 generations of culturing. Moreover, the plasmids carrying the heterologous alr genes could be stably maintained in wild-type strains of L. plantarum and L. lactis by selection for resistance to D-cycloserine, a competitive inhibitor of Alr (600 and 200 micro g/ml, respectively). In addition, a plasmid carrying the L. plantarum alr gene under control of the regulated nisA promoter was constructed to demonstrate that D-cycloserine resistance of L. lactis is linearly correlated to the alr expression level. Finally, the L. lactis alr gene controlled by the nisA promoter, together with the nisin-regulatory genes nisRK, were integrated into the chromosome of L. plantarum Deltaalr. The resulting strain could grow in the absence of D-alanine only when expression of the alr gene was induced with nisin.

A survey of the prevalence of selected bacteria in wild birds

USGS Publications Warehouse

Brittingham, M.C.; Temple, S.A.; Duncan, R.M.

1988-01-01

We determined the prevalence of six genera of bacteria from a sample of 387 cloacal swabs from 364 passerines and woodpeckers. The prevalence of bacteria were as follows: Escherichia coli (1%), Pseudomonas spp. (22%), Salmonella spp. (0%), Staphylococcus spp. (15%), Streptococcus spp. (18%), and Yersinia spp. (1%). The prevalence of Streptococcus spp. was higher in omnivorous species than in granivorous species (20% versus 8%). Individuals captured at feeders had a lower prevalence of both Streptococcus spp. (15% versus 33%) and Escherichia coli (0.5% versus 4%) than birds that did not have access to feeders. These differences are probably not due to the feeder per se, but instead to other site related differences. The prevalence of bacteria did not differ between male and female black-capped chickadees, Parus atricapillus. For 279 color marked black-capped chickadees, we calculated the cumulative mortality rate during 12 wk following swabbing. Although the cumulative mortality rates of infected birds were consistently higher than the rates of non-infected birds, none of these differences were significant. Infections may cause slight reductions in survival rates, but we were not able to confirm this with our data.

Cleaning, resistant bacteria, and antibiotic prescribing in residential aged care facilities.

PubMed

Cowan, Raquel U; Kishan, Divya; Walton, Aaron L; Sneath, Emmy; Cheah, Thomas; Butwilowsky, Judith; Friedman, N Deborah

2016-03-01

Residents of residential aged care facilities (RACFs) are at risk of colonization and infection with multidrug-resistant bacteria, and antibiotic prescribing is often inappropriate and not based on culture-proven infection. We describe low levels of resident colonization and environmental contamination with resistant gram-negative bacteria in RACFs, but high levels of empirical antibiotic use not guided by microbiologic culture. This research highlights the importance of antimicrobial stewardship and environmental cleaning in aged care facilities. Copyright © 2016 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Comparing Selections of Environmental Variables for Ecological Studies: A Focus on Terrain Attributes.

PubMed

Lecours, Vincent; Brown, Craig J; Devillers, Rodolphe; Lucieer, Vanessa L; Edinger, Evan N

2016-01-01

Selecting appropriate environmental variables is a key step in ecology. Terrain attributes (e.g. slope, rugosity) are routinely used as abiotic surrogates of species distribution and to produce habitat maps that can be used in decision-making for conservation or management. Selecting appropriate terrain attributes for ecological studies may be a challenging process that can lead users to select a subjective, potentially sub-optimal combination of attributes for their applications. The objective of this paper is to assess the impacts of subjectively selecting terrain attributes for ecological applications by comparing the performance of different combinations of terrain attributes in the production of habitat maps and species distribution models. Seven different selections of terrain attributes, alone or in combination with other environmental variables, were used to map benthic habitats of German Bank (off Nova Scotia, Canada). 29 maps of potential habitats based on unsupervised classifications of biophysical characteristics of German Bank were produced, and 29 species distribution models of sea scallops were generated using MaxEnt. The performances of the 58 maps were quantified and compared to evaluate the effectiveness of the various combinations of environmental variables. One of the combinations of terrain attributes-recommended in a related study and that includes a measure of relative position, slope, two measures of orientation, topographic mean and a measure of rugosity-yielded better results than the other selections for both methodologies, confirming that they together best describe terrain properties. Important differences in performance (up to 47% in accuracy measurement) and spatial outputs (up to 58% in spatial distribution of habitats) highlighted the importance of carefully selecting variables for ecological applications. This paper demonstrates that making a subjective choice of variables may reduce map accuracy and produce maps that do not

Autochthonous bioaugmentation with environmental samples rich in hydrocarbonoclastic bacteria for bench-scale bioremediation of oily seawater and desert soil.

PubMed

Ali, Nedaa; Dashti, Narjes; Salamah, Samar; Al-Awadhi, Husain; Sorkhoh, Naser; Radwan, Samir

2016-05-01

Oil-contaminated seawater and desert soil batches were bioaugmented with suspensions of pea (Pisum sativum) rhizosphere and soil with long history of oil pollution. Oil consumption was measured by gas-liquid chromatography. Hydrocarbonoclastic bacteria in the bioremediation batches were counted using a mineral medium with oil vapor as a sole carbon source and characterized by their 16S ribosomal RNA (rRNA)-gene sequences. Most of the oil was consumed during the first 2-4 months, and the oil-removal rate decreased or ceased thereafter due to nutrient and oxygen depletion. Supplying the batches with NaNO3 (nitrogen fertilization) at a late phase of bioremediation resulted in reenhanced oil consumption and bacterial growth. In the seawater batches bioaugmented with rhizospheric suspension, the autochthonous rhizospheric bacterial species Microbacterium oxidans and Rhodococcus spp. were established and contributed to oil-removal. The rhizosphere-bioaugmented soil batches selectively favored Arthrobacter nitroguajacolicus, Caulobacter segnis, and Ensifer adherens. In seawater batches bioaugmented with long-contaminated soil, the predominant oil-removing bacterium was the marine species Marinobacter hydrocarbonoclasticus. In soil batches on the other hand, the autochthonous inhabitants of the long-contaminated soil, Pseudomonas and Massilia species were established and contributed to oil removal. It was concluded that the use of rhizospheric bacteria for inoculating seawater and desert soil and of bacteria in long-contaminated soil for inoculating desert soil follows the concept of "autochthonous bioaugmentation." Inoculating seawater with bacteria in long-contaminated soil, on the other hand, merits the designation "allochthonous bioaugmentation."

Amphibian skin may select for rare environmental microbes

PubMed Central

Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Cormier, Guy; Jensen, Roderick V; Belden, Lisa K

2014-01-01

Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment. PMID:24858782

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment

PubMed Central

Kiseleva, Larisa; Briliute, Justina; Khilyas, Irina V.; Simpson, David J. W.; Fedorovich, Viacheslav; Cohen, M.; Goryanin, Igor

2015-01-01

Some bacteria can carry out anaerobic respiration by depositing electrons on external materials, such as electrodes, thereby creating an electrical current. Into the anode chamber of microbial fuel cells (MFCs) having abiotic air-cathodes we inoculated microorganisms cultured from a magnetic particle-enriched portion of a marine tidal sediment, reasoning that since some external electron acceptors are ferromagnetic, electrogenic bacteria should be found in their vicinity. Two MFCs, one inoculated with a mixed bacterial culture and the other with an axenic culture of a helical bacterium isolated from the magnetic particle enrichment, termed strain HJ, were operated for 65 d. Both MFCs produced power, with production from the mixed culture MFC exceeding that of strain HJ. Strain HJ was identified as a Thalassospira sp. by transmission electron microscopic analysis and 16S rRNA gene comparisons. An MFC inoculated with strain HJ and operated in open circuit produced 47% and 57% of the maximal power produced from MFCs inoculated with the known electrogen Geobacter daltonii and the magnetotactic bacterium Desulfamplus magnetomortis, respectively. Further investigation will be needed to determine whether bacterial populations associated with magnetic particles within marine sediments are enriched for electrogens. PMID:26504814

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment.

PubMed

Kiseleva, Larisa; Briliute, Justina; Khilyas, Irina V; Simpson, David J W; Fedorovich, Viacheslav; Cohen, M; Goryanin, Igor

2015-01-01

Some bacteria can carry out anaerobic respiration by depositing electrons on external materials, such as electrodes, thereby creating an electrical current. Into the anode chamber of microbial fuel cells (MFCs) having abiotic air-cathodes we inoculated microorganisms cultured from a magnetic particle-enriched portion of a marine tidal sediment, reasoning that since some external electron acceptors are ferromagnetic, electrogenic bacteria should be found in their vicinity. Two MFCs, one inoculated with a mixed bacterial culture and the other with an axenic culture of a helical bacterium isolated from the magnetic particle enrichment, termed strain HJ, were operated for 65 d. Both MFCs produced power, with production from the mixed culture MFC exceeding that of strain HJ. Strain HJ was identified as a Thalassospira sp. by transmission electron microscopic analysis and 16S rRNA gene comparisons. An MFC inoculated with strain HJ and operated in open circuit produced 47% and 57% of the maximal power produced from MFCs inoculated with the known electrogen Geobacter daltonii and the magnetotactic bacterium Desulfamplus magnetomortis, respectively. Further investigation will be needed to determine whether bacterial populations associated with magnetic particles within marine sediments are enriched for electrogens.

Airborne bacteria and fungi associated with waste-handling work.

PubMed

Park, Donguk; Ryu, Seunghun; Kim, Shinbum; Byun, Hyaejeong; Yoon, Chungsik; Lee, Kyeongmin

2013-01-01

Municipal workers handling household waste are potentially exposed to a variety of toxic and pathogenic substances, in particular airborne bacteria, gram-negative bacteria (GNB), and fungi. However, relatively little is known about the conditions under which exposure is facilitated. This study assessed levels of airborne bacteria, GNB, and fungi, and examined these in relation to the type of waste-handling activity (collection, transfer, transport, and sorting at the waste preprocessing plant), as well as a variety of other environmental and occupational factors. Airborne microorganisms were sampled using an Andersen single-stage sampler equipped with agar plates containing the appropriate nutritional medium and then cultured to determine airborne levels. Samples were taken during collection, transfer, transport, and sorting of household waste. Multiple regression analysis was used to identify environmental and occupational factors that significantly affect airborne microorganism levels during waste-handling activities. The "type of waste-handling activity" was the only factor that significantly affected airborne levels of bacteria and GNB, accounting for 38% (P = 0.029) and 50% (P = 0.0002) of the variation observed in bacteria and GNB levels, respectively. In terms of fungi, the type of waste-handling activity (R2 = 0.76) and whether collection had also occurred on the day prior to sampling (P < 0.0001, R2 = 0.78) explained most of the observed variation. Given that the type of waste-handling activity was significantly correlated with levels of bacteria, GNB, and fungi, we suggest that various engineering, administrative, and regulatory measures should be considered to reduce the occupational exposure to airborne microorganisms in the waste-handling industry.

Assessment System for Junior High Schools in Taiwan to Select Environmental Education Facilities and Sites

ERIC Educational Resources Information Center

Ho, Shyue-Yung; Chen, Wen-Te; Hsu, Wei-Ling

2017-01-01

Environmental education is essential for people to pursue sustainable development. In Taiwan, environmental education is taught to students until they graduate from junior high school. This study was conducted to establish an assessment system for junior high schools to select appropriate environmental education facilities and sites. A mix of…

Environmental Education in the Elementary School. A Selection of Articles Reprinted from Science and Children.

ERIC Educational Resources Information Center

Shugrue, Sylvia K., Comp.; Lamberton, Berenice, Comp.

Included in this document are a selection of articles reprinted from SCIENCE AND CHILDREN. They focus on environmental education in the elementary school, and present a number of environmental perspectives. Those concerning general or background information are: an examination of environmental education: children's attitudes about the environment;…

Exogenous fatty acid metabolism in bacteria.

PubMed

Yao, Jiangwei; Rock, Charles O

2017-10-01

Bacterial type II fatty acid synthesis (FASII) is a target for novel antibiotic development. All bacteria encode for mechanisms to incorporate exogenous fatty acids, and some bacteria can use exogenous fatty acids to bypass FASII inhibition. Bacteria encode three different mechanisms for activating exogenous fatty acids for incorporation into phospholipid synthesis. Exogenous fatty acids are converted into acyl-CoA in Gammaproteobacteria such as E. coli. Acyl-CoA molecules constitute a separate pool from endogenously synthesized acyl-ACP. Acyl-CoA can be used for phospholipid synthesis or broken down by β-oxidation, but cannot be used for lipopolysaccharide synthesis. Exogenous fatty acids are converted into acyl-ACP in some Gram-negative bacteria. The resulting acyl-ACP undergoes the same fates as endogenously synthesized acyl-ACP. Exogenous fatty acids are converted into acyl-phosphates in Gram-positive bacteria, and can be used for phospholipid synthesis or become acyl-ACP. Only the order Lactobacillales can use exogenous fatty acids to bypass FASII inhibition. FASII shuts down completely in presence of exogenous fatty acids in Lactobacillales, allowing Lactobacillales to synthesize phospholipids entirely from exogenous fatty acids. Inhibition of FASII cannot be bypassed in other bacteria because FASII is only partially down-regulated in presence of exogenous fatty acid or FASII is required to synthesize essential metabolites such as β-hydroxyacyl-ACP. Certain selective pressures such as FASII inhibition or growth in biofilms can select for naturally occurring one step mutations that attenuate endogenous fatty acid synthesis. Although attempts have been made to estimate the natural prevalence of these mutants, culture-independent metagenomic methods would provide a better estimate. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Characterizing relationships among fecal indicator bacteria ...

EPA Pesticide Factsheets

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

The effects of low-level ionizing radiation and copper exposure on the incidence of antibiotic resistance in lentic biofilm bacteria.

PubMed

McArthur, J Vaun; Dicks, Christian A; Bryan, A Lawrence; Tuckfield, R Cary

2017-09-01

Environmental reservoirs of antibiotic resistant bacteria are poorly understood. Understanding how the environment selects for resistance traits in the absence of antibiotics is critical in developing strategies to mitigate this growing menace. Indirect or co-selection of resistance by environmental pollution has been shown to increase antibiotic resistance. However no attention has been given to the effects of low-level ionizing radiation or the interactions between radiation and heavy metals on the maintenance or selection for antibiotic resistance (AR) traits. Here we explore the effect of radiation and copper on antibiotic resistance. Bacteria were collected from biofilms in two ponds - one impacted by low-level radiocesium and the other an abandoned farm pond. Through laboratory controlled experiments we examined the effects of increasing concentrations of copper on the incidence of antibiotic resistance. Differences were detected in the resistance profiles of the controls from each pond. Low levels (0.01 mM) of copper sulfate increased resistance but 0.5 mM concentrations of copper sulfate depressed the AR response in both ponds. A similar pattern was observed for levels of multiple antibiotic resistance per isolate. The first principal component response of isolate exposure to multiple antibiotics showed significant differences among the six isolate treatment combinations. These differences were clearly visualized through a discriminant function analysis, which showed distinct antibiotic resistance response patterns based on the six treatment groups. Copyright © 2017 Elsevier Ltd. All rights reserved.

Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria

USDA-ARS?s Scientific Manuscript database

The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater- and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hotspot for pr...

Fecal Indicator Bacteria and Environmental Observations: Validation of Virtual Beach

EPA Science Inventory

Contamination of recreational waters by fecal material is often assessed using indicator bacteria such as enterococci. Enumeration based on culturing methods can take up to 48 hours to complete, limiting the accuracy of water quality evaluations. Molecular microbial techniques em...

Analysis of magnetite crystals and inclusion bodies inside magnetotactic bacteria from different environmental locations

NASA Astrophysics Data System (ADS)

Oestreicher, Z.; Lower, B.; Lower, S.; Bazylinski, D. A.

2011-12-01

Biomineralization occurs throughout the living world; a few common examples include iron oxide in chiton teeth, calcium carbonate in mollusk shells, calcium phosphate in animal bones and teeth, silica in diatom shells, and magnetite crystals inside the cells of magnetotactic bacteria. Biologically controlled mineralization is characterized by biominerals that have species-specific properties such as: preferential crystallographic orientation, consistent particle size, highly ordered spatial locations, and well-defined composition and structure. It is well known that magnetotactic bacteria synthesize crystals of magnetite inside of their cells, but how they mineralize the magnetite is poorly understood. Magnetosomes have a species-specific morphology that is due to specific proteins involved in the mineralization process. In addition to magnetite crystals, magnetotactic bacteria also produce inclusion bodies or granules that contain different elements, such as phosphorus, calcium, and sulfur. In this study we used the transmission electron microscope to analyze the structure of magnetite crystals and inclusion bodies from different species of magnetotactic bacteria in order to determine the composition of the inclusion bodies and to ascertain whether or not the magnetite crystals contain elements other than iron and oxygen. Using energy dispersive spectroscopy we found that different bacteria from different environments possess inclusion bodies that contain different elements such as phosphorus, calcium, barium, magnesium, and sulfur. These differences may reflect the conditions of the environment in which the bacteria inhabit.

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea

PubMed Central

Rieck, Angelika; Herlemann, Daniel P. R.; Jürgens, Klaus; Grossart, Hans-Peter

2015-01-01

Many studies on bacterial community composition (BCC) do not distinguish between particle-associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16 S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. “Shannon and Simpson indices” showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently. PMID:26648911

Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome.

PubMed

Pierella Karlusich, Juan J; Ceccoli, Romina D; Graña, Martín; Romero, Héctor; Carrillo, Néstor

2015-02-16

Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-containing flavodoxin, is a widespread strategy employed by photosynthetic microorganisms to overcome environmental adversities. The flavodoxin gene was lost in the course of plant evolution, but its reintroduction in transgenic plants confers increased tolerance to environmental stress and iron starvation, raising the question as to why a genetic asset with obvious adaptive value was not kept by natural selection. Phylogenetic analyses reveal that the evolutionary history of flavodoxin is intricate, with several horizontal gene transfer events between distant organisms, including Eukarya, Bacteria, and Archaea. The flavodoxin gene is unevenly distributed in most algal lineages, with flavodoxin-containing species being overrepresented in iron-limited regions and scarce or absent in iron-rich environments. Evaluation of cyanobacterial genomic and metagenomic data yielded essentially the same results, indicating that there was little selection pressure to retain flavodoxin in iron-rich coastal/freshwater phototrophs. Our results show a highly dynamic evolution pattern of flavodoxin tightly connected to the bioavailability of iron. Evidence presented here also indicates that the high concentration of iron in coastal and freshwater habitats may have facilitated the loss of flavodoxin in the freshwater ancestor of modern plants during the transition of photosynthetic organisms from the open oceans to the firm land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria.

PubMed

Shrout, Joshua D; Scheetz, Todd E; Casavant, Thomas L; Parkin, Gene F

2005-04-01

Recent studies have shown that perchlorate (ClO(4) (-)) can be degraded by some pure-culture and mixed-culture bacteria with the addition of hydrogen. This paper describes the isolation of two hydrogen-utilizing perchlorate-degrading bacteria capable of using inorganic carbon for growth. These autotrophic bacteria are within the genus Dechloromonas and are the first Dechloromonas species that are microaerophilic and incapable of growth at atmospheric oxygen concentrations. Dechloromonas sp. JDS5 and Dechloromonas sp. JDS6 are the first perchlorate-degrading autotrophs isolated from a perchlorate-contaminated site. Measured hydrogen thresholds were higher than for other environmentally significant, hydrogen-utilizing, anaerobic bacteria (e.g., halorespirers). The chlorite dismutase activity of these bacteria was greater for autotrophically grown cells than for cells grown heterotrophically on lactate. These bacteria used fumarate as an alternate electron acceptor, which is the first report of growth on an organic electron acceptor by perchlorate-reducing bacteria.

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects.

PubMed

Sabater-Muñoz, Beatriz; Toft, Christina; Alvarez-Ponce, David; Fares, Mario A

2017-06-01

An open question in evolutionary biology is how does the selection-drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host-symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shift.

Opposing selection and environmental variation modify optimal timing of breeding.

PubMed

Tarwater, Corey E; Beissinger, Steven R

2013-09-17

Studies of evolution in wild populations often find that the heritable phenotypic traits of individuals producing the most offspring do not increase proportionally in the population. This paradox may arise when phenotypic traits influence both fecundity and viability and when there is a tradeoff between these fitness components, leading to opposing selection. Such tradeoffs are the foundation of life history theory, but they are rarely investigated in selection studies. Timing of breeding is a classic example of a heritable trait under directional selection that does not result in an evolutionary response. Using a 22-y study of a tropical parrot, we show that opposing viability and fecundity selection on the timing of breeding is common and affects optimal breeding date, defined by maximization of fitness. After accounting for sampling error, the directions of viability (positive) and fecundity (negative) selection were consistent, but the magnitude of selection fluctuated among years. Environmental conditions (rainfall and breeding density) primarily and breeding experience secondarily modified selection, shifting optimal timing among individuals and years. In contrast to other studies, viability selection was as strong as fecundity selection, late-born juveniles had greater survival than early-born juveniles, and breeding later in the year increased fitness under opposing selection. Our findings provide support for life history tradeoffs influencing selection on phenotypic traits, highlight the need to unify selection and life history theory, and illustrate the importance of monitoring survival as well as reproduction for understanding phenological responses to climate change.

Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates.

PubMed Central

Lowe, S E; Jain, M K; Zeikus, J G

1993-01-01

Anaerobic bacteria include diverse species that can grow at environmental extremes of temperature, pH, salinity, substrate toxicity, or available free energy. The first evolved archaebacterial and eubacterial species appear to have been anaerobes adapted to high temperatures. Thermoanaerobes and their stable enzymes have served as model systems for basic and applied studies of microbial cellulose and starch degradation, methanogenesis, ethanologenesis, acetogenesis, autotrophic CO2 fixation, saccharidases, hydrogenases, and alcohol dehydrogenases. Anaerobes, unlike aerobes, appear to have evolved more energy-conserving mechanisms for physiological adaptation to environmental stresses such as novel enzyme activities and stabilities and novel membrane lipid compositions and functions. Anaerobic syntrophs do not have similar aerobic bacterial counterparts. The metabolic end products of syntrophs are potent thermodynamic inhibitors of energy conservation mechanisms, and they require coordinated consumption by a second partner organism for species growth. Anaerobes adapted to environmental stresses and their enzymes have biotechnological applications in organic waste treatment systems and chemical and fuel production systems based on biomass-derived substrates or syngas. These kinds of anaerobes have only recently been examined by biologists, and considerably more study is required before they are fully appreciated by science and technology. Images PMID:8336675

Occurrence of tributyltin (TBT)-resistant bacteria is not related to TBT pollution in Mekong River and coastal sediment: with a hypothesis of selective pressure from suspended solid.

PubMed

Suehiro, Fujiyo; Mochizuki, Hiroko; Nakamura, Shinji; Iwata, Hisato; Kobayashi, Takeshi; Tanabe, Shinsuke; Fujimori, Yoshifumi; Nishimura, Fumitake; Tuyen, Bui Cach; Tana, Touch Seang; Suzuki, Satoru

2007-07-01

Tributyltin (TBT) is organotin compound that is toxic to aquatic life ranging from bacteria to mammals. This study examined the concentration of TBT in sediment from and near the Mekong River and the distribution of TBT-resistant bacteria. TBT concentrations ranged from <2.4 to 2.4 ng/g (dry wt) in river sediment and <2.4-15 ng g(-1) (dry wt) in harbor sediment. Viable count of total bacteria ranged from 2.0 x 10(4) to 1.4 x 10(7)cfu/g, and counts of TBT-resistant bacteria ranged <1.0 x 10(2) to 2.5 x 10(4)cfu/g. The estimated occurrence rate of TBT-resistant bacteria ranged from <0.01 to 34% and was highest in upstream sites in Cambodia. The occurrences of TBT in the sediment and of TBT-resistant bacteria were unrelated, and chemicals other than TBT might induce TBT resistance. TBT-resistant bacteria were more abundant in the dry season than in the rainy season. Differences in the selection process of TBT-resistant bacteria between dry and rainy seasons were examined using an advection-diffusion model of a suspended solid (SS) that conveys chemicals. The estimated dilution-diffusion time over a distance of 120 km downstream from a release site was 20 days during dry season and 5 days during rainy season, suggesting that bacteria at the sediment surface could be exposed to SS for longer periods during dry season.

Pawtucket R.I. Group Selected for EPA Environmental Workforce Development and Job Training Program Grant

EPA Pesticide Factsheets

Groundwork Rhode Island, a Pawtucket-based organization, was one of 17 groups selected today by the U.S. Environmental Protection Agency (EPA) to share $3.3 million to operate environmental job training programs for local citizens.

Isolation and characterization of biosurfactant production under extreme environmental conditions by alkali-halo-thermophilic bacteria from Saudi Arabia

PubMed Central

Elazzazy, Ahmed M.; Abdelmoneim, T.S.; Almaghrabi, O.A.

2014-01-01

Twenty three morphologically distinct microbial colonies were isolated from soil and sea water samples, which were collected from Jeddah region, Saudi Arabia for screening of the most potent biosurfactant strains. The isolated bacteria were selected by using different methods as drop collapse test, oil displacement test, blue agar test, blood hemolysis test, emulsification activity and surface tension. The results showed that the ability of Virgibacillus salarius to grow and reduce surface tension under a wide range of pH, salinities and temperatures gives bacteria isolate an advantage in many applications such as pharmaceutical, cosmetics, food industries and bioremediation in marine environment. The biosurfactant production by V. salarius decreased surface tension and emulsifying activity (30 mN/m and 80%, respectively). In addition to reducing the production cost of biosurfactants by tested several plant-derived oils such as jatropha oil, castor oils, jojoba oil, canola oil and cottonseed oil. In this respect the feasibility to reusing old frying oil of sunflower for production rhamnolipids and sophorolipids, their use that lead to solve many ecological and industrial problems. PMID:26150754

Isolation and characterization of biosurfactant production under extreme environmental conditions by alkali-halo-thermophilic bacteria from Saudi Arabia.

PubMed

Elazzazy, Ahmed M; Abdelmoneim, T S; Almaghrabi, O A

2015-07-01

Twenty three morphologically distinct microbial colonies were isolated from soil and sea water samples, which were collected from Jeddah region, Saudi Arabia for screening of the most potent biosurfactant strains. The isolated bacteria were selected by using different methods as drop collapse test, oil displacement test, blue agar test, blood hemolysis test, emulsification activity and surface tension. The results showed that the ability of Virgibacillus salarius to grow and reduce surface tension under a wide range of pH, salinities and temperatures gives bacteria isolate an advantage in many applications such as pharmaceutical, cosmetics, food industries and bioremediation in marine environment. The biosurfactant production by V. salarius decreased surface tension and emulsifying activity (30 mN/m and 80%, respectively). In addition to reducing the production cost of biosurfactants by tested several plant-derived oils such as jatropha oil, castor oils, jojoba oil, canola oil and cottonseed oil. In this respect the feasibility to reusing old frying oil of sunflower for production rhamnolipids and sophorolipids, their use that lead to solve many ecological and industrial problems.

Quantitative and Qualitative Analysis of Bacteria in Er(III) Solution by Thin-Film Magnetopheresis

PubMed Central

Zborowski, Maciej; Tada, Yoko; Malchesky, Paul S.; Hall, Geraldine S.

1993-01-01

Magnetic deposition, quantitation, and identification of bacteria reacting with the paramagnetic trivalent lanthanide ion, Er3+, was evaluated. The magnetic deposition method was dubbed thin-film magnetopheresis. The optimization of the magnetic deposition protocol was accomplished with Escherichia coli as a model organism in 150 mM NaCl and 5 mM ErCl3 solution. Three gram-positive bacteria, Staphylococcus epidermidis, Staphylococcus saprophyticus, and Enterococcus faecalis, and four gram-negative bacteria, E. coli, Pseudomonas aeruginosa, Proteus mirabilis, and Klebsiella pneumoniae, were subsequently investigated. Quantitative analysis consisted of the microscopic cell count and a scattered-light scanning of the magnetically deposited material aided by the computer data acquisition system. Qualitative analysis consisted of Gram stain differentiation and fluorescein isothiocyanate staining in combination with selected antisera against specific types of bacteria on the solid substrate. The magnetic deposition protocol allowed quantitative detection of E. coli down to the concentration of 105 CFU ml-1, significant in clinical diagnosis applications such as urinary tract infections. Er3+ did not interfere with the typical appearance of the Gram-stained bacteria nor with the antigen recognition by the antibody in the immunohistological evaluations. Indirect antiserum-fluorescein isothiocyanate labelling correctly revealed the presence of E. faecalis and P. aeruginosa in the magnetically deposited material obtained from the mixture of these two bacterial species. On average, the reaction of gram-positive organisms was significantly stronger to the magnetic field in the presence of Er3+ than the reaction of gram-negative organisms. The thin-film magnetophoresis offers promise as a rapid method for quantitative and qualitative analysis of bacteria in solutions such as urine or environmental water. Images PMID:16348916

Bacteria interface pickering emulsions stabilized by self-assembled bacteria-chitosan network.

PubMed

Wongkongkatep, Pravit; Manopwisedjaroen, Khajohnpong; Tiposoth, Perapon; Archakunakorn, Somwit; Pongtharangkul, Thunyarat; Suphantharika, Manop; Honda, Kohsuke; Hamachi, Itaru; Wongkongkatep, Jirarut

2012-04-03

An oil-in-water Pickering emulsion stabilized by biobased material based on a bacteria-chitosan network (BCN) was developed for the first time in this study. The formation of self-assembled BCN was possible due to the electrostatic interaction between negatively charged bacterial cells and polycationic chitosan. The BCN was proven to stabilize the tetradecane/water interface, promoting formation of highly stable oil-in-water emulsion (o/w emulsion). We characterized and visualized the BCN stabilized o/w emulsions by scanning electron microscopy (SEM) and laser scanning confocal microscopy (LSCM). Due to the sustainability and low environmental impact of chitosan, the BCN-based emulsions open up opportunities for the development of an environmental friendly new interface material as well as the novel type of microreactor utilizing bacterial cells network.

Changes in Attitudes Toward Environmental Education and Selected Teaching Behaviors of Teachers Participating in Environmental Education Workshops.

ERIC Educational Resources Information Center

Myer, Teresa A.

This study examined four teacher in-service environmental education programs to: (1) suggest a workable evaluative model for such programs; (2) assess their content with respect to stated activities and objectives; and (3) determine whether or not the experiences correlated with changes in selected teaching behaviors. The research design included…

Dielectrophoretic sample preparation for environmental monitoring of microorganisms: Soil particle removal.

PubMed

Fatoyinbo, Henry O; McDonnell, Martin C; Hughes, Michael P

2014-07-01

Detection of pathogens from environmental samples is often hampered by sensors interacting with environmental particles such as soot, pollen, or environmental dust such as soil or clay. These particles may be of similar size to the target bacterium, preventing removal by filtration, but may non-specifically bind to sensor surfaces, fouling them and causing artefactual results. In this paper, we report the selective manipulation of soil particles using an AC electrokinetic microfluidic system. Four heterogeneous soil samples (smectic clay, kaolinitic clay, peaty loam, and sandy loam) were characterised using dielectrophoresis to identify the electrical difference to a target organism. A flow-cell device was then constructed to evaluate dielectrophoretic separation of bacteria and clay in a continous flow through mode. The average separation efficiency of the system across all soil types was found to be 68.7% with a maximal separation efficiency for kaolinitic clay at 87.6%. This represents the first attempt to separate soil particles from bacteria using dielectrophoresis and indicate that the technique shows significant promise; with appropriate system optimisation, we believe that this preliminary study represents an opportunity to develop a simple yet highly effective sample processing system.

Identification and selection of Environmental Performance Indicators for sustainable port development.

PubMed

Puig, Martí; Wooldridge, Chris; Darbra, Rosa Mari

2014-04-15

In this paper an identification and selection of Environmental Performance Indicators (EPIs) in port areas has been conducted. A comprehensive inventory of existing EPIs in use in the seaport sector has been identified for monitoring performance of operational (e.g. dust, noise, dredging, and waste), managerial (e.g. certification, compliance, and complaints) and environmental condition (e.g. air, water, sediment and ecosystems). These indicators have been filtered against specific criteria and have been assessed and evaluated by port stakeholders in order to obtain a final set of indicators suitable to be implemented at EU level. A user friendly tool has been developed specifically to assist port authorities in calculating and reporting the proposed indicators. This study has drawn on major research projects to blend academic research with input from marine professionals in order to identify, select, evaluate and validate EPIs that are acceptable and feasible to the sector, and practicable in their application and implementation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria

PubMed Central

Sabrina Pankey, M; Foxall, Randi L; Ster, Ian M; Perry, Lauren A; Schuster, Brian M; Donner, Rachel A; Coyle, Matthew; Cooper, Vaughn S; Whistler, Cheryl A

2017-01-01

Host immune and physical barriers protect against pathogens but also impede the establishment of essential symbiotic partnerships. To reveal mechanisms by which beneficial organisms adapt to circumvent host defenses, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri by colonization and growth within the light organs of the squid Euprymna scolopes. Serial squid passaging of bacteria produced eight distinct mutations in the binK sensor kinase gene, which conferred an exceptional selective advantage that could be demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion that were mediated by cell-associated matrices including symbiotic polysaccharide (Syp) and cellulose. binK variation also altered quorum sensing, raising the threshold for luminescence induction. Preexisting coordinated regulation of symbiosis traits by BinK presented an efficient solution where altered BinK function was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations. DOI: http://dx.doi.org/10.7554/eLife.24414.001 PMID:28447935

Comparison of DOT-ELISA and Standard-ELISA for Detection of the Vibrio cholerae Toxin in Culture Supernatants of Bacteria Isolated from Human and Environmental Samples.

PubMed

Meza-Lucas, Antonio; Pérez-Villagómez, María-Fernanda; Martínez-López, José-Patricio; García-Rodea, Ricardo; Martínez-Castelán, María-Guadalupe; Escobar-Gutiérrez, Alejandro; de-la-Rosa-Arana, Jorge-Luis; Villanueva-Zamudio, Altagracia

2016-09-01

A comparison of DOT-ELISA and Standard-ELISA was made for detection of Vibrio cholerae toxin in culture supernatants of bacteria isolated from human and environmental samples. A total of 293 supernatants were tested in a double blind assay. A correlation of 100 % was obtained between both techniques. The cholera toxin was found in 20 Inaba and 3 Ogawa strains. Positive samples were from seafood (17 samples), potable water (1 sample) and sewage (5 samples). The DOT-ELISA was useful as the standard-ELISA to confirm the presence of cholera toxin in the environmental samples.

Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

PubMed Central

Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

2015-01-01

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes.

PubMed

Fauteux, Lisa; Cottrell, Matthew T; Kirchman, David L; Borrego, Carles M; Garcia-Chaves, Maria Carolina; Del Giorgio, Paul A

2015-01-01

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

Bio-prospectus of cadmium bioadsorption by lactic acid bacteria to mitigate health and environmental impacts.

PubMed

Kumar, Narendra; Kumari, Vandna; Ram, Chand; Thakur, Kiran; Tomar, Sudhir Kumar

2018-02-01

Foodstuffs and water are the key sources of cadmium biomagnifiaction. The available strategies to mitigate this problem are unproductive and expensive for practical large-scale use. Biological decontamination of metals through environmental microbes has been known since long time, whereas lactic acid bacteria (LAB) have not been extensively studied for this purpose. The LAB are known for maintaining homeostasis and suppression of pathogens in humans and animals. They also play a vital role in bioremediation of certain heavy metals. Recently in-vivo research findings strongly complement the in-vitro results in relation to decreased total body cadmium burden in animal model. This review summarizes the currently available information on impact of toxic metal (Cd) on human and animal health as well as cadmium sequestration through microbes placed broadly, whereas preeminent attention grabbed on LAB-cadmium interaction to explore their possible role in bioremediation of cadmium from foods and environment to safeguard human as well as environment health.

Exploitation of Endophytic Bacteria to Enhance the Phytoremediation Potential of the Wetland Helophyte Juncus acutus

PubMed Central

Syranidou, Evdokia; Christofilopoulos, Stavros; Gkavrou, Georgia; Thijs, Sofie; Weyens, Nele; Vangronsveld, Jaco; Kalogerakis, Nicolas

2016-01-01

This study investigated the potential of indigenous endophytic bacteria to improve the efficiency of the wetland helophyte Juncus acutus to deal with a mixed pollution consisting of emerging organic contaminants (EOCs) and metals. The beneficial effect of bioaugmentation with selected endophytic bacteria was more prominent in case of high contamination: most of the inoculated plants (especially those inoculated with the mixed culture) removed higher percentages of organics and metals from the liquid phase in shorter times compared to the non-inoculated plants without exhibiting significant oxidative stress. When exposed to the lower concentrations, the tailored mixed culture enhanced the performance of the plants to decrease the organics and metals from the water. The composition of the root endophytic community changed in response to increased levels of contaminants while the inoculated bacteria did not modify the community structure. Our results indicate that the synergistic relationships between endophytes and the macrophyte enhance plants’ performance and may be exploited in constructed wetlands treating water with mixed contaminations. Taking into account that the concentrations of EOCs used in this study are much higher than the average contents of typical wastewaters, we can conclude that the macrophyte J. acutus with the aid of a mixed culture of tailored endophytic bacteria represents a suitable environmentally friendly alternative for treating pharmaceuticals and metals. PMID:27458433

Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids.

PubMed

Knief, Claudia; Altendorf, Karlheinz; Lipski, André

2003-11-01

A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur-oxidizing and iron-oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography-mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis-7-hexadecenoic acid (16:1 cis7) and 11-methyl hexadecanoic acid (16:0 11methyl), which are as-yet not known for any sulphide-oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide-oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.

Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

PubMed

Ding, Jing; Fu, Liang; Ding, Zhao-Wei; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

2016-01-01

The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage.

Ciprofloxacin Residues in Municipal Biosolid Compost Do Not Selectively Enrich Populations of Resistant Bacteria

PubMed Central

Youngquist, Caitlin P.; Liu, Jinxin; Orfe, Lisa H.; Jones, Stephen S.

2014-01-01

Biosolids and livestock manure are valuable high-carbon soil amendments, but they commonly contain antibiotic residues that might persist after land application. While composting reduces the concentration of extractable antibiotics in these materials, if the starting concentration is sufficiently high then remaining residues could impact microbial communities in the compost and soil to which these materials are applied. To examine this issue, ciprofloxacin was added to biosolid compost feedstock to achieve a total concentration of 19 ppm, approximately 5-fold higher than that normally detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) (1 to 3.5 ppm). This feedstock was placed into mesh bags that were buried in aerated compost bays. Once a week, a set of bags was removed and analyzed (treated and untreated, three replicates of each; 4 weeks). Addition of ciprofloxacin had no effect on the recovery of resistant bacteria at any time point (P = 0.86), and a separate bioassay showed that aqueous extractions from materials with an estimated 59 ppm ciprofloxacin had no effect on the growth of a susceptible strain of Escherichia coli (P = 0.28). Regression analysis showed that growth of the susceptible strain of E. coli can be reduced given a sufficiently high concentration of ciprofloxacin (P < 0.007), a result that is consistent with adsorption being the primary mechanism of sequestration. While analytical methods detected biologically significant concentrations of ciprofloxacin in the materials tested here, the culture-based methods were consistent with the materials having sufficient adsorptive capacity to prevent typical concentrations of ciprofloxacin residues from selectively enriching populations of resistant bacteria. PMID:25261519

A Protein Nanopore-Based Approach for Bacteria Sensing

NASA Astrophysics Data System (ADS)

Apetrei, Aurelia; Ciuca, Andrei; Lee, Jong-kook; Seo, Chang Ho; Park, Yoonkyung; Luchian, Tudor

2016-11-01

We present herein a first proof of concept demonstrating the potential of a protein nanopore-based technique for real-time detection of selected Gram-negative bacteria ( Pseudomonas aeruginosa or Escherichia coli) at a concentration of 1.2 × 108 cfu/mL. The anionic charge on the bacterial outer membrane promotes the electrophoretically driven migration of bacteria towards a single α-hemolysin nanopore isolated in a lipid bilayer, clamped at a negative electric potential, and followed by capture at the nanopore's mouth, which we found to be described according to the classical Kramers' theory. By using a specific antimicrobial peptide as a putative molecular biorecognition element for the bacteria used herein, we suggest that the detection system can combine the natural sensitivity of the nanopore-based sensing techniques with selective biological recognition, in aqueous samples, and highlight the feasibility of the nanopore-based platform to provide portable, sensitive analysis and monitoring of bacterial pathogens.

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

NASA Technical Reports Server (NTRS)

Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

1985-01-01

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

Magnetotactic bacteria in marine sediments: clues from recent cores from Brazilian Coast

NASA Astrophysics Data System (ADS)

Jovane, L.; Pellizari, V. H.; Brandini, F. P.; Braga, E. D. S.; Freitas, G. R.; Benites, M.; Rodelli, D.; Giorgioni, M.; Iacoviello, F.; Ruffato, D. G.; Lins, U.

2014-12-01

The magnetic properties (first order reversal curves, ferromagnetic resonance and decomposition of saturation remanent magnetization acquisition) of marine magnetotactic bacteria, in conjunction with geophysical, geochemical and oceanographic data from the Brazilian Coast, provide interesting insights regarding the primary productivity distribution in oceans. This finding suggests that magnetite produced by some magnetotactic bacteria retains magnetic properties in relation to the crystallographic structure of the magnetic phase produced and thus might represent a "magnetic fingerprint" for the presence of magnetotactic bacteria. The use of those magnetic properties is a non-destructive, new technology that might allow for the identification and presence of specific species or types of magnetotactic bacteria in certain environments such as sediment. We will also show some preliminary results on the biogeochemical factors that control magnetotactic bacterial populations, documenting the environment and the preservation of bacterial magnetite, which dominates the palaeomagnetic signal throughout recent sediments from Brazilian Coast. We searched for magnetotactic bacteria in order to understand the ecosystems and environmental change related to their presence in sediments. We studied magnetotactic bacterial concentration and geophysical, geochemical and oceanographic results in marine settings measuring crucially nutrients availability in the water column and in sediments, on particulate delivery to the seafloor, to understand the environmental condition that allow the presence of magnetotactic bacteria and magnetosomes in sediments.

Screening and biological characteristics of fufenozide degrading bacteria

NASA Astrophysics Data System (ADS)

Xu, Chenhao; Gong, Mingfu; Guan, Qinlan; Deng, Xia; Deng, Hongyan; Huang, Jiao

2018-04-01

Fufenozide was a novel pesticide for the control of Lepidoptera pests, which was highly toxic to silkworm. Fufenozide-contaminated soil samples were collected and the bacteria that degrade fufenozide were isolated and screened by selective medium. The colony characteristics, cell characteristics and degradation characteristics in different concentrations fufenozide of the fufenozide degrading bacteria were studied. The results indicated that seven strains of fufenozide degradeing bacteria, named as DDH01, DDH03, DDH04, DDH04, DDH05, DDH07 and DDH07 respectively, were isolated from soil contaminated with fufenozide. DDH01, DDH02, DDH04 and DDH05 of seven fufenozide degrading bacteria, was gram-positive bacteria, and DDH03, DDH06 and DDH07 was gram-negative bacteria. All of seven strains of fufenozide degrading bacteria were not spores, weeks flagella, rod-shaped bacteria. DDH06 and DDH07 had capsules, and the remaining five strains had not capsule. The colonies formed by seven strains of fufenozide degradation bacteria on beef extract peptone medium plate were milky white colonies with irregular edges, thinner lawn, smaller colony with smooth surface. The growth of 7 strains of fufenozide degradation bacteria was significantly affected by the concentration of fufenozide, All of 7 strains grown in the range from 0.00025 g/mL to 1 g/mL of 10% fufenozide suspension. DDH2 was the best among the 7 strains of fufenozide degrading bacteria grown in 10% fufenozide suspension medium.

COUNCIL FOR REGULATORY ENVIRONMENTAL MODELING (CREM) PILOT WATER QUALITY MODEL SELECTION TOOL

EPA Science Inventory

EPA's Council for Regulatory Environmental Modeling (CREM) is currently supporting the development of a pilot model selection tool that is intended to help the states and the regions implement the total maximum daily load (TMDL) program. This tool will be implemented within the ...

Thermal control of virulence factors in bacteria: A hot topic

PubMed Central

Lam, Oliver; Wheeler, Jun; Tang, Christoph M

2014-01-01

Pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. Thermal regulation can be achieved at the level of DNA, RNA or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. Understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often influenced by complex regulatory networks involving multiple transcription factors in bacteria. Here we highlight some recent insights into thermal regulation of virulence in pathogenic bacteria. We focus on bacteria which cause disease in mammalian hosts, which are at a significantly higher temperature than the outside environment. We outline the mechanisms of thermal regulation and how understanding this fundamental aspect of the biology of bacteria has implications for pathogenesis and human health. PMID:25494856

Selectively enhanced expression of prophenoloxidase activating enzyme 1 (PPAE1) at a bacteria clearance site in the white shrimp, Litopenaeus vannamei

PubMed Central

2011-01-01

Background The prophenoloxidase-activating (PO activating) system plays an important role in the crustacean innate immunity, particularly in wound healing and pathogen defense. A key member of this system is prophenoloxidase-activating enzyme (PPAE), which is the direct activator of prophenoloxidase (proPO). Despite their importance in crustacean PO activating system, the studies on them remain limited. Results Here we report on a PPAE of white shrimp, Litopenaeus vannamei (lvPPAE1), which showed 94% similarity to PPAE1 of Penaeus monodon. We found that lvPPAE1 in fluid hemocytes was down regulated after challenge by Vibrio harveyi but was enhanced when shrimps were exposed to a bacteria-rich environment for long-term. In vivo gene silence of lvPPAE1 by RNAi can significantly reduce the phenoloxidase activity (PO) and increase the susceptibility of shrimps to V. harveyi. Although lvPPAE1 was down-regulated in fluid hemocytes by Vibrio challenge, its expression increased significantly in gill after bacteria injection, which is the primary bacteria-clearance tissue. Conclusion Suppressed expression in fluid hemocytes and enhanced expression in gill indicates selectively enhanced expression at the bacterial clearance site. This is a novel feature for PPAE expression. The results will contribute to our understanding of the PO activating system in crustaceans. PMID:22208405

Biomagnetic Recovery and Bioaccumulation of Selenium Granules in Magnetotactic Bacteria.

PubMed

Tanaka, Masayoshi; Knowles, William; Brown, Rosemary; Hondow, Nicole; Arakaki, Atsushi; Baldwin, Stephen; Staniland, Sarah; Matsunaga, Tadashi

2016-07-01

Using microorganisms to remove waste and/or neutralize pollutants from contaminated water is attracting much attention due to the environmentally friendly nature of this methodology. However, cell recovery remains a bottleneck and a considerable challenge for the development of this process. Magnetotactic bacteria are a unique group of organisms that can be manipulated by an external magnetic field due to the presence of biogenic magnetite crystals formed within their cells. In this study, we demonstrated an account of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria alongside and independent of magnetite crystal biomineralization when grown in a medium containing selenium oxyanion (SeO3 (2-)). Quantitative analysis shows that magnetotactic bacteria accumulate the largest amount of target molecules (Se) per cell compared with any other previously reported nonferrous metal/metalloid. For example, 2.4 and 174 times more Se is accumulated than Te taken up into cells and Cd(2+) adsorbed onto the cell surface, respectively. Crucially, the bacteria with high levels of Se accumulation were successfully recovered with an external magnetic field. The biomagnetic recovery and the effective accumulation of target elements demonstrate the potential for application in bioremediation of polluted water. The development of a technique for effective environmental water remediation is urgently required across the globe. A biological remediation process of waste removal and/or neutralization of pollutant from contaminated water using microorganisms has great potential, but cell recovery remains a bottleneck. Magnetotactic bacteria synthesize magnetic particles within their cells, which can be recovered by a magnetic field. Herein, we report an example of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria independent of magnetic particle synthesis. The cells were able to

Race-dependent association of sulfidogenic bacteria with colorectal cancer.

PubMed

Yazici, Cemal; Wolf, Patricia G; Kim, Hajwa; Cross, Tzu-Wen L; Vermillion, Karin; Carroll, Timothy; Augustus, Gaius J; Mutlu, Ece; Tussing-Humphreys, Lisa; Braunschweig, Carol; Xicola, Rosa M; Jung, Barbara; Llor, Xavier; Ellis, Nathan A; Gaskins, H Rex

2017-11-01

Colorectal cancer (CRC) incidence is higher in African Americans (AAs) compared with non-Hispanic whites (NHWs). A diet high in animal protein and fat is an environmental risk factor for CRC development. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC. Hydrogen sulfide, produced by autochthonous sulfidogenic bacteria, triggers proinflammatory pathways and hyperproliferation, and is genotoxic. We hypothesised that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AA and NHW. Colonic biopsies from uninvolved or healthy mucosa from CRC cases and tumour-free controls were collected prospectively from five medical centres in Chicago for association studies. Sulfidogenic bacterial abundance in uninvolved colonic mucosa of AA and NHW CRC cases was compared with normal mucosa of AA and NHW controls. In addition, 16S rDNA sequencing was performed in AA cases and controls. Correlations were examined among bacterial targets, race, disease status and dietary intake. AAs harboured a greater abundance of sulfidogenic bacteria compared with NHWs regardless of disease status. Bilophila wadsworthia -specific dsrA was more abundant in AA cases than controls. Linear discriminant analysis of 16S rRNA gene sequences revealed five sulfidogenic genera that were more abundant in AA cases. Fat and protein intake and daily servings of meat were significantly higher in AAs compared with NHWs, and multiple dietary components correlated with a higher abundance of sulfidogenic bacteria. These results implicate sulfidogenic bacteria as a potential environmental risk factor contributing to CRC development in AAs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Bacteria Provide Cleanup of Oil Spills, Wastewater

NASA Technical Reports Server (NTRS)

2010-01-01

Through Small Business Innovation Research (SBIR) contracts with Marshall Space Flight Center, Micro-Bac International Inc., of Round Rock, Texas, developed a phototrophic cell for water purification in space. Inside the cell: millions of photosynthetic bacteria. Micro-Bac proceeded to commercialize the bacterial formulation it developed for the SBIR project. The formulation is now used for the remediation of wastewater systems and waste from livestock farms and food manufacturers. Strains of the SBIR-derived bacteria also feature in microbial solutions that treat environmentally damaging oil spills, such as that resulting from the catastrophic 2010 Deepwater Horizon oil rig explosion in the Gulf of Mexico.

Working with bacteria and putting bacteria to work: The biopolitics of synthetic biology for energy in the United Kingdom.

PubMed

McLeod, Carmen; Nerlich, Brigitte; Mohr, Alison

2017-08-01

The UK government has made significant investment into so called 'fourth-generation' biofuel technologies. These biofuels are based on engineering the metabolic pathways of bacteria in order to create products compatible with existing infrastructure. Bacteria play an important role in what is promoted as a potentially new biological industrial revolution, which could address some of the negative environmental legacies of the last. This article presents results from ethnographic research with synthetic biologists who are challenged with balancing the curiosity-driven and intrinsically fulfilling scientific task of working with bacteria, alongside the policy-driven task of putting bacteria to work for extrinsic economic gains. In addition, the scientists also have to balance these demands with a new research governance framework, Responsible Research and Innovation, which envisions technoscientific innovation will be responsive to societal concerns and work in collaboration with stakeholders and members of the public. Major themes emerging from the ethnographic research revolve around stewardship, care, responsibility and agency. An overall conflict surfaces between individual agents assuming responsibility for 'stewarding' bacteria, against funding systems and structures imposing responsibility for economic growth. We discuss these findings against the theoretical backdrop of a new concept of 'energopolitics' and an anthropology of ethics and responsibility.

How long can culturable bacteria and total DNA persist in environmental waters? The role of sunlight and solid particles.

PubMed

Gutiérrez-Cacciabue, Dolores; Cid, Alicia G; Rajal, Verónica B

2016-01-01

In this work, sunlight inactivation of two indicator bacteria in freshwater, with and without solid particles, was studied and the persistence of culturable cells and total DNA was compared. Environmental water was used to prepare two matrices, with and without solid particles, which were spiked with Escherichia coli and Enterococcus faecalis. These matrices were used to prepare microcosm bags that were placed in two containers: one exposed to sunlight and the other in the dark. During one month, samples were removed from each container and detection was done by membrane filter technique and real-time PCR. Kinetic parameters were calculated to assess sunlight effect. Indicator bacteria without solid particles exposed to sunlight suffered an immediate decay (<4h) compared with the ones which were shielded from them. In addition, the survival of both bacteria with solid particles varied depending on the situation analyzed (T99 from 3 up to 60days), being always culturable E. coli more persistent than E. faecalis. On the other side, E. faecalis DNA persisted much longer than culturable cells (T99>40h in the dark with particles). In this case active cells were more prone to sunlight than total DNA and the protective effect of solid particles was also observed. Results highlight that the effects caused by the parameters which describe the behavior of culturable microorganisms and total DNA in water are different and must be included in simulation models but without forgetting that these parameters will also depend on bacterial properties, sensitizers, composition, type, and uses of the aquatic environment under assessment. Copyright © 2015 Elsevier B.V. All rights reserved.

A general procedure to generate models for urban environmental-noise pollution using feature selection and machine learning methods.

PubMed

Torija, Antonio J; Ruiz, Diego P

2015-02-01

The prediction of environmental noise in urban environments requires the solution of a complex and non-linear problem, since there are complex relationships among the multitude of variables involved in the characterization and modelling of environmental noise and environmental-noise magnitudes. Moreover, the inclusion of the great spatial heterogeneity characteristic of urban environments seems to be essential in order to achieve an accurate environmental-noise prediction in cities. This problem is addressed in this paper, where a procedure based on feature-selection techniques and machine-learning regression methods is proposed and applied to this environmental problem. Three machine-learning regression methods, which are considered very robust in solving non-linear problems, are used to estimate the energy-equivalent sound-pressure level descriptor (LAeq). These three methods are: (i) multilayer perceptron (MLP), (ii) sequential minimal optimisation (SMO), and (iii) Gaussian processes for regression (GPR). In addition, because of the high number of input variables involved in environmental-noise modelling and estimation in urban environments, which make LAeq prediction models quite complex and costly in terms of time and resources for application to real situations, three different techniques are used to approach feature selection or data reduction. The feature-selection techniques used are: (i) correlation-based feature-subset selection (CFS), (ii) wrapper for feature-subset selection (WFS), and the data reduction technique is principal-component analysis (PCA). The subsequent analysis leads to a proposal of different schemes, depending on the needs regarding data collection and accuracy. The use of WFS as the feature-selection technique with the implementation of SMO or GPR as regression algorithm provides the best LAeq estimation (R(2)=0.94 and mean absolute error (MAE)=1.14-1.16 dB(A)). Copyright © 2014 Elsevier B.V. All rights reserved.

Use of strategic environmental assessment in the site selection process for a radioactive waste disposal facility in Slovenia.

PubMed

Dermol, Urška; Kontić, Branko

2011-01-01

The benefits of strategic environmental considerations in the process of siting a repository for low- and intermediate-level radioactive waste (LILW) are presented. The benefits have been explored by analyzing differences between the two site selection processes. One is a so-called official site selection process, which is implemented by the Agency for radwaste management (ARAO); the other is an optimization process suggested by experts working in the area of environmental impact assessment (EIA) and land-use (spatial) planning. The criteria on which the comparison of the results of the two site selection processes has been based are spatial organization, environmental impact, safety in terms of potential exposure of the population to radioactivity released from the repository, and feasibility of the repository from the technical, financial/economic and social point of view (the latter relates to consent by the local community for siting the repository). The site selection processes have been compared with the support of the decision expert system named DEX. The results of the comparison indicate that the sites selected by ARAO meet fewer suitability criteria than those identified by applying strategic environmental considerations in the framework of the optimization process. This result stands when taking into account spatial, environmental, safety and technical feasibility points of view. Acceptability of a site by a local community could not have been tested, since the formal site selection process has not yet been concluded; this remains as an uncertain and open point of the comparison. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effects of environmental variables on invasive amphibian activity: Using model selection on quantiles for counts

USGS Publications Warehouse

Muller, Benjamin J.; Cade, Brian S.; Schwarzkoph, Lin

2018-01-01

Many different factors influence animal activity. Often, the value of an environmental variable may influence significantly the upper or lower tails of the activity distribution. For describing relationships with heterogeneous boundaries, quantile regressions predict a quantile of the conditional distribution of the dependent variable. A quantile count model extends linear quantile regression methods to discrete response variables, and is useful if activity is quantified by trapping, where there may be many tied (equal) values in the activity distribution, over a small range of discrete values. Additionally, different environmental variables in combination may have synergistic or antagonistic effects on activity, so examining their effects together, in a modeling framework, is a useful approach. Thus, model selection on quantile counts can be used to determine the relative importance of different variables in determining activity, across the entire distribution of capture results. We conducted model selection on quantile count models to describe the factors affecting activity (numbers of captures) of cane toads (Rhinella marina) in response to several environmental variables (humidity, temperature, rainfall, wind speed, and moon luminosity) over eleven months of trapping. Environmental effects on activity are understudied in this pest animal. In the dry season, model selection on quantile count models suggested that rainfall positively affected activity, especially near the lower tails of the activity distribution. In the wet season, wind speed limited activity near the maximum of the distribution, while minimum activity increased with minimum temperature. This statistical methodology allowed us to explore, in depth, how environmental factors influenced activity across the entire distribution, and is applicable to any survey or trapping regime, in which environmental variables affect activity.

Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations.

PubMed

van der Ha, David; Vanwonterghem, Inka; Hoefman, Sven; De Vos, Paul; Boon, Nico

2013-03-01

Due to the increasing atmospheric concentration of the greenhouse gas methane, more knowledge is needed on the management of methanotrophic communities. While most studies have focused on the characteristics of the methane-oxidizing bacteria (MOB), less is known about their interactions with the associated heterotrophs. Interpretative tools based on denaturing gradient gel electrophoresis allowed to evaluate the influence of copper-an important enzymatic regulator for MOB-on the activity and composition of the bacterial community. Over 30 days, enrichments with 0.1, 1.0 and 10 μM Cu(2+) respectively, showed comparable methane oxidation activities. The different copper concentrations did not create major shifts in the methanotrophic communities, as a Methylomonas sp. was able to establish dominance at all different copper concentrations by switching between both known methane monooxygenases. The associated heterotrophic communities showed continuous shifts, but over time all cultures evolved to a comparable composition, independent of the copper concentration. This indicates that the MOB selected for certain heterotrophs, possibly fulfilling vital processes such as removal of toxic compounds. The presence of a large heterotrophic food web indirectly depending on methane as sole carbon and energy source was confirmed by a clone library wherein MOB only formed a minority of the identified species.

Selected historic agricultural data important to environmental quality in the United States

USGS Publications Warehouse

Grey, Katia M.; Capel, Paul D.; Baker, Nancy T.; Thelin, Gail P.

2012-01-01

This report and the accompanying tables summarize some of the important changes in American agriculture in the form of a timeline and a compilation of selected annual time-series data that can be broadly related to environmental quality. Although these changes have been beneficial for increasing agricultural production, some of them have resulted in environmental concerns. The agriculture timeline is divided into four categories (1) crop and animal changes, (2) mechanical changes, (3) biological and chemical changes, and (4) regulatory and societal changes. The timeline attempts to compile events that have had a lasting impact on agriculture in the United States. The events and data presented in this report may help to improve the connections between agricultural activist and environmental concerns.

Plant-bacteria partnerships for the remediation of persistent organic pollutants.

PubMed

Arslan, Muhammad; Imran, Asma; Khan, Qaiser Mahmood; Afzal, Muhammad

2017-02-01

High toxicity, bioaccumulation factor and widespread dispersal of persistent organic pollutants (POPs) cause environmental and human health hazards. The combined use of plants and bacteria is a promising approach for the remediation of soil and water contaminated with POPs. Plants provide residency and nutrients to their associated rhizosphere and endophytic bacteria. In return, the bacteria support plant growth by the degradation and detoxification of POPs. Moreover, they improve plant growth and health due to their innate plant growth-promoting mechanisms. This review provides a critical view of factors that affect absorption and translocation of POPs in plants and the limitations that plant have to deal with during the remediation of POPs. Moreover, the synergistic effects of plant-bacteria interactions in the phytoremediation of organic pollutants with special reference to POPs are discussed.

A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria.

PubMed

Winans, Nathan J; Walter, Alec; Chouaia, Bessem; Chaston, John M; Douglas, Angela E; Newell, Peter D

2017-09-01

Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two habitat types are ecologically and evolutionarily distinct is largely unknown. This study investigated the scale and pattern of genetic differentiation between bacteria of the family Acetobacteraceae isolated from the guts of Drosophila fruit flies, plant material and industrial fermentations. Genome-scale analysis of the phylogenetic relationships and predicted functions was conducted on 44 Acetobacteraceae isolates, including newly sequenced genomes from 18 isolates from wild and laboratory Drosophila. Isolates from the external environment and Drosophila could not be assigned to distinct phylogenetic groups, nor are their genomes enriched for any different sets of genes or category of predicted gene functions. In contrast, analysis of bacteria from laboratory Drosophila showed they were genetically distinct in their universal capacity to degrade uric acid (a major nitrogenous waste product of Drosophila) and absence of flagellar motility, while these traits vary among wild Drosophila isolates. Analysis of the competitive fitness of Acetobacter discordant for these traits revealed a significant fitness deficit for bacteria that cannot degrade uric acid in culture with Drosophila. We propose that, for wild populations, frequent cycling of Acetobacter between Drosophila and the external environment prevents genetic differentiation by maintaining selection for traits adaptive in both the gut and external habitats. However, laboratory isolates bear the signs of adaptation to persistent association with the Drosophila host under tightly defined environmental conditions. © 2017 John Wiley & Sons Ltd.

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation.

PubMed

Almeida, Luis Gustavo de; Moraes, Luiz Alberto Beraldo de; Trigo, José Roberto; Omoto, Celso; Cônsoli, Fernando Luis

2017-01-01

The exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized the gut microbiota associated with insect-resistant lines carry pesticide degrading bacteria, and predicted they carry bacteria selected to degrade pesticides they were resistant to. We isolated and accessed the pesticide-degrading capacity of gut bacteria from the gut of fifth instars of Spodoptera frugiperda strains resistant to lambda-cyhalothrin, deltamethrin, chlorpyrifos ethyl, spinosad and lufenuron, using insecticide-selective media. Sixteen isolates belonging to 10 phylotypes were obtained, from which four were also associated with the susceptible strain. However, growth of gut bacteria associated with larvae from the susceptible strain was not obtained in any of the insecticide-based selective media tested. Growth of isolates was affected by the concentration of insecticides in the media, and all grew well up to 40 μg/ml. The insecticide-degrading capacity of selected isolates was assessed by GC or LC-MS/MS analyses. In conclusion, resistant strains of S. frugiperda are an excellent reservoir of insecticide-degrading bacteria with bioremediation potential. Moreover, gut-associated bacteria are subjected to the selection pressure imposed by insecticides on their hosts and may influence the metabolization of pesticides in insects.

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation

PubMed Central

de Almeida, Luis Gustavo; de Moraes, Luiz Alberto Beraldo; Trigo, José Roberto; Omoto, Celso

2017-01-01

The exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized the gut microbiota associated with insect-resistant lines carry pesticide degrading bacteria, and predicted they carry bacteria selected to degrade pesticides they were resistant to. We isolated and accessed the pesticide-degrading capacity of gut bacteria from the gut of fifth instars of Spodoptera frugiperda strains resistant to lambda-cyhalothrin, deltamethrin, chlorpyrifos ethyl, spinosad and lufenuron, using insecticide-selective media. Sixteen isolates belonging to 10 phylotypes were obtained, from which four were also associated with the susceptible strain. However, growth of gut bacteria associated with larvae from the susceptible strain was not obtained in any of the insecticide-based selective media tested. Growth of isolates was affected by the concentration of insecticides in the media, and all grew well up to 40 μg/ml. The insecticide-degrading capacity of selected isolates was assessed by GC or LC-MS/MS analyses. In conclusion, resistant strains of S. frugiperda are an excellent reservoir of insecticide-degrading bacteria with bioremediation potential. Moreover, gut-associated bacteria are subjected to the selection pressure imposed by insecticides on their hosts and may influence the metabolization of pesticides in insects. PMID:28358907

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE PAGES

Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...

2017-08-04

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justice, N. B.; Sczesnak, A.; Hazen, T. C.

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow.

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations ( F ST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a , a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

Characterization of Integrons and Sulfonamide Resistance Genes among Bacteria from Drinking Water Distribution Systems in Southwestern Nigeria.

PubMed

Adesoji, Ayodele T; Ogunjobi, Adeniyi A; Olatoye, Isaac O

2017-01-01

The emergence of antibiotic resistance among pathogenic bacteria in clinical and environmental settings is a global problem. Many antibiotic resistance genes are located on mobile genetic elements such as plasmids and integrons, enabling their transfer among a variety of bacterial species. Water distribution systems may be reservoirs for the spread of antibiotic resistance. Bacteria isolated from raw, treated, and municipal tap water samples from selected water distribution systems in south-western Nigeria were investigated using the point inoculation method with seeded antibiotics, PCR amplification, and sequencing for the determination of bacterial resistance profiles and class 1/2 integrase genes and gene cassettes, respectively. sul1,sul2, and sul3 were detected in 21.6, 27.8, and 0% of the isolates, respectively (n = 162). Class 1 and class 2 integrons were detected in 21.42 and 3.6% of the isolates, respectively (n = 168). Genes encoding resistance to aminoglycosides (aadA2, aadA1, and aadB), trimethoprim (dfrA15, dfr7, and dfrA1), and sulfonamide (sul1) were detected among bacteria with class 1 integrons, while genes that encodes resistance to strepthothricin (sat2) and trimethoprim (dfrA15) were detected among bacteria with class 2 integrons. Bacteria from these water samples are a potential reservoir of multidrug-resistant traits including sul genes and mobile resistance elements, i.e. the integrase gene. © 2016 S. Karger AG, Basel.

Basic Information for EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM)

EPA Pesticide Factsheets

Contains basic information on the role and origins of the Selected Analytical Methods including the formation of the Homeland Security Laboratory Capacity Work Group and the Environmental Evaluation Analytical Process Roadmap for Homeland Security Events

Airborne bacteria in the atmosphere: Presence, purpose, and potential

NASA Astrophysics Data System (ADS)

Smets, Wenke; Moretti, Serena; Denys, Siegfried; Lebeer, Sarah

2016-08-01

Numerous recent studies have highlighted that the types of bacteria present in the atmosphere often show predictable patterns across space and time. These patterns can be driven by differences in bacterial sources of the atmosphere and a wide range of environmental factors, including UV intensity, precipitation events, and humidity. The abundance of certain bacterial taxa is of interest, not only for their ability to mediate a range of chemical and physical processes in the atmosphere, such as cloud formation and ice nucleation, but also for their implications -both beneficial and detrimental-for human health. Consequently, the widespread importance of airborne bacteria has stimulated the search for their applicability. Improving air quality, modelling the dispersal of airborne bacteria (e.g. pathogens) and biotechnological purposes are already being explored. Nevertheless, many technological challenges still need to be overcome to fully understand the roles of airborne bacteria in our health and global ecosystems.

Implementing sponge physiological and genomic information to enhance the diversity of its culturable associated bacteria.

PubMed

Lavy, Adi; Keren, Ray; Haber, Markus; Schwartz, Inbar; Ilan, Micha

2014-02-01

In recent years new approaches have emerged for culturing marine environmental bacteria. They include the use of novel culture media, sometimes with very low-nutrient content, and a variety of growth conditions such as temperature, oxygen levels, and different atmospheric pressures. These approaches have largely been neglected when it came to the cultivation of sponge-associated bacteria. Here, we used physiological and environmental conditions to reflect the environment of sponge-associated bacteria along with genomic data of the prominent sponge symbiont Candidatus Poribacteria sp. WGA-4E, to cultivate bacteria from the Red Sea sponge Theonella swinhoei. Designing culturing conditions to fit the metabolic needs of major bacterial taxa present in the sponge, through a combined use of diverse culture media compositions with aerobic and microaerophilic states, and addition of antibiotics, yielded higher diversity of the cultured bacteria and led to the isolation of novel sponge-associated and sponge-specific bacteria. In this work, 59 OTUs of six phyla were isolated. Of these, 22 have no close type strains at the species level (< 97% similarity of 16S rRNA gene sequence), representing novel bacteria species, and some are probably new genera and even families. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Abundance and Genetic Diversity of Aerobic Anoxygenic Phototrophic Bacteria of Coastal Regions of the Pacific Ocean

PubMed Central

Ritchie, Anna E.

2012-01-01

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by the pufM gene biomarker, are most abundant near shore and in areas with high chlorophyll or Synechococcus abundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and uncultured pufM gene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities. PMID:22307290

Bacteria-based concrete: from concept to market

NASA Astrophysics Data System (ADS)

Wiktor, V.; Jonkers, H. M.

2016-08-01

The concept of self-healing concrete—a concrete which can autonomously repair itself after crack formation, with no or limited human intervention—has received a lot of attention over the past 10 years as it could help structures to last longer and at a lower maintenance cost. This paper gives an overview on the key aspects and recent advances in the development of the bacteria-based self-healing concrete developed at the University of Technology of Delft (The Netherlands). Research started with the screening and selection of concrete compatible bacteria and nutrients. Several types of encapsulated bacteria and nutrients have been developed and tested. The functionality of these healing agents was demonstrated by showing metabolic activity of activated bacterial spores by oxygen consumption measurements and by regain of material functionality in form of regain of water tightness. Besides development of bacteria-based self-healing concrete, a bacteria-based repair mortar and liquid system were developed for the treatment of aged concrete structures. Field trials have been carried out with either type of bacteria-based systems and the promising results have led to a spinoff company Basilisk Self-Healing Concrete with the aim to further develop these systems and bring them to the market.

A selective medium for the isolation of Microbacterium species in oral cavities.

PubMed

Tsuzukibashi, Osamu; Uchibori, Satoshi; Kobayashi, Taira; Saito, Masanori; Umezawa, Koji; Ohta, Mitsuhiro; Shinozaki-Kuwahara, Noriko

2015-09-01

The genus Microbacterium has been isolated from the environment, dairy goods, and human clinical specimens. Although, in our previous studies, some Microbacterium species were infrequently detected in oral samples collected from humans, there is currently no report that these organisms, which are capable of causing serious systemic infections, were isolated from the human oral cavity. The aim of the present study was to develop a selective medium to isolate the representative Microbacterium species most frequently detected in human clinical specimens, and reveal the distribution of individual Microbacterium species in the oral cavity. The growth recoveries of representative Microbacterium species on the selective medium, designated as MSM, were sufficient. Moreover, the growth of other representative oral bacteria was markedly inhibited on the selective medium. The proportion of Microbacterium species in the saliva samples of 60 subjects, 20 of whom were removable denture wearers, was then examined. The proportion of these organisms was also examined in environmental samples obtained by swabbing 20 washstands. PCR primers were designed for representative Microbacterium species. The genus Microbacterium was detected in 45% of the saliva and denture plaque samples collected from the twenty removable denture wearers, but was absent in the saliva of the forty non-denture wearers. On the other hand, these organisms were detected in all environmental samples. The genus Microbacterium accounted for 0.00003%, 0.0001%, and 12.6% of the total cultivable bacteria number on the BHI medium in the saliva and denture plaque samples of removable denture wearers and in the environmental samples, respectively. The most predominant Microbacterium species in all positive samples was Microbacterium oxydans. These results indicated that the genus Microbacterium was not a part of the normal flora in the human oral cavity, except for subjects wearing dentures that were contaminated by the

Reducing the environmental impact of poultry breeding by genetic selection.

PubMed

de Verdal, H; Mignon-Grasteau, S; Bastianelli, D; Même, N; Le Bihan-Duval, E; Narcy, A

2013-02-01

Improving the sustainability of poultry production involves limiting its environmental impact and maintaining effectiveness. It has recently been shown that genetic selection on the ability of chickens to digest wheat at 23 d of age can decrease chicken excretion without decreasing BW at this age. The aim of this study was to check whether selection on digestibility modified excretion and growth performance over the whole production cycle. The 2 divergent lines selected for high (D+) and low (D-) apparent metabolizable energy corrected for 0 N balance (AMEn) values were compared with a reference line used at the beginning of the selection experiment (RL) to evaluate the potential excretion improvement that could be expected with such selection. These 3 lines were therefore compared for growth and excretion (raw and relative to feed intake, fresh and dry excreta weights, and moisture content of excreta) from 4 to 53 d. Between 4 and 7 d, 17 and 21 d, and 49 and 53 d, AMEn and N and P excretion rates were also compared between the 3 lines. Furthermore, body composition (breast meat and abdominal fat yields), bone breaking strength, and meat quality traits (lightness, redness, yellowness, and ultimate pH) were compared between lines at 53 d. Over the whole rearing period, D+ birds excreted significantly less fresh and dry excreta (-56 and -61%) than D- and RL birds (-6 and -26%). Similarly, N and P excretion rates of D+ birds were 13% to 30% less than those of D- birds and 12% to 19% less than RL birds, depending on age. These excretion differences may be related to the differential development of the gastrointestinal tract. Differences between lines were already present at 7 d for relative gizzard weight and the weight of the upper to the lower part of the gastrointestinal tract ratio. Anatomic differences were maximum at 23 d for all traits except for relative weight of the duodenum. At slaughter age, BW, breast and fat yields, and meat color did not differ between

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Pyle, B. H.; Lisle, J. T.; Broadaway, S. C.

1999-01-01

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between

Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model.

PubMed

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Jeong, Jaehak; Pachepsky, Yakov A

2018-02-15

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export. Bacteria survival in manure is simulated as a two-stage process separately for each manure application event. In-stream microbial fate and transport processes include bacteria release from streambeds due to sediment resuspension during high flow events, active release from the streambed sediment during low flow periods, bacteria settling with sediment, and survival. Default parameter values were selected from published databases and evaluated based on field observations. The APEX model with the newly developed microbial fate and transport module was applied to simulate fate and transport of the fecal indicator bacterium Escherichia coli in the Toenepi watershed, New Zealand that was monitored for seven years. The stream network of the watershed ran through grazing lands with daily bovine waste deposition. Results show that the APEX with the bacteria module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water as affected by various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Published by Elsevier B.V.

Toxicity Evaluation of Pig Slurry Using Luminescent Bacteria and Zebrafish

PubMed Central

Chen, Wenyan; Cai, Qiang; Zhao, Yuan; Zheng, Guojuan; Liang, Yuting

2014-01-01

Biogas slurry has become a serious pollution problem and anaerobic digestion is widely applied to pig manure treatment for environmental protection and energy recovery. To evaluate environmental risk of the emission of biogas slurry, luminescent bacteria (Vibrio fischeri), larvae and embryos of zebrafish (Danio rerio) were used to detect the acute and development toxicity of digested and post-treated slurry. Then the ability of treatment process was evaluated. The results showed that digested slurry displayed strong toxicity to both zebrafish and luminescent bacteria, while the EC50 for luminescent bacteria and the LC50 for larvae were only 6.81% (v/v) and 1.95% (v/v) respectively, and embryonic development was inhibited at just 1% (v/v). Slurry still maintained a high level of toxicity although it had been treated by membrane bioreactor (MBR), while the LC50 of larvae was 75.23% (v/v) and there was a little effect on the development of embryos and V. fischeri; the results also revealed that the zebrafish larvae are more sensitive than embryos and luminescent bacteria to pig slurry. Finally, we also found the toxicity removal rate was higher than 90% after the treatment of MBR according to toxicity tests. In conclusion, further treatment should be used in pig slurry disposal or reused of final effluent. PMID:24995598

Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network.

PubMed

Sikkink, Kristin L; Reynolds, Rose M; Cresko, William A; Phillips, Patrick C

2015-05-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. © 2015 The Author(s).

ENVIRONMENTALLY INDUCED CHANGES IN CORRELATED RESPONSES TO SELECTION REVEAL VARIABLE PLEIOTROPY ACROSS A COMPLEX GENETIC NETWORK

PubMed Central

Sikkink, Kristin L.; Reynolds, Rose M.; Cresko, William A.; Phillips, Patrick C.

2017-01-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. PMID:25809411

A selective and sensitive D-xylose electrochemical biosensor based on xylose dehydrogenase displayed on the surface of bacteria and multi-walled carbon nanotubes modified electrode.

PubMed

Li, Liang; Liang, Bo; Shi, Jianguo; Li, Feng; Mascini, Marco; Liu, Aihua

2012-03-15

A novel Nafion/bacteria-displaying xylose dehydrogenase (XDH)/multi-walled carbon nanotubes (MWNTs) composite film-modified electrode was fabricated and applied for the sensitive and selective determination of d-xylose (INS 967), where the XDH-displayed bacteria (XDH-bacteria) was prepared using a newly identified ice nucleation protein from Pseudomonas borealis DL7 as an anchoring motif. The XDH-displayed bacteria can be used directly, eliminating further enzyme-extraction and purification, thus greatly improved the stability of the enzyme. The optimal conditions for the construction of biosensor were established: homogeneous Nafion-MWNTs composite dispersion (10 μL) was cast onto the inverted glassy carbon electrode, followed by casting 10-μL of XDH-bacteria aqueous solution to stand overnight to dry, then a 5-μL of Nafion solution (0.05 wt%) is syringed to the electrode surface. The bacteria-displaying XDH could catalyze the oxidization of xylose to xylonolactone with coenzyme NAD(+) in 0.1M PBS buffer (pH7.4), where NAD(+) (nicotinamide adenine dinucleotide) is reduced to NADH (the reduced form of nicotinamide adenine dinucleotide). The resultant NADH is further electrocatalytically oxidized by MWNTs on the electrode, resulting in an obvious oxidation peak around 0.50 V (vs. Ag/AgCl). In contrast, the bacteria-XDH-only modified electrode showed oxidation peak at higher potential of 0.7 V and less sensitivity. Therefore, the electrode/MWNTs/bacteria-XDH/Nafion exhibited good analytical performance such as long-term stability, a wide dynamic range of 0.6-100 μM and a low detection limit of 0.5 μM D-xylose (S/N=3). No interference was observed in the presence of 300-fold excess of other saccharides including D-glucose, D-fructose, D-maltose, D-galactose, D-mannose, D-sucrose, and D-cellbiose as well as 60-fold excess of L-arabinose. The proposed microbial biosensor is stable, specific, sensitive, reproducible, simple, rapid and cost-effective, which holds

Draft Environmental Impact Statement. MX Deployment Area Selection and Land Withdrawal/Acquisition DEIS. Volume IV. Part I. Environmental Consequences to the Study Regions and Operating Base Vicinities.

DTIC Science & Technology

1980-12-01

consequences such that the ecosystem will not recover at all, (7) are the consequences such that the impact may be large but the recovery process...Bswe $Vicinitoe MLWI Impact Analysis Process DEPLOYMENT AREA SELECTION AND LAND WITHDRAWAL/ ACQUISITION DISI, DEPARTMENT OF THE AmR F1ORC ’oritinax...Subtitle) S. TYPE OF REPORT & PERIOD COVEREDDraft Environmental Impact Statement-MX Deployment Area Selection-Environmental Draft-December 80 Consequences

Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments

PubMed Central

Amachi, Seigo; Kamagata, Yoichi; Kanagawa, Takahiro; Muramatsu, Yasuyuki

2001-01-01

Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here we report that a wide variety of bacteria including terrestrial and marine bacteria are capable of methylating the environmental level of iodide (0.1 μM). Of the strains tested, Rhizobium sp. strain MRCD 19 was chosen for further analysis, and it was found that the cell extract catalyzed the methylation of iodide with S-adenosyl-l-methionine as the methyl donor. These results strongly indicate that bacteria contribute to iodine transfer from the terrestrial and marine ecosystems into the atmosphere. PMID:11375186

Prevalence and persistence of potentially pathogenic and antibiotic resistant bacteria during anaerobic digestion treatment of cattle manure.

PubMed

Resende, Juliana Alves; Silva, Vânia Lúcia; de Oliveira, Tamara Lopes Rocha; de Oliveira Fortunato, Samuel; da Costa Carneiro, Jailton; Otenio, Marcelo Henrique; Diniz, Cláudio Galuppo

2014-02-01

Anaerobic digestion figures as a sustainable alternative to avoid discharge of cattle manure in the environment, which results in biogas and biofertilizer. Persistence of potentially pathogenic and drug-resistant bacteria during anaerobic digestion of cattle manure was evaluated. Selective cultures were performed for enterobacteria (ENT), non-fermenting Gram-negative rods (NFR) and Gram-positive cocci (GPC). Antimicrobial susceptibility patterns were determined and a decay of all bacterial groups was observed after 60days. Multidrug-resistant bacteria were detected both the influent and effluent. GPC, the most prevalent group was highly resistant against penicillin and levofloxacin, whereas resistance to ampicillin, ampicillin-sulbactam and chloramphenicol was frequently observed in the ENT and NFR groups. The data point out the need of discussions to better address management of biodigesters and the implementation of sanitary and microbiological safe treatments of animal manures to avoid consequences to human, animal and environmental health. Copyright © 2013 Elsevier Ltd. All rights reserved.

Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth.

PubMed

Daquigan, Ninalynn; Grim, Christopher J; White, James R; Hanes, Darcy E; Jarvis, Karen G

2016-01-01

Culture based methods are commonly employed to detect pathogens in food and environmental samples. These methods are time consuming and complex, requiring multiple non-selective and selective enrichment broths, and usually take at least 1 week to recover and identify pathogens. Improving pathogen detection in foods is a primary goal for regulatory agencies and industry. Salmonella detection in food relies on a series of culture steps in broth formulations optimized to resuscitate Salmonella and reduce the abundance of competitive bacteria. Examples of non-selective pre-enrichment broths used to isolate Salmonella from food include Lactose, Universal Pre-enrichment, BPW, and Trypticase Soy broths. Tetrathionate (TT) and Rappaport-Vassiliadis (RV) broths are employed after a 24-h non-selective enrichment to select for Salmonella and hamper the growth of competitive bacteria. In this study, we tested a new formulation of TT broth that lacks brilliant green dye and has lower levels of TT . We employed this TT broth formulation in conjunction with a 6-h non-selective pre-enrichment period and determined that Salmonella recovery was possible one day earlier than standard food culture methods. We tested the shortened culture method in different non-selective enrichment broths, enumerated Salmonella in the non-selective enrichments, and used 16S rRNA gene sequencing to determine the proportional abundances of Salmonella in the TT and RV selective enrichments. Together these data revealed that a 6-h non-selective pre-enrichment reduces the levels of competitive bacteria inoculated into the selective TT and RV broths, enabling the recovery of Salmonella 1 day earlier than standard culture enrichment methods.

Agriculture and food animals as a source of antimicrobial-resistant bacteria

PubMed Central

Economou, Vangelis; Gousia, Panagiota

2015-01-01

One of the major breakthroughs in the history of medicine is undoubtedly the discovery of antibiotics. Their use in animal husbandry and veterinary medicine has resulted in healthier and more productive farm animals, ensuring the welfare and health of both animals and humans. Unfortunately, from the first use of penicillin, the resistance countdown started to tick. Nowadays, the infections caused by antibiotic-resistant bacteria are increasing, and resistance to antibiotics is probably the major public health problem. Antibiotic use in farm animals has been criticized for contributing to the emergence of resistance. The use and misuse of antibiotics in farm animal settings as growth promoters or as nonspecific means of infection prevention and treatment has boosted antibiotic consumption and resistance among bacteria in the animal habitat. This reservoir of resistance can be transmitted directly or indirectly to humans through food consumption and direct or indirect contact. Resistant bacteria can cause serious health effects directly or via the transmission of the antibiotic resistance traits to pathogens, causing illnesses that are difficult to treat and that therefore have higher morbidity and mortality rates. In addition, the selection and proliferation of antibiotic-resistant strains can be disseminated to the environment via animal waste, enhancing the resistance reservoir that exists in the environmental microbiome. In this review, an effort is made to highlight the various factors that contribute to the emergence of antibiotic resistance in farm animals and to provide some insights into possible solutions to this major health issue. PMID:25878509

Environmental factors influencing the development and spread of antibiotic resistance

PubMed Central

Kristiansson, Erik; Larsson, D G Joakim

2017-01-01

Abstract Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans. PMID:29069382

Anaerobic bacteria

MedlinePlus

Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Brook I. Diseases caused by non-spore-forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman-Cecil ...

Growth of saprotrophic fungi and bacteria in soil.

PubMed

Rousk, Johannes; Bååth, Erland

2011-10-01

Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A heuristic approach using multiple criteria for environmentally benign 3PLs selection

NASA Astrophysics Data System (ADS)

Kongar, Elif

2005-11-01

Maintaining competitiveness in an environment where price and quality differences between competing products are disappearing depends on the company's ability to reduce costs and supply time. Timely responses to rapidly changing market conditions require an efficient Supply Chain Management (SCM). Outsourcing logistics to third-party logistics service providers (3PLs) is one commonly used way of increasing the efficiency of logistics operations, while creating a more "core competency focused" business environment. However, this alone may not be sufficient. Due to recent environmental regulations and growing public awareness regarding environmental issues, 3PLs need to be not only efficient but also environmentally benign to maintain companies' competitiveness. Even though an efficient and environmentally benign combination of 3PLs can theoretically be obtained using exhaustive search algorithms, heuristics approaches to the selection process may be superior in terms of the computational complexity. In this paper, a hybrid approach that combines a multiple criteria Genetic Algorithm (GA) with Linear Physical Weighting Algorithm (LPPW) to be used in efficient and environmentally benign 3PLs is proposed. A numerical example is also provided to illustrate the method and the analyses.

Environmental considerations in the selection of isolation gowns: A life cycle assessment of reusable and disposable alternatives.

PubMed

Vozzola, Eric; Overcash, Michael; Griffing, Evan

2018-04-11

Isolation gowns serve a critical role in infection control by protecting healthcare workers, visitors, and patients from the transfer of microorganisms and body fluids. The decision of whether to use a reusable or disposable garment system is a selection process based on factors including sustainability, barrier effectiveness, cost, and comfort. Environmental sustainability is increasingly being used in the decision-making process. Life cycle assessment is the most comprehensive and widely used tool used to evaluate environmental performance. The environmental impacts of market-representative reusable and disposable isolation gown systems were compared using standard life cycle assessment procedures. The basis of comparison was 1,000 isolation gown uses in a healthcare setting. The scope included the manufacture, use, and end-of-life stages of the gown systems. At the healthcare facility, compared to the disposable gown system, the reusable gown system showed a 28% reduction in energy consumption, a 30% reduction in greenhouse gas emissions, a 41% reduction in blue water consumption, and a 93% reduction in solid waste generation. Selecting reusable garment systems may result in significant environmental benefits compared to selecting disposable garment systems. By selecting reusable isolation gowns, healthcare facilities can add these quantitative benefits directly to their sustainability scorecards. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Environmental Control Of A Genetic Process

NASA Technical Reports Server (NTRS)

Khosla, Chaitan; Bailey, James E.

1991-01-01

E. coli bacteria altered to contain DNA sequence encoding production of hemoglobin made to produce hemoglobin at rates decreasing with increases in concentration of oxygen in culture media. Represents amplification of part of method described in "Cloned Hemoglobin Genes Enhance Growth Of Cells" (NPO-17517). Manipulation of promoter/regulator DNA sequences opens promising new subfield of recombinant-DNA technology for environmental control of expression of selected DNA sequences. New recombinant-DNA fusion gene products, expression vectors, and nucleotide-base sequences will emerge. Likely applications include such aerobic processes as manufacture of cloned proteins and synthesis of metabolites, production of chemicals by fermentation, enzymatic degradation, treatment of wastes, brewing, and variety of oxidative chemical reactions.

Integration of non-oral bacteria into in vitro oral biofilms.

PubMed

Thurnheer, Thomas; Belibasakis, Georgios N

2015-01-01

Biofilms are polymicrobial communities that grow on surfaces in nature. Oral bacteria can spontaneously form biofilms on the surface of teeth, which may compromise the health of the teeth, or their surrounding (periodontal) tissues. While the oral bacteria exhibit high tropism for their specialized ecological niche, it is not clear if bacteria that are not part of the normal oral microbiota can efficiently colonize and grow within oral biofilms. By using an in vitro "supragingival" biofilm model of 6 oral species, this study aimed to investigate if 3 individual bacterial species that are not part of the normal oral microbiota (Eschericia coli, Staphylococcus aureus, Enterococcus faecails) and one not previously tested oral species (Aggregatibacter actinomycetemcomitans) can be incorporated into this established supragingival biofilm model. Staphylococcus aureus and A. actinomycetemcomitans were able to grow efficiently in the biofilm, without disrupting the growth of the remaining species. They localized in sparse small aggregates within the biofilm mass. Enterococcus faecalis and E. coli were both able to populate the biofilm at high numbers, and suppressed the growth of A. oris and S. mutants. Enterococcus faecalis was arranged in a chain-like conformation, whereas E. coli was densely and evenly spread throughout the biofilm mass. In conclusion, it is possible for selected species that are not part of the normal oral microbiota to be introduced into an oral biofilm, under the given experimental micro-environmental conditions. Moreover, the equilibrated incorporation of A. actinomycetemcomitans and S. aureus in this oral biofilm model could be a useful tool in the study of aggressive periodontitis and peri-implantitis, in which these organisms are involved, respectively.

Non-invasive determination of conjugative transfer of plasmids bearing antibiotic-resistance genes in biofilm-bound bacteria: effects of substrate loading and antibiotic selection

PubMed Central

Ma, Hongyan; Bryers, James D.

2012-01-01

Biofilms cause much of all human microbial infections. Attempts to eradicate biofilm-based infections rely on disinfectants and antibiotics. Unfortunately, biofilm bacteria are significantly less responsive to antibiotic stressors than their planktonic counterparts. Sublethal doses of antibiotics can actually enhance biofilm formation. Here, we have developed a non-invasive microscopic image analyses to quantify plasmid conjugation within a developing biofilm. Corroborating destructive samples were analyzed by a cultivation-independent flow cytometry analysis and a selective plate count method to cultivate transconjugants. Increases in substrate loading altered biofilm 3-D architecture and subsequently affected the frequency of plasmid conjugation (decreases at least two times) in the absence of any antibiotic selective pressure. More importantly, donor populations in biofilms exposed to a sublethal dose of kanamycin exhibited enhanced transfer efficiency of plasmids containing the kanamycin resistance gene, up to tenfold. However, when stressed with a different antibiotic, imipenem, transfer of plasmids containing the kanR+ gene was not enhanced. These preliminary results suggest biofilm bacteria “sense” antibiotics to which they are resistant, which enhances the spread of that resistance. Confocal scanning microscopy coupled with our non-invasive image analysis was able to estimate plasmid conjugative transfer efficiency either averaged over the entire biofilm landscape or locally with individual biofilm clusters. PMID:22669634

Are Uncultivated Bacteria Really Uncultivable?

PubMed Central

Puspita, Indun Dewi; Kamagata, Yoichi; Tanaka, Michiko; Asano, Kozo; Nakatsu, Cindy H.

2012-01-01

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency. PMID:23059723

Importance of lactic acid bacteria in Asian fermented foods

PubMed Central

2011-01-01

Lactic acid bacteria play important roles in various fermented foods in Asia. Besides being the main component in kimchi and other fermented foods, they are used to preserve edible food materials through fermentation of other raw-materials such as rice wine/beer, rice cakes, and fish by producing organic acids to control putrefactive microorganisms and pathogens. These bacteria also provide a selective environment favoring fermentative microorganisms and produce desirable flavors in various fermented foods. This paper discusses the role of lactic acid bacteria in various non-dairy fermented food products in Asia and their nutritional and physiological functions in the Asian diet. PMID:21995342

Selection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures.

PubMed

Zanirati, Débora Ferreira; Abatemarco, Mário; Sandes, Sávio Henrique de Cicco; Nicoli, Jacques Robert; Nunes, Álvaro Cantini; Neumann, Elisabeth

2015-04-01

Brazilian kefir is a homemade fermented beverage that is obtained by incubating milk or a brown sugar solution with kefir grains that contribute their different microbiological compositions. It is highly important to isolate and characterize microorganisms from Brazilian kefir grains to obtain starter cultures for the industrial production of a standardized commercial kefir. Thus, the present study aimed to isolate lactic acid bacteria from eight kefir grains that were propagated in milk or sugar solutions from five different locations in Brazil and to select Lactobacillus isolates based on desirable in vitro probiotic properties. One hundred eight isolates from both substrates were identified by amplified ribosomal DNA restriction analysis and/or 16S rRNA gene sequencing and were determined to belong to the following 11 species from the genera: Lactococcus, Leuconostoc, Lactobacillus (L.), and Oenococcus. Leuconostoc mesenteroides, Lactobacillus kefiri, and Lactobacillus kefiranofaciens were isolated only from milk grains, whereas Lactobacillus perolens, Lactobacillus parafarraginis, Lactobacillus diolivorans, and Oenococcus oeni were isolated exclusively from sugar water grains. When the microbial compositions of four kefir grains were evaluated with culture-independent analyses, L. kefiranofaciens was observed to predominant in milk grains, whereas Lactobacillus hilgardii was most abundant in sugar water kefir. Unfortunately, L. hilgardii was not isolated from any grain, although this bacteria was detected with a culture-independent methodology. Fifty-two isolated Lactobacilli were tested for gastric juice and bile salt tolerance, antagonism against pathogens, antimicrobial resistance, and surface hydrophobicity. Three Lactobacillus strains (L. kefiranofaciens 8U, L. diolivorans 1Z, and Lactobacillus casei 17U) could be classified as potential probiotics. In conclusion, several lactic acid bacteria that could be used in combination with yeasts as starter

Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

PubMed

Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

2015-12-01

The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

DOEpatents

Apel, William A.; Dugan, Patrick R.

1995-01-01

An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

DOEpatents

Apel, William A.; Dugan, Patrick R.

1995-04-04

An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria

DOEpatents

Ooteghem, Suellen Van

2005-09-13

A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

Functional genomics of lactic acid bacteria: from food to health

PubMed Central

2014-01-01

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health. PMID:25186768

Functional genomics of lactic acid bacteria: from food to health.

PubMed

Douillard, François P; de Vos, Willem M

2014-08-29

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

Environmental and economic evaluation of selective non-catalytic reduction of nitrogen oxides

NASA Astrophysics Data System (ADS)

Parchevskii, V. M.; Shchederkina, T. E.; Proshina, A. O.

2017-11-01

There are two groups of atmosphere protecting measures: technology (primary) and treatment (secondary). When burning high-calorie low-volatile brands of coals in the furnaces with liquid slag removal to achieve emission standards required joint use of these two methods, for example, staged combustion and selective non-catalytic reduction recovery (SNCR). For the economically intelligent combination of these two methods it is necessary to have information not only about the environmental performance of each method, but also the operating costs per unit of reduced emission. The authors of this report are made an environmental-economic analysis of SNCR on boiler Π-50P Kashirskaya power station. The obtained results about the dependence of costs from the load of the boiler and the mass emissions of nitrogen oxides then approximates into empirical formulas, is named as environmental and economic characteristics, which is suitable for downloading into controllers and other control devices for subsequent implementation of optimal control of emissions to ensure compliance with environmental regulations at the lowest cost at any load of the boiler.

Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes

NASA Astrophysics Data System (ADS)

Etayash, Hashem; Khan, M. F.; Kaur, Kamaljit; Thundat, Thomas

2016-10-01

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a concentration of single cell per μl. Trapped Escherichia coli in the microchannel shows a distinct nanomechanical response when exposed to antibiotics. This approach, which combines enrichment with three different modes of detection, can serve as a platform for the development of a portable, high-throughput device for use in the real-time detection of bacteria and their response to antibiotics.

Isolation, identification and characterization of lignin-degrading bacteria from Qinling, China.

PubMed

Yang, C-X; Wang, T; Gao, L-N; Yin, H-J; Lü, X

2017-12-01

Lignin is an aromatic heteropolymer forming a physical barrier and it is a big challenge in biomass utilization. This paper first investigated lignin-degradation bacteria from rotten wood in Qinling Mountain. Nineteen potential strains were selected and ligninolytic enzyme activities were determined over 84 h. Strains that had higher enzyme activities were selected. Further, the biodegradation of wheat straw lignin and alkali lignin was evaluated indicating that Burkholderia sp. H1 had the highest capability. It was confirmed by gel permeation chromatography and field emission scanning electron microscope that alkali lignin was depolymerized into small fragments. The degraded products were analysed using gas chromatography-mass spectrometry. The total ion chromatograph of products treated for 7 days showed the formation of aromatic compounds, an important intermediate from lignin degradation. Interestingly, they disappeared in 15 days while the aldehyde and ester compounds increased. The results suggest that the lignin-degrading bacteria are abundant in rotten wood and strain H1 has high potential to break down lignin. The diversity of lignin-degrading bacteria in Qinling Mountain is revealed. The study of Burkholderia sp. H1 expands the range of bacteria for lignin degradation and provides novel bacteria for application to lignocellulosic biomass. © 2017 The Society for Applied Microbiology.

Impedimetric detection of pathogenic Gram-positive bacteria using an antimicrobial peptide from class IIa bacteriocins.

PubMed

Etayash, Hashem; Jiang, Keren; Thundat, Thomas; Kaur, Kamaljit

2014-02-04

Real-time, label-free detection of Gram-positive bacteria with high selectivity and sensitivity is demonstrated using an interdigitated impedimetric array functionalized with naturally produced antimicrobial peptide from class IIa bacteriocins. The antimicrobial peptide, leucocin A, was chemically synthesized and covalently immobilized on interdigitated gold microelectrodes via the interaction between the C-terminal carboxylic acid of the peptide and free amines of a preattached thiolated linker. Exposing the peptide sensor to various concentrations of Gram-positive bacteria generated reproducible impedance spectra that detected peptide-bacteria interactions at a concentration of 1 cell/μL. The peptide sensor also selectively detected Listeria monocytogenes from other Gram-positive strains at a concentration of 10(3) cfu mL(-1). The study highlights that short peptide ligands from bacteriocin class offer high selectivity in bacterial detection and can be used in developing a robust, portable biosensor device to efficiently detect pathogenic Gram-positive bacteria in food samples.

Selection, validation and utility of pathogen surrogate bacteria used in food safety challenge studies: A Review

USDA-ARS?s Scientific Manuscript database

Non-pathogenic surrogate bacteria are prevalently used in a variety of food challenge studies in place of foodborne pathogens such as Listeria monocytogenes, Salmonella, Escherichia coli O157:H7, and Clostridium botulinum, due to safety and sanitary concerns. Surrogate bacteria should demonstrate si...

Selective Discrimination of Key Enzymes of Pathogenic and Nonpathogenic Bacteria on Autonomously Reporting Shape-Encoded Hydrogel Patterns.

PubMed

Jia, Zhiyuan; Sukker, Issa; Müller, Mareike; Schönherr, Holger

2018-02-14

This work reports on a new approach to rapidly and selectively detect and discriminate enzymes of pathogenic from those of nonpathogenic bacteria using a patterned autonomously reporting hydrogel on a transparent support, in which the selectivity has been encoded by the pattern shape to enable facile detection by a color change at one single wavelength. In particular, enzyme-responsive chitosan hydrogel layers that report the presence of the enzymes β-glucuronidase (β-Gus) and β-galactosidase (β-Gal), produced by the nonvirulent Escherichia coli K12 and the food-borne biosafety level 3 pathogen enterohemorrhagic E. coli, respectively, via the blue color of an indigo dye were patterned by two complementary strategies. The comparison of the functionalization of patterned chitosan patches on a solid support with two chromogenic substrates on one hand and the area-selective conjugation of the substrates on the other hand showed that the two characteristic enzymes could indeed be rapidly and selectively discriminated. The limits of detection of the highly stable sensing layers for an observation time of 60 min using a spectrophotometer correspond to enzyme concentrations of β-Gus and β-Gal of ≤5 and ≤3 nM, respectively, and to ≤62 and ≤33 nM for bare eye detection in nonoptimized sensor patches. These results confirm the applicability of this approach, which is compatible with the simple measurement of optical density at one single wavelength only as well as with parallel, multiplexed detection, to differentiate the enzymes secreted by a highly pathogenic E. coli from a nonpathogenic E. coli on the basis of specifically secreted enzymes. Hence, a general approach for the rapid and selective detection of enzymes of different bacterial species for potential applications in food safety as well as point-of-care microbiological diagnostics is described.

Plant-microbe interactions driven by exometabolite preferences of rhizosphere bacteria

NASA Astrophysics Data System (ADS)

Zhalnina, K.; Louie, K. B.; Mansoori, N.; Hao, Z.; Gao, J.; Cho, H. J.; Karaoz, U.; Loqué, D.; Bowen, B.; Firestone, M.; Brodie, E.; Northen, T.

2016-12-01

It is known that rhizosphere bacteria can impact important processes during plant development. In `return' plants release substantial quantities of soluble C into the soil surrounding its roots, attracting bacteria and other soil organisms. Given the potential beneficial and detrimental consequences of stimulating high densities of organisms adjacent to newly formed root, regulating the chemical composition of exudates would represent a potential means of plant selection for beneficial microorganisms. If exudate resource composition functions to select specific microorganisms, then one would expect that substrate specialization exists within the rhizosphere microbiome. Here we provide evidence that in the rhizosphere of wild oats (Avena barbata), specific metabolites are exuded that are preferentially used by selected bacteria in rhizosphere and this substrate specialization, together with the changing composition of root exudates, drives the observed successional patterns. To investigate the relationship between exudates and rhizosphere bacteria we first analyzed exudate composition of hydroponically grown plants using LC-MS/MS based metabolomics. We then designed a medium to simulate plant exudates and using this medium we examined the substrate preferences of a diversity of rhizosphere bacterial isolates. We then assessed the ability of soil isolates to consume exudate components by LC-MS/MS based metabolomics. These substrate preferences were then related to genomic features and successional patterns of bacteria in the Avena rhizosphere. The major fraction of plant exudates was found to be composed of amino- and carboxylic acids, sugars, nucleosides, quaternary amines and plant hormones. Amino acids, sugars and nucleosides were consumed by all analyzed isolates. However, isolates that were preferentially stimulated by plant growth, revealed substrate utilization preferences towards aromatic organic acids, while those not responding to growing roots did not

Probing minority population of antibiotic-resistant bacteria.

PubMed

Huang, Tianxun; Zheng, Yan; Yan, Ya; Yang, Lingling; Yao, Yihui; Zheng, Jiaxin; Wu, Lina; Wang, Xu; Chen, Yuqing; Xing, Jinchun; Yan, Xiaomei

2016-06-15

The evolution and spread of antibiotic-resistant pathogens has become a major threat to public health. Advanced tools are urgently needed to quickly diagnose antibiotic-resistant infections to initiate appropriate treatment. Here we report the development of a highly sensitive flow cytometric method to probe minority population of antibiotic-resistant bacteria via single cell detection. Monoclonal antibody against TEM-1 β-lactamase and Alexa Fluor 488-conjugated secondary antibody were used to selectively label resistant bacteria green, and nucleic acid dye SYTO 62 was used to stain all the bacteria red. A laboratory-built high sensitivity flow cytometer (HSFCM) was applied to simultaneously detect the side scatter and dual-color fluorescence signals of single bacteria. By using E. coli JM109/pUC19 and E. coli JM109 as the model systems for antibiotic-resistant and antibiotic-susceptible bacteria, respectively, as low as 0.1% of antibiotic-resistant bacteria were accurately quantified. By monitoring the dynamic population change of a bacterial culture with the administration of antibiotics, we confirmed that under the antimicrobial pressure, the original low population of antibiotic-resistant bacteria outcompeted susceptible strains and became the dominant population after 5hours of growth. Detection of antibiotic-resistant infection in clinical urine samples was achieved without cultivation, and the bacterial load of susceptible and resistant strains can be faithfully quantified. Overall, the HSFCM-based quantitative method provides a powerful tool for the fundamental studies of antibiotic resistance and holds the potential to provide rapid and precise guidance in clinical therapies. Copyright © 2016 Elsevier B.V. All rights reserved.

Sulfur cycling and metabolism of phototrophic and filamentous sulfur bacteria

NASA Technical Reports Server (NTRS)

Guerrero, R.; Brune, D.; Poplawski, R.; Schmidt, T. M.

1985-01-01

Phototrophic sulfur bacteria taken from different habitate (Alum Rock State Park, Palo Alto salt marsh, and Big Soda Lake) were grown on selective media, characterized by morphological and pigment analysis, and compared with bacteria maintained in pure culture. A study was made of the anaerobic reduction of intracellular sulfur globules by a phototrophic sulfur bacterium (Chromatium vinosum) and a filamentous aerobic sulfur bacterium (Beggiatoa alba). Buoyant densities of different bacteria were measured in Percoll gradients. This method was also used to separate different chlorobia in mixed cultures and to assess the relative homogeneity of cultures taken directly or enriched from natural samples (including the purple bacterial layer found at a depth of 20 meters at Big Soda Lake.) Interactions between sulfide oxidizing bacteria were studied.

Manufacture and characterization of functional emmer beverages fermented by selected lactic acid bacteria.

PubMed

Coda, Rossana; Rizzello, Carlo Giuseppe; Trani, Antonio; Gobbetti, Marco

2011-05-01

Autochthonous lactic acid bacteria from emmer flour were screened based on the kinetic of acidification and used to ferment beverages containing emmer flour, emmer gelatinized flour, and emmer malt at percentages ranging 5-30% (wt/wt). Preliminarily, the concentration of raw flour and malt was selected based on sensory analysis. Different protocols were set up for the manufacture of four different beverages which used Lactobacillus plantarum 6E as the starter. Emmer beverages were mainly differentiated based on the concentration of organic acids, carbohydrates, amino acids, dietary fibers, vitamins, antioxidant and phytase activities, and volatiles and sensory profiles. Wheat flour bread was used as the control to determine the hydrolysis index (HI=100), as an indirect estimation of the glycemic index. The beverage made with 30% (wt/wt) of gelatinized flour showed an HI of 56%, its viscosity was improved by using an EPS-producing strain and it allowed the survival of the potential probiotic Lactobacillus rhamnosus SP1 at cell density of ca. 5 × 10(8) cfu/ml throughout storage at 4 °C. Among the exploited biotechnological options, this latter beverage could be considered as a promising novel functional food. Copyright © 2010 Elsevier Ltd. All rights reserved.

A comparative study of selected Georgia elementary principals' perceptions of environmental knowledge

NASA Astrophysics Data System (ADS)

Campbell, Joyce League

This study sought to establish baseline data on environmental knowledge, opinions, and perceptions of elementary principals and to make comparisons based on academic success rankings of schools and to national results. The self-reported study looked at 200 elementary principals in the state of Georgia. The population selected for the study included principals from the 100 top and 100 bottom academically ranked elementary schools as reported in the Georgia Public Policy Foundation Report Card for Parents. Their scores on the NEETF/Roper Environmental Knowledge Survey were compared between these two Georgia groups and to a national sample. Georgia elementary principals' scores were compared to environmental programs evident in their schools. The two Georgia groups were also compared on environmental opinion and perception responses on mandates, programs in schools and time devoted to these, environmental education as a priority, and the impact of various factors on the strength of environmental studies in schools. Georgia elementary principals leading schools at the bottom of the academic performance scale achieved environmental knowledge scores comparable to the national sample. However, principals of academically successful schools scored significantly higher on environmental knowledge than their colleagues from low performing schools (p < .05) and higher than the national sample (p < .001). Both Georgia principal groups strongly support a mandated environmental education curriculum for Georgia. The two groups were comparable on distributions of time devoted to environmental education across grade levels; however, principals from the more successful schools reported significantly (p < .01) greater amounts of time allotted to environmental studies. Both groups reported the same variety of environmental programs and practices evident in their schools and similar participation in these activities at various grade levels. Most significant (p < .01) was the comparison

Estimating the burden of disease attributable to four selected environmental risk factors in South Africa.

PubMed

Norman, Rosana; Bradshaw, Debbie; Lewin, Simon; Cairncross, Eugene; Nannan, Nadine; Vos, Theo

2010-01-01

The first South African National Burden of Disease study quantified the underlying causes of premature mortality and morbidity experienced in South Africa in the year 2000. This was followed by a Comparative Risk Assessment to estimate the contributions of 17 selected risk factors to burden of disease in South Africa. This paper describes the health impact of exposure to four selected environmental risk factors: unsafe water, sanitation and hygiene; indoor air pollution from household use of solid fuels; urban outdoor air pollution and lead exposure. The study followed World Health Organization comparative risk assessment methodology. Population-attributable fractions were calculated and applied to revised burden of disease estimates (deaths and disability adjusted life years, [DALYs]) from the South African Burden of Disease study to obtain the attributable burden for each selected risk factor. The burden attributable to the joint effect of the four environmental risk factors was also estimated taking into account competing risks and common pathways. Monte Carlo simulation-modeling techniques were used to quantify sampling, uncertainty. Almost 24 000 deaths were attributable to the joint effect of these four environmental risk factors, accounting for 4.6% (95% uncertainty interval 3.8-5.3%) of all deaths in South Africa in 2000. Overall the burden due to these environmental risks was equivalent to 3.7% (95% uncertainty interval 3.4-4.0%) of the total disease burden for South Africa, with unsafe water sanitation and hygiene the main contributor to joint burden. The joint attributable burden was especially high in children under 5 years of age, accounting for 10.8% of total deaths in this age group and 9.7% of burden of disease. This study highlights the public health impact of exposure to environmental risks and the significant burden of preventable disease attributable to exposure to these four major environmental risk factors in South Africa. Evidence

Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector

PubMed Central

Dickson, Laura B.; Jiolle, Davy; Minard, Guillaume; Moltini-Conclois, Isabelle; Volant, Stevenn; Ghozlane, Amine; Bouchier, Christiane; Ayala, Diego; Paupy, Christophe; Moro, Claire Valiente; Lambrechts, Louis

2017-01-01

Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector. PMID:28835919

Increased production of outer membrane vesicles by cultured freshwater bacteria in response to ultraviolet radiation.

PubMed

Gamalier, Juliana P; Silva, Thiago P; Zarantonello, Victor; Dias, Felipe F; Melo, Rossana C N

2017-01-01

Secretion of membrane vesicles is an important biological process of both eukaryotic and prokaryotic cells. This process has been characterized in pathogenic bacteria, but is less clear in non-pathogenic bacteria from aquatic ecosystems. Here, we investigated, for the first time, the process of formation of outer membranes vesicles (OMVs), nanoscale vesicles extruded from the outer membrane (OM) of gram-negative bacteria, in cultures of freshwater bacteria after exposure or not to ultraviolet radiation (UVR) as an environmental stressor. Non-axenic cultures of freshwater bacteria isolated from a Brazilian aquatic ecosystem (Funil reservoir) were exposed or not to UVR (UVA+UVB) over a 3h period, during which cell density, viability and ultrastructure were analyzed. First, we showed that UVR induce bacterial death. UVR triggered significant negative effect on cell density after 3h of UVR treatment. This decrease was directly associated with cell death as revealed by a cell viability fluorescent probe that enables the distinction of live/dead bacteria. Transmission electron microscopy (TEM) revealed changes indicative of cell death after 3h of UVR exposure, with significant increase of damaged cells compared to the control group. Second, we demonstrated that gram-negative bacteria release OMVs during normal growth and after UVR exposure. OMVs were clearly identified as round, membrane-bound vesicles budding off from the bacterial OM as isolated or clustered vesicles or free in the extracellular medium. Remarkably, quantitative TEM analyses showed that bacteria respond to UVR with increased formation of OMVs. Moreover, while OMVs numbers per intact or damaged cell did not differ in the untreated group, UVR led to a higher vesiculation by bacteria in process of death. This means that degenerating bacteria release OMVs before lysis and that this secretion might be an adaptive/protective response to rapid changes in environmental conditions such as UV radiation. Copyright

Isolation of antifungal bacteria from Japanese fermented soybeans, natto.

PubMed

Murata, Daichi; Sawano, Sayaka; Ohike, Tatsuya; Okanami, Masahiro; Ano, Takashi

2013-12-01

An inhibitory effect of a traditional Japanese fermented food, natto, was found against plant pathogens such as Rhizoctonia solani and Fusarium oxysporum, and the bacteria which showed inhibition were isolated from the natto. Among isolated bacteria, BC-1 and GAc exhibited a strong antagonistic effect in vitro against plant pathogens on an agar medium. The supernatant of bacterial culture also showed strong activity against R. solani, which meant the antimicrobial substances were produced and secreted into the medium. Both of the bacteria were estimated as Bacillus amyloliquefaciens from a partial sequence of the 16s rRNA gene. High performance liquid chromatography analysis clearly showed the production of the lipopeptide antibiotic iturin A by BC-1 and GAc. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Natural soil reservoirs for human pathogenic and fecal indicator bacteria

USGS Publications Warehouse

Boschiroli, Maria L; Falkinham, Joseph; Favre-Bonte, Sabine; Nazaret, Sylvie; Piveteau, Pascal; Sadowsky, Michael J.; Byappanahalli, Muruleedhara; Delaquis, Pascal; Hartmann, Alain

2016-01-01

Soils receive inputs of human pathogenic and indicator bacteria through land application of animal manures or sewage sludge, and inputs by wildlife. Soil is an extremely heterogeneous substrate and contains meso- and macrofauna that may be reservoirs for bacteria of human health concern. The ability to detect and quantify bacteria of human health concern is important in risk assessments and in evaluating the efficacy of agricultural soil management practices that are protective of crop quality and protective of adjacent water resources. The present chapter describes the distribution of selected Gram-positive and Gram-negative bacteria in soils. Methods for detecting and quantifying soilborne bacteria including extraction, enrichment using immunomagnetic capture, culturing, molecular detection and deep sequencing of metagenomic DNA to detect pathogens are overviewed. Methods for strain phenotypic and genotypic characterization are presented, as well as how comparison with clinical isolates can inform the potential for human health risk.

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk

DOE Office of Scientific and Technical Information (OSTI.GOV)

O’Connor, Roberta M.; Fung, Jennifer M.; Sharp, Koty H.

In animals, gut microbes are essential for digestion. Here in this paper, we show that bacteria outside the gut can also play a critical role in digestion. In shipworms, wood-eating marine bivalves, endosymbiotic bacteria are found within specialized cells in the gills. We show that these endosymbionts produce wood-degrading enzymes that are selectively transported to the shipworm’s bacteria-free gut, where wood digestion occurs. Because only selected wood-degrading enzymes are transported, the shipworm system naturally identifies those endosymbiont enzymes most relevant to lignocellulose deconstruction without interference from other microbial proteins. Furthermore, this work expands the known biological repertoire of bacterial endosymbiontsmore » to include digestion of food and identifies previously undescribed enzymes and enzyme combinations of potential value to biomass-based industries, such as cellulosic biofuel production.« less

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk

DOE PAGES

O’Connor, Roberta M.; Fung, Jennifer M.; Sharp, Koty H.; ...

2014-11-10

In animals, gut microbes are essential for digestion. Here in this paper, we show that bacteria outside the gut can also play a critical role in digestion. In shipworms, wood-eating marine bivalves, endosymbiotic bacteria are found within specialized cells in the gills. We show that these endosymbionts produce wood-degrading enzymes that are selectively transported to the shipworm’s bacteria-free gut, where wood digestion occurs. Because only selected wood-degrading enzymes are transported, the shipworm system naturally identifies those endosymbiont enzymes most relevant to lignocellulose deconstruction without interference from other microbial proteins. Furthermore, this work expands the known biological repertoire of bacterial endosymbiontsmore » to include digestion of food and identifies previously undescribed enzymes and enzyme combinations of potential value to biomass-based industries, such as cellulosic biofuel production.« less

Remediation of Acid Mine Drainage with Sulfate Reducing Bacteria

ERIC Educational Resources Information Center

Hauri, James F.; Schaider, Laurel A.

2009-01-01

Sulfate reducing bacteria have been shown to be effective at treating acid mine drainage through sulfide production and subsequent precipitation of metal sulfides. In this laboratory experiment for undergraduate environmental chemistry courses, students design and implement a set of bioreactors to remediate acid mine drainage and explain observed…

Algae-bacteria interactions: Evolution, ecology and emerging applications.

PubMed

Ramanan, Rishiram; Kim, Byung-Hyuk; Cho, Dae-Hyun; Oh, Hee-Mock; Kim, Hee-Sik

2016-01-01

Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions - from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae-roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal-bacterial interactions to various environmental and bio-technological applications. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A METHOD TO DETECT VIABLE HELICOBACTER PYLORI BACTERIA IN GROUNDWATER

EPA Science Inventory

The inability to detect the presence of viable Helicobacter pylori bacteria in environmental waters has hindered the public health community in assessing the role water may playin the transmission of this pathogen. This work describes a cultural enrichment method coupled with an...

Current Issues in Environmental Education and Environmental Studies. Volume VIII. Selected Papers from the Annual Conference of the National Association for Environmental Education (11th, Silver Bay, New York, October 15-20, 1982).

ERIC Educational Resources Information Center

Sacks, Arthur B.; And Others

Provided in three major sections are selected papers presented at the 1982 Conference of the National Association for Environmental Education. The first part contains four invited addresses on environmental issues and two symposium papers related to the Global 2000 Report to the President. Topics of addresses focus on education/citizen…

Carbohydrate profiling of bacteria by gas chromatography-mass spectrometry and their trace detection in complex matrices by gas chromatography-tandem mass spectrometry.

PubMed

Fox, A

1999-05-28

Bacterial cellular polysaccharides are composed of a variety of sugar monomers. These sugars serve as chemical markers to identify specific species or genera or to determine their physiological status. Some of these markers can also be used for trace detection of bacteria or their constituents in complex clinical or environmental matrices. Analyses are performed, in our hands, employing hydrolysis followed by the alditol acetate derivatization procedure. Substantial improvements have been made to sample preparation including simplification and computer-controlled automation. For characterization of whole cell bacterial hydrolysates, sugars are analyzed by gas chromatography-mass spectrometry (GC-MS). Simple chromatograms are generated using selected ion monitoring (SIM). Using total ion GC-MS, sugars can be readily identified. In more complex clinical and environmental samples, markers for bacteria are present at sufficiently low concentrations that more advanced instrumentation, gas chromatography-tandem mass spectrometry (GC-MS-MS), is preferred for optimal analysis. Using multiple reaction monitoring, MS-MS is used (replacing more conventional SIM) to ignore extraneous chromatographic peaks. Triple quadrupole and ion trap GC-MS-MS instruments have both been used successfully. Absolute chemical identification of sugar markers at trace levels is achieved, using MS-MS, by the product spectrum.

Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

PubMed

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil

PubMed Central

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

Horizontal functional gene transfer from bacteria to fishes.

PubMed

Sun, Bao-Fa; Li, Tong; Xiao, Jin-Hua; Jia, Ling-Yi; Liu, Li; Zhang, Peng; Murphy, Robert W; He, Shun-Min; Huang, Da-Wei

2015-12-22

Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.

Antimicrobial-resistant bacteria in wild game in Slovenia

NASA Astrophysics Data System (ADS)

Križman, M.; Kirbiš, A.; Jamnikar-Ciglenečki, U.

2017-09-01

Wildlife is usually not exposed to clinically-used antimicrobial agents but can acquire antimicrobial resistance throughout contact with humans, domesticated animals and environments. Samples of faeces from intestines (80 in total) were collected from roe deer (52), wild boars (11), chamois (10) red deer (6) and moufflon (1). After culture on ChromID extended spectrum β-lactamase (ESBL) plates to select for growth of ESBL-producing bacteria, 25 samples produced bacterial colonies for further study. Six species of bacteria were identified from the 25 samples: Stenotrophomonas maltophilia, Serratia fonticola, Stenotrophomonas nitritireducens, Enterococcus faecium, Enterococcus faecalis and Escherichia coli. Two ESBL enzymes were amplified from group TEM and three from group CTX-M-1. Undercooked game meat and salami can be a source of resistant bacteria when animals are not eviscerated properly.

Distribution and decline of human pathogenic bacteria in soil after application in irrigation water and the potential for soil-splash-mediated dispersal onto fresh produce.

PubMed

Monaghan, J M; Hutchison, M L

2012-05-01

To improve our understanding of the survival and splash-mediated transfer of zoonotic agents and faecal indicator bacteria introduced into soils used for crop cultivation via contaminated irrigation waters. Zoonotic agents and an Escherichia coli marker bacterium were inoculated into borehole water, which was applied to two different soil types in early-, mid- and late summer. Decline of the zoonotic agents was influenced by soil type. Marker bacteria applied to columns of two soil types in irrigation water did not concentrate at the surface of the soils. Decline of zoonotic agents at the surface was influenced by soil type and environmental conditions. Typically, declines were rapid and bacteria were not detectable after 5 weeks. Selective agar strips were used to determine that the impact of water drops 24-87 μl could splash marker bacteria from soil surfaces horizontal distances of at least 25 cm and heights of 20 cm. Soil splash created by rain-sized water droplets can transfer enteric bacteria from soil to ready-to-eat crops. Persistence of zoonotic agents was reduced at the hottest part of the growing season when irrigation is most likely. Soil splash can cause crop contamination. We report the penetration depths and seasonally influenced declines of bacteria applied in irrigation water into two soil types. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

PubMed Central

Mortimer, Monika; Petersen, Elijah J.; Buchholz, Bruce A.; Holden, Patricia A.

2016-01-01

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstrate separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. The optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation. PMID:27917301

Removal of bacteria from stallion semen by colloid centrifugation.

PubMed

Morrell, J M; Klein, C; Lundeheim, N; Erol, E; Troedsson, M H T

2014-02-01

Bacteria (environmental contaminants and occasionally potential pathogens) are found in most stallion ejaculates and may negatively affect sperm quality during storage. Since the use of antibiotics can lead to the development of resistance, an alternative means of microbial control is desirable. The removal of bacteria from stallion semen using Single Layer Centrifugation through Androcoll-E was investigated. Known doses of cultured bacteria were added to freshly collected ejaculates (15mL aliquots) before processing by Single Layer Centrifugation. The resulting sperm pellets and controls (not processed by Single Layer Centrifugation) were cultured and the bacteria identified. In experiment 1, doses of E. coli from 2×10(2) to 2×10(7) colony forming units were added to aliquots of semen. In experiment 2, Taylorella equigenitalis or a mix of E. coli, Klebsiella pneumoniae and Streptococcus equi subsp. zooepidemicus (approximately 7×10(6), 5×10(6), and 6×10(6)cfu, respectively) were added to 15mL aliquots of semen. In experiment 1, more than 90% of the bacteria were removed where loading doses were >×10(4)cfu/mL. In experiment 2, varying proportions of different bacteria were removed, ranging from 68% for naturally occurring Corynebacterium spp. to >97% for added cultured E. coli. Thus, Single Layer Centrifugation can separate spermatozoa from many, but not all bacteria in stallion ejaculates and could be a useful alternative to adding antibiotics to semen extenders to control bacterial contamination. However, further research is needed to determine the effect of small numbers of bacteria on sperm quality. Copyright © 2014 Elsevier B.V. All rights reserved.

Production of biodegradable plastic by polyhydroxybutyrate (PHB) accumulating bacteria using low cost agricultural waste material.

PubMed

Getachew, Anteneh; Woldesenbet, Fantahun

2016-12-12

Polyhydroxybutyrates (PHBs) are macromolecules synthesized by bacteria. They are inclusion bodies accumulated as reserve materials when the bacteria grow under different stress conditions. Because of their fast degradability under natural environmental conditions, PHBs are selected as alternatives for production of biodegradable plastics. The aim of this work was to isolate potential PHB producing bacteria, evaluate PHB production using agro-residues as carbon sources. Among fifty bacterial strains isolated from different localities, ten PHB accumulating strains were selected and compared for their ability to accumulate PHB granules inside their cells. Isolate Arba Minch Waste Water (AWW) identified as Bacillus spp was found to be the best producer. The optimum pH, temperature, and incubation period for best PHB production by the isolate were 7, 37 °C, and 48 h respectively at 150 rpm. PHB production was best with glucose as carbon source and peptone as nitrogen source. The strain was able to accumulate 55.6, 51.6, 37.4 and 25% PHB when pretreated sugar cane bagasse, corn cob, teff straw (Eragrostis tef) and banana peel were used as carbon sources respectively. Fourier transform-infrared authentication results of the extracted and purified PHB identified its functional units as C-H, CH 2 , C=O and C-O groups. UV-Vis spectrophotometric analysis and biodegradability test confirmed the similarity of the extract with standard PHB and its suitability for bioplastic production. The isolated Bacillus sp can be used for feasible production of PHB using agro-residues especially sugarcane bagasse which can reduce the production cost in addition to reducing the disposal problem of these substrates. The yield of PHB can further be boosted by optimization of production parameters as substrates.

Association of time under immunosuppression and different immunosuppressive medication on periodontal parameters and selected bacteria of patients after solid organ transplantation.

PubMed

Schmalz, G; Berisha, L; Wendorff, H; Widmer, F; Marcinkowski, A; Teschler, H; Sommerwerck, U; Haak, R; Kollmar, O; Ziebolz, D

2018-05-01

Aim of this study was to investigate the association of the time under immunosuppression and different immunosuppressive medication on periodontal parameters and selected periodontal pathogenic bacteria of immunosuppressed patients after solid organ transplantation (SOT). 169 Patients after SOT (lung, liver or kidney) were included and divided into subgroups according their time under (0-1, 1-3, 3-6, 6-10 and >10 years) and form of immunosuppression (Tacrolimus, Cyclosporine, Mycophenolate, Glucocorticoids, Sirolimus and monotherapy vs. combination). Periodontal probing depth (PPD) and clinical attachment loss (CAL) were assessed. Periodontal disease severity was classified as healthy/mild, moderate or severe periodontitis. Subgingival biofilm samples were investigated for eleven selected potentially periodontal pathogenic bacteria using polymerasechainreaction. The mean PPD and CAL as well as prevalence of Treponema denticola and Capnocytophaga species was shown to be different but heterogeneous depending on time under immunosuppression (p<0.05). Furthermore, only the medication with Cyclosporine was found to show worse periodontal condition compared to patients without Cyclosporine (p<0.05). Prevalence of Porphyromonas gingivalis, Tannerella forsythia and Fusobacterium nucleatum was reduced and prevalence of Parvimonas micra and Capnocytophaga species was increased in patients under immunosuppression with Glucocorticoids, Mycophenolate as well as combination therapy. Time under and form of immunosuppression might have an impact on the clinical periodontal and microbiological parameters of patients after SOT. Patients under Cyclosporine medication should receive increased attention. Differences in subgingival biofilm, but not in clinical parameters were found for Glucocorticoids, Mycophenolate and combination therapy, making the clinical relevance of this finding unclear.

Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria.

PubMed

Kartal, Boran; Geerts, Wim; Jetten, Mike S M

2011-01-01

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite under anoxic conditions. The anammox process is currently used to remove ammonium from wastewater and contributes significantly to the loss of fixed nitrogen from the oceans. In this chapter, we focus on the ecophysiology of anammox bacteria and describe new methodologies to grow these microorganisms. Now, it is possible to enrich anammox bacteria up to 95% with a membrane bioreactor that removes forces of selection for fast settling aggregates and facilitates the growth of planktonic cells. The biomass from this system has a high anaerobic ammonium oxidation rate (50 fmol NH(4)(+) · cell(-1) day(-1)) and is suitable for many ecophysiological and molecular experiments. A high throughput Percoll density gradient centrifugation protocol may be applied on this biomass for further enrichment (>99.5%) of anammox bacteria. Furthermore, we provide an up-to-date list of commonly used primers and introduce protocols for quantification and detection of functional genes of anammox bacteria in their natural environment. Copyright © 2011 Elsevier Inc. All rights reserved.

Adaptations of indigenous bacteria to fuel contamination in karst aquifers in south-central Kentucky

USGS Publications Warehouse

Byl, Thomas D.; Metge, David W.; Agymang, Daniel T.; Bradley, Michael W.; Hileman, Gregg; Harvey, Ronald W.

2014-01-01

The karst aquifer systems in southern Kentucky can be dynamic and quick to change. Microorganisms that live in these unpredictable aquifers are constantly faced with environmental changes. Their survival depends upon adaptations to changes in water chemistry, taking advantage of positive stimuli and avoiding negative environmental conditions. The U.S. Geological Survey conducted a study in 2001 to determine the capability of bacteria to adapt in two distinct regions of water quality in a karst aquifer, an area of clean, oxygenated groundwater and an area where the groundwater was oxygen depleted and contaminated by jet fuel. Water samples containing bacteria were collected from one clean well and two jet fuel contaminated wells in a conduit-dominated karst aquifer. Bacterial concentrations, enumerated through direct count, ranged from 500,000 to 2.7 million bacteria per mL in the clean portion of the aquifer, and 200,000 to 3.2 million bacteria per mL in the contaminated portion of the aquifer over a twelve month period. Bacteria from the clean well ranged in size from 0.2 to 2.5 mm, whereas bacteria from one fuel-contaminated well were generally larger, ranging in size from 0.2 to 3.9 mm. Also, bacteria collected from the clean well had a higher density and, consequently, were more inclined to sink than bacteria collected from contaminated wells. Bacteria collected from the clean portion of the karst aquifer were predominantly (,95%) Gram-negative and more likely to have flagella present than bacteria collected from the contaminated wells, which included a substantial fraction (,30%) of Gram-positive varieties. The ability of the bacteria from the clean portion of the karst aquifer to biodegrade benzene and toluene was studied under aerobic and anaerobic conditions in laboratory microcosms. The rate of fuel biodegradation in laboratory studies was approximately 50 times faster under aerobic conditions as compared to anaerobic, sulfur-reducing conditions. The

Regulating the Intersection of Metabolism and Pathogenesis in Gram-positive Bacteria

PubMed Central

RICHARDSON, ANTHONY R.; SOMERVILLE, GREG A.; SONENSHEIN, ABRAHAM L.

2015-01-01

Pathogenic bacteria must contend with immune systems that actively restrict the availability of nutrients and cofactors, and create a hostile growth environment. To deal with these hostile environments, pathogenic bacteria have evolved or acquired virulence determinants that aid in the acquisition of nutrients. This connection between pathogenesis and nutrition may explain why regulators of metabolism in nonpathogenic bacteria are used by pathogenic bacteria to regulate both metabolism and virulence. Such coordinated regulation is presumably advantageous because it conserves carbon and energy by aligning synthesis of virulence determinants with the nutritional environment. In Gram-positive bacterial pathogens, at least three metabolite-responsive global regulators, CcpA, CodY, and Rex, have been shown to coordinate the expression of metabolism and virulence genes. In this chapter, we discuss how environmental challenges alter metabolism, the regulators that respond to this altered metabolism, and how these regulators influence the host-pathogen interaction. PMID:26185086

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors.

PubMed

Demeter, Marc A; Lemire, Joseph A; Mercer, Sean M; Turner, Raymond J

2017-03-01

Bacteria are often found tolerating polluted environments. Such bacteria may be exploited to bioremediate contaminants in controlled ex situ reactor systems. One potential strategic goal of such systems is to harness microbes directly from the environment such that they exhibit the capacity to markedly degrade organic pollutants of interest. Here, the use of biofilm cultivation techniques to inoculate and activate moving bed biofilm reactor (MBBR) systems for the degradation of polycyclic aromatic hydrocarbons (PAHs) was explored. Biofilms were cultivated from 4 different hydrocarbon contaminated sites using a minimal medium spiked with the 16 EPA identified PAHs. Overall, all 4 inoculant sources resulted in biofilm communities capable of tolerating the presence of PAHs, but only 2 of these exhibited enhanced PAH catabolic gene prevalence coupled with significant degradation of select PAH compounds. Comparisons between inoculant sources highlighted the dependence of this method on appropriate inoculant screening and biostimulation efforts. Copyright © 2016 Elsevier Ltd. All rights reserved.

Motility analysis of bacteria-based microrobot (bacteriobot) using chemical gradient microchamber.

PubMed

Park, Daechul; Park, Sung Jun; Cho, Sunghoon; Lee, Yeonkyung; Lee, Yu Kyung; Min, Jung-Joon; Park, Bang Ju; Ko, Seong Young; Park, Jong-Oh; Park, Sukho

2014-01-01

A bacteria-based microrobot (bacteriobot) was proposed and investigated as a new type of active drug delivery system because of its useful advantages, such as active tumor targeting, bacteria-mediated tumor diagnosis, and therapy. In this study, we fabricated a bacteriobot with enhanced motility by selective attachment of flagellar bacteria (Salmonella typhimurium). Through selective bovine serum albumin (BSA) pattering on hydrophobic polystyrene (PS) microbeads, many S. typhimurium could be selectively attached only on the unpatterned surface of PS microbead. For the evaluation of the chemotactic motility of the bacteriobot, we developed a microfluidic chamber which can generate a stable concentration gradient of bacterial chemotactic chemicals. Prior to the evaluation of the bacteriobot, we first evaluated the directional chemotactic motility of S. typhimurium using the proposed microfluidic chamber, which contained a bacterial chemo-attractant (L-aspartic acid) and a chemo-repellent (NiSO4 ), respectively. Compared to density of the control group in the microfluidic chamber without any chemical gradient, S. typhimurium increased by about 16% in the L-aspartic acid gradient region and decreased by about 22% in the NiSO4 gradient region. Second, we evaluated the bacteriobot's directional motility by using this microfluidic chamber. The chemotactic directional motility of the bacteriobot increased by 14% and decreased by 13% in the concentration gradients of L-aspartic acid and NiSO4 , respectively. These results confirm that the bacteriobot with selectively patterned S. typhimurium shows chemotaxis motility very similar to that of S. typhimurium. Moreover, the directional motilities of the bacteria and bacteriobot could be demonstrated quantitatively through the proposed microfluidic chamber. © 2013 Wiley Periodicals, Inc.

Phenotypic switching in bacteria

NASA Astrophysics Data System (ADS)

Merrin, Jack

Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

Microplate freeze-dried cyanobacterial bioassay for fresh-waters environmental monitoring.

PubMed

Martín-Betancor, Keila; Durand, Marie-José; Thouand, Gérald; Leganés, Francisco; Fernández-Piñas, Francisca; Rodea-Palomares, Ismael

2017-12-01

Microorganisms have been very useful in environmental monitoring due to their constant sensing of the surrounding environment, their easy maintenance and low cost. Some freeze-dried toxicity kits based on naturally bioluminescent bacteria are commercially available and commonly used to assess the toxicity of environmental samples such as Microtox (Aliivibrio fischeri) or ToxScreen (Photobacterium leiognathi), however, due to the marine origin of these bacteria, they could not be the most appropriate for fresh-waters monitoring. Cyanobacteria are one of the most representative microorganisms of aquatic environments, and are well suited for detecting contaminants in aqueous samples. This study presents the development and application of the first freeze-dried cyanobacterial bioassay for fresh-water contaminants detection. The effects of different cell growth phases, cryoprotectant solutions, freezing protocols, rehydration solutions and incubation conditions methods were evaluated and the best combination of these parameters for freeze-drying was selected. The study includes detailed characterization of sensitivity towards reference pollutants, as well as, comparison with the standard assays. Moreover, long-term viability and sensitivity were evaluated after 3 years of storage. Freeze-dried cyanobacteria showed, in general, higher sensitivity than the standard assays and viability of the cells remained after 3 years of storage. Finally, the validation of the bioassay using a wastewater sample was also evaluated. Freeze-drying of cyanobacteria in 96-well plates presents a simple, fast and multi-assay method for environmental monitoring. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sorption of lead onto two gram-negative marine bacteria in seawater

USGS Publications Warehouse

Harvey, Ronald W.; Leckie, James O.

1985-01-01

Laboratory adsorption experiments performed at environmentally significant lead (Pb) and cell concentrations indicate that the marine bacteria examined have significant binding capacities for Pb. However, the behavior governing Pb sorption onto gram-negative bacteria in seawater may be quite complex. The sorption kinetics appear to involve two distinct phases, i.e., a rapid removal of Pb from solution within the first few minutes, followed by a slow but nearly constant removal over many hours. Also, the average binding coefficient, calculated for Pb sorption onto bacteria and a measure of binding intensity, increases with decreasing sorption density (amounts of bacteria-associated Pb per unit bacterial surface) at low cell concentrations (105 cells ml−1), but decreases with decreasing sorption density at higher cell concentrations (107 cells ml−1). The latter effect is apparently due to the production of significant amounts of extra-cellular organics at high cell concentrations that compete directly with bacterial surfaces for available lead. Lead toxicity and active uptake by marine bacteria did not appear significant at the Pb concentrations used.

Distribution, genetic diversity and antibiotic resistance of clinically important bacteria from the environment of a tertiary hospital.

PubMed

Phoon, Hannah Y P; Hussin, Hazilawati; Hussain, Baizurah Mohd; Lim, Shu Yong; Woon, Jia Jie; Er, Yi Xian; Thong, Kwai Lin

2018-03-11

Hospital environments are potential reservoirs of bacteria associated with nosocomial infections. Here, we determined the distribution of cultivable environmental bacteria of clinical importance from a Malaysian tertiary hospital and to investigate their resistotypes and genotypes. Swab and fluid samples (n=358) from healthcare workers' hands, frequently touched surfaces, medical equipment, patients' immediate surroundings, ward sinks and toilets and solutions or fluids of 12 selected wards were collected. Biochemical tests, PCR and 16S rRNA sequencing were used for identification after isolation from CHROMagar TM Orientation medium. Clinically important bacteria such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter spp., Pseudomonas aeruginosa, and Enterobacter spp. were further characterised by disk diffusion method and REP-PCR. The 32 Gram negative and 21 Gram positive bacteria species identified were widely distributed in the hospital environment. Staphylococci were predominant followed by Bacillus spp., and P. aeruginosa. Frequently touched surfaces, medical equipment and ward sinks and toilets were the top three sources of bacterial species. Nine S. aureus, four Acinetobacter spp., one K. pneumoniae, and one Enterobacter spp., were multidrug resistant (MDR). The ESKAPE organisms were genetically diverse and widely dispersed across the hospital wards. An MDR MRSA clone was detected in a surgical ward isolation room. The large variety of cultivable, clinically important bacteria, especially the genetically related MDR S. aureus, K. pneumoniae, Acinetobacter spp., and Enterobacter spp. from various sampling sites indicated that the surfaces and fomites in the hospital were potential exogenous sources of nosocomial infections in the hospital. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Chemical Modification and Detoxification of the Pseudomonas aeruginosa Toxin 2-Heptyl-4-hydroxyquinoline N-Oxide by Environmental and Pathogenic Bacteria.

PubMed

Thierbach, Sven; Birmes, Franziska S; Letzel, Matthias C; Hennecke, Ulrich; Fetzner, Susanne

2017-09-15

2-Heptyl-4-hydroxyquinoline N-oxide (HQNO), a major secondary metabolite and virulence factor produced by the opportunistic pathogen Pseudomonas aeruginosa, acts as a potent inhibitor of respiratory electron transfer and thereby affects host cells as well as microorganisms. In this study, we demonstrate the previously unknown capability of environmental and pathogenic bacteria to transform and detoxify this compound. Strains of Arthrobacter and Rhodococcus spp. as well as Staphylococcus aureus introduced a hydroxyl group at C-3 of HQNO, whereas Mycobacterium abscessus, M. fortuitum, and M. smegmatis performed an O-methylation, forming 2-heptyl-1-methoxy-4-oxoquinoline as the initial metabolite. Bacillus spp. produced the glycosylated derivative 2-heptyl-1-(β-d-glucopyranosydyl)-4-oxoquinoline. Assaying the effects of these metabolites on cellular respiration and on quinol oxidase activity of membrane fractions revealed that their EC 50 values were up to 2 orders of magnitude higher than that of HQNO. Furthermore, cellular levels of reactive oxygen species were significantly lower in the presence of the metabolites than under the influence of HQNO. Therefore, the capacity to transform HQNO should lead to a competitive advantage against P. aeruginosa. Our findings contribute new insight into the metabolic diversity of bacteria and add another layer of complexity to the metabolic interactions which likely contribute to shaping polymicrobial communities comprising P. aeruginosa.

Selection of facility location under environmental damage priority and using ELECTRE method.

PubMed

Gundogdu, Ceren Erdin

2011-03-01

In the recent years, the environmental problems have reached to a vital extent, which is pushing the boundaries and far beyond daily evaluations. Industrial plants, the energy sources and uncontrolled release of pollutant gases (SO2, CO2 etc.) in the production stage have the greatest share in the occurrence of unfavorable environmental conditions. For this reason, the dimension of the problems that may arise in the production stage of industrial plants is directly related to the selection of facility location. In this study, geographical regions (a total of 7 regions) of our country have been analyzed in terms of environmental values based on their basins and the unfavorable environmental problems that are currently being experienced. Considered as such, with the directives of an expert group composed of nature scientists, the criteria and alternative areas are determined using the data gathered on ecosystem, basin characteristics, and land types. Since the primary goal is to keep the environmental damages at the minimum level, comprehensive definition of the problem is constructed by consultation of the expert group and the criteria are determined. Considering the fact that it will prevent the drawbacks generated by making decisions depending on certain stereotypes toa great extent, ELECTRE (Elimination and Choice Translating Reality English - Elimination Et Choix Traduisant la Realite) method is used to determine in which geographic region our country's industrial plants should be located.

Micro-zooplankton grazing as a means of fecal bacteria removal in stormwater BMPs.

PubMed

Burtchett, Jade M; Mallin, Michael A; Cahoon, Lawrence B

2017-06-01

A priority for environmental managers is control of stormwater runoff pollution, especially fecal microbial pollution. This research was designed to determine if fecal bacterial grazing by micro-zooplankton is a significant control on fecal bacteria in aquatic best management practices (BMPs); if grazing differs between a wet detention pond and a constructed wetland; and if environmental factors enhance grazing. Both 3-day grazing tests and 24-h dilution assays were used to determine grazing differences between the two types of BMP. Micro-zooplankton grazing was a stronger bacteria removal mechanism in stormwater wetlands rich in aquatic vegetation compared to a standard wet detention pond, although grazing was important in detention ponds as well. Our experiments indicated that the majority of grazers that fed on fecal bacteria were <20 μm in size. Grazing rates were positively correlated with fecal coliform abundance and increased water temperatures. Enumeration of grazers demonstrated that protozoans were significantly more abundant among wetland vegetation than in open water, and open wetland waters contained more flagellates and dinoflagellates than open wet detention pond waters. Grazing on fecal bacteria in BMPs is enhanced by aquatic vegetation, and grazing in aquatic BMPs in warmer climates should be greater than in cooler climates.

Assessment of Environmental Contamination with Pathogenic Bacteria at a Hospital Laundry Facility.

PubMed

Michael, Karen E; No, David; Daniell, William E; Seixas, Noah S; Roberts, Marilyn C

2017-11-10

Little is known about exposure to pathogenic bacteria among industrial laundry workers who work with soiled clinical linen. To study worker exposures, an assessment of surface contamination was performed at an industrial laundry facility serving hospitals in Seattle, WA, USA. Surface swab samples (n = 240) from the environment were collected during four site visits at 3-month intervals. These samples were cultured for Clostridium difficile, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE). Voluntary participation of 23 employees consisted of nasal swabs for detection of MRSA, observations during work, and questionnaires. Contamination with all three pathogens was observed in both dirty (laundry handling prior to washing) and clean areas (subsequent to washing). The dirty area had higher odds of overall contamination (≥1 pathogen) than the clean area (odds ratio, OR = 18.0, 95% confidence interval 8.9-36.5, P < 0.001). The odds of contamination were high for each individual pathogen: C. difficile, OR = 15.5; MRSA, OR = 14.8; and VRE, OR = 12.6 (each, P < 0.001). The highest odds of finding surface contamination occurred in the primary and secondary sort areas where soiled linens were manually sorted by employees (OR = 63.0, P < 0.001). The study substantiates that the laundry facility environment can become contaminated by soiled linens. Workers who handle soiled linen may have a higher risk of exposure to C. difficile, MRSA, and VRE than those who handle clean linens. Improved protocols for prevention and reduction of environmental contamination were implemented because of this study. © The Author 2017. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples.

PubMed

Meir-Gruber, Lital; Manor, Yossi; Gefen-Halevi, Shiraz; Hindiyeh, Musa Y; Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples

PubMed Central

Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage. PMID:27780222

Succession sequence of lactic acid bacteria driven by environmental factors and substrates throughout the brewing process of Shanxi aged vinegar.

PubMed

Zheng, Yu; Mou, Jun; Niu, Jiwei; Yang, Shuai; Chen, Lin; Xia, Menglei; Wang, Min

2018-03-01

Lactic acid bacteria (LAB) are essential microbiota for the fermentation and flavor formation of Shanxi aged vinegar, a famous Chinese traditional cereal vinegar that is manufactured using open solid-state fermentation (SSF) technology. However, the dynamics of LAB in this SSF process and the underlying mechanism remain poorly understood. Here, the diversity of LAB and the potential driving factors of the entire process were analyzed by combining culture-independent and culture-dependent methods. Canonical correlation analysis indicated that ethanol, acetic acid, and temperature that result from the metabolism of microorganisms serve as potential driving factors for LAB succession. LAB strains were periodically isolated, and the characteristics of 57 isolates on environmental factor tolerance and substrate utilization were analyzed to understand the succession sequence. The environmental tolerance of LAB from different stages was in accordance with their fermentation conditions. Remarkable correlations were identified between LAB growth and environmental factors with 0.866 of ethanol (70 g/L), 0.756 of acetic acid (10 g/L), and 0.803 of temperature (47 °C). More gentle or harsh environments (less or more than 60 or 80 g/L of ethanol, 5 or 20 g/L of acetic acid, and 30 or 55 °C temperature) did not affect the LAB succession. The utilization capability evaluation of the 57 isolates for 95 compounds proved that strains from different fermentation stages exhibited different predilections on substrates to contribute to the fermentation at different stages. Results demonstrated that LAB succession in the SSF process was driven by the capabilities of environmental tolerance and substrate utilization.

Identification and discrimination of Pseudomonas aeruginosa bacteria grown in blood and bile by laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Rehse, Steven J.; Diedrich, Jonathan; Palchaudhuri, Sunil

2007-10-01

Pseudomonas aeruginosa bacteria colonies have been analyzed by laser-induced breakdown spectroscopy using nanosecond laser pulses. LIBS spectra were obtained after transferring the bacteria from a nutrient-rich culture medium to a nutrient-free agar plate for laser ablation. To study the dependence of the LIBS spectrum on growth and environmental conditions, colonies were cultured on three different nutrient media: a trypticase soy agar (TSA) plate, a blood agar plate, and a medium chosen deliberately to induce bacteria membrane changes, a MacConkey agar plate containing bile salts. Nineteen atomic and ionic emission lines in the LIBS spectrum, which was dominated by inorganic elements such as calcium, magnesium and sodium, were used to identify and classify the bacteria. A discriminant function analysis was used to discriminate between the P. aeruginosa bacteria and two strains of E. coli: a non-pathogenic environmental strain and the pathogenic strain enterohemorrhagic E. coli 0157:H7 (EHEC). Nearly identical spectra were obtained from P. aeruginosa grown on the TSA plate and the blood agar plate, while the bacteria grown on the MacConkey plate exhibited easily distinguishable differences from the other two. All P. aeruginosa samples, independent of initial growth conditions, were readily discriminated from the two E. coli strains.

Space Environmental Effects on the Optical Properties of Selected Transparent Polymers

NASA Technical Reports Server (NTRS)

Edwards, David L.; Willowby, Douglas J.; Hubbs, Whitney C.; Piszczor, Michael F., Jr.; Bowden, Mary L.

1997-01-01

Transparent polymer films are currently considered for use as solar concentrating lenses for spacecraft power and propulsion systems. These polymer films concentrate solar energy onto energy conversion devices such as solar cells and thermal energy systems. Conversion efficiency is directly related to the polymer transmission. Space environmental effects will decrease the transmission and thus reduce the conversion efficiency. This investigation focuses on the effects of ultraviolet and charged particle radiation on the transmission of selected transparent polymers. Multiple candidate polymer samples were exposed to near ultraviolet (NUV) radiation to screen the materials and select optimum materials for further study. All materials experienced transmission degradation of varying degree. A method was developed to normalize the transmission loss and thus rank the materials according to their tolerance of NUV. Teflon(Tm) FEP and Teflon(Tm) PFA were selected for further study. These materials were subjected to a combined charged particle dose equivalent to 5 years in a typical geosynchronous Earth orbit (GEO). Results from these NUV screening tests and the 5 year GEO equivalent dose are presented.

Precision genome engineering in lactic acid bacteria

PubMed Central

2014-01-01

Innovative new genome engineering technologies for manipulating chromosomes have appeared in the last decade. One of these technologies, recombination mediated genetic engineering (recombineering) allows for precision DNA engineering of chromosomes and plasmids in Escherichia coli. Single-stranded DNA recombineering (SSDR) allows for the generation of subtle mutations without the need for selection and without leaving behind any foreign DNA. In this review we discuss the application of SSDR technology in lactic acid bacteria, with an emphasis on key factors that were critical to move this technology from E. coli into Lactobacillus reuteri and Lactococcus lactis. We also provide a blueprint for how to proceed if one is attempting to establish SSDR technology in a lactic acid bacterium. The emergence of CRISPR-Cas technology in genome engineering and its potential application to enhancing SSDR in lactic acid bacteria is discussed. The ability to perform precision genome engineering in medically and industrially important lactic acid bacteria will allow for the genetic improvement of strains without compromising safety. PMID:25185700

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, R.L.

1995-05-30

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, Richard L.

1995-01-01

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Antibacterial clay against gram-negative antibiotic resistant bacteria.

PubMed

Zarate-Reyes, Luis; Lopez-Pacheco, Cynthia; Nieto-Camacho, Antonio; Palacios, Eduardo; Gómez-Vidales, Virginia; Kaufhold, Stephan; Ufer, Kristian; García Zepeda, Eduardo; Cervini-Silva, Javiera

2018-01-15

Antibiotic resistant bacteria persist throughout the world because they have evolved the ability to express various defense mechanisms to cope with antibiotics and the immune system; thus, low-cost strategies for the treatment of these bacteria are needed, such as the usage of environmental minerals. This paper reports the antimicrobial properties of a clay collected from Brunnenberg, Germany, that is composed of ferroan saponite with admixtures of quartz, feldspar and calcite as well as exposed or hidden (layered at inner regions) nano Fe(0). Based on the growth curves (log phase) of six antibiotic resistant bacteria (4 gram-negative and 2 gram-positive), we concluded that the clay acted as a bacteriostat; however, the clay was only active against the gram-negative bacteria (except for resilient Klebsiella pneumonia). The bacteriostatic mode of action was evidenced by the initial lack of Colony Forming Units on agar plates with growth registered afterward, certainly after 24h, and can be explained because interactions between membrane lipopolysaccharides and the siloxane surfaces of the clay. Labile or bioavailable Fe in the clay (extracted by EDTA or DFO-B) induced the quantitative production of HO as well as oxidative stress, which, nevertheless, did not account for by its bacteriostatic activity. Copyright © 2017 Elsevier B.V. All rights reserved.

Efflux-Mediated Drug Resistance in Bacteria: an Update

PubMed Central

Li, Xian-Zhi; Nikaido, Hiroshi

2010-01-01

Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome although they can also be plasmid-encoded. A previous article (Li X-Z and Nikaido H, Drugs, 2004; 64[2]: 159–204) had provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past five years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria. PMID:19678712

Infection Vibrio sp. Bacteria on Kappaphycus Seaweed Varieties Brown and Green

NASA Astrophysics Data System (ADS)

Irmawati, Yuni; Sudirjo, Fien

2017-10-01

Disease in seaweed or ice-ice, until today is still a major problem in the cultivation of seaweed. Changes in extreme environmental conditions is a trigger factor of ice-ice, which can result in seaweed susceptible to infection with pathogenic microorganisms, such as bacteria Vibrio sp. This research aims to determine the bacteria Vibrio sp. infection in seaweed Kappaphycus varieties of brown and green. Vibrio sp. bacteria isolated in the infected seaweed thallus ice-ice, grown on TCBS media, purification, gram staining and biochemical tests. Vibrio sp. infected to seaweed Kappaphycus brown and green varieties in containers controlled by different density, 105 CFU/ml, 106 CFU/ml and 107CFU/ml. Observations were made to change clinical effect in thallus seaweed for 14 days of observation. The results obtained show that the levels of infection bacteria Vibrio sp. higher in seaweed Kappaphycus green varieties both in density 105 CFU/ml, 106 CFU/ml and 107CFU/ml, when compared with varieties brown.

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna.

PubMed

Peerakietkhajorn, Saranya; Tsukada, Koji; Kato, Yasuhiko; Matsuura, Tomoaki; Watanabe, Hajime

2015-04-01

The filter-feeding crustacean Daphnia is a key organism in freshwater ecosystems. Here, we report the effect of symbiotic bacteria on ecologically important life history traits, such as population dynamics and longevity, in Daphnia magna. By disinfection of the daphniid embryos with glutaraldehyde, aposymbiotic daphniids were prepared and cultured under bacteria-free conditions. Removal of bacteria from the daphniids was monitored by quantitative polymerase chain reaction for bacterial 16S rRNA gene. The population of aposymbiotic daphniids was reduced 10-folds compared with that of the control daphniids. Importantly, re-infection with symbiotic bacteria caused daphniids to regain bacteria and increase their fecundity to the level of the control daphniids, suggesting that symbiotic bacteria regulate Daphnia fecundity. To identify the species of symbiotic bacteria, 16S rRNA genes of bacteria in daphniids were sequenced. This revealed that 50% of sequences belonged to the Limnohabitans sp. of the Betaproteobacteria class and that the diversity of bacterial taxa was relatively low. These results suggested that symbiotic bacteria have a beneficial effect on D. magna, and that aposymbiotic Daphnia are useful tools in understanding the role of symbiotic bacteria in the environmental responses and evolution of their hosts. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Investigating Bacterial Sources of Toxicity as an Environmental Contributor to Dopaminergic Neurodegeneration

PubMed Central

Caldwell, Kim A.; Tucci, Michelle L.; Armagost, Jafa; Hodges, Tyler W.; Chen, Jue; Memon, Shermeen B.; Blalock, Jeana E.; DeLeon, Susan M.; Findlay, Robert H.; Ruan, Qingmin; Webber, Philip J.; Standaert, David G.; Olson, Julie B.; Caldwell, Guy A.

2009-01-01

Parkinson disease (PD) involves progressive neurodegeneration, including loss of dopamine (DA) neurons from the substantia nigra. Select genes associated with rare familial forms of PD function in cellular pathways, such as the ubiquitin-proteasome system (UPS), involved in protein degradation. The misfolding and accumulation of proteins, such as α-synuclein, into inclusions termed Lewy Bodies represents a clinical hallmark of PD. Given the predominance of sporadic PD among patient populations, environmental toxins may induce the disease, although their nature is largely unknown. Thus, an unmet challenge surrounds the discovery of causal or contributory neurotoxic factors that could account for the prevalence of sporadic PD. Bacteria within the order Actinomycetales are renowned for their robust production of secondary metabolites and might represent unidentified sources of environmental exposures. Among these, the aerobic genera, Streptomyces, produce natural proteasome inhibitors that block protein degradation and may potentially damage DA neurons. Here we demonstrate that a metabolite produced by a common soil bacterium, S. venezuelae, caused DA neurodegeneration in the nematode, Caenorhabditis elegans, which increased as animals aged. This metabolite, which disrupts UPS function, caused gradual degeneration of all neuronal classes examined, however DA neurons were particularly vulnerable to exposure. The presence of DA exacerbated toxicity because neurodegeneration was attenuated in mutant nematodes depleted for tyrosine hydroxylase (TH), the rate-limiting enzyme in DA production. Strikingly, this factor caused dose-dependent death of human SH-SY5Y neuroblastoma cells, a dopaminergic line. Efforts to purify the toxic activity revealed that it is a highly stable, lipophilic, and chemically unique small molecule. Evidence of a robust neurotoxic factor that selectively impacts neuronal survival in a progressive yet moderate manner is consistent with the etiology

Enumeration and Identification of Coliform Bacteria Injured by Chlorine or Fungicide Mixed with Agricultural Water.

PubMed

Izumi, Hidemi; Nakata, Yuji; Inoue, Ayano

2016-10-01

Chemical sanitizers may induce no injury (bacteria survive), sublethal injury (bacteria are injured), or lethal injury (bacteria die). The proportion of coliform bacteria that were injured sublethally by chlorine and fungicide mixed with agricultural water (pond water), which was used to dilute the pesticide solution, was evaluated using the thin agar layer (TAL) method. In pure cultures of Enterobacter cloacae , Escherichia coli , and E. coli O157:H7 (representing a human pathogen), the percentage of chlorine-injured cells was 69 to 77% for dilute electrolyzed water containing an available chlorine level of 2 ppm. When agricultural water was mixed with electrolyzed water, the percentage of injured coliforms in agricultural water was 75%. The isolation and identification of bacteria on TAL and selective media suggested that the chlorine stress caused injury to Enterobacter kobei . Of the four fungicide products tested, diluted to their recommended concentrations, Topsin-M, Sumilex, and Oxirane caused injury to coliform bacteria in pure cultures and in agricultural water following their mixture with each pesticide, whereas Streptomycin did not induce any injury to the bacteria. The percentage of injury was 45 to 97% for Topsin-M, 80 to 87% for Sumilex, and 50 to 97% for Oxirane. A comparison of the coliforms isolated from the pesticide solutions and then grown on either TAL or selective media indicated the possibility of fungicide-injured Rahnella aquatilis , Yersinia mollaretii , and E. coli . These results suggest the importance of selecting a suitable sanitizer and the necessity of adjusting the sanitizer concentration to a level that will kill the coliforms rather than cause sanitizer-induced cell injury that can result in the recovery of the coliforms.

Temporal evolution of the environmental performance of implementing selective collection in municipal waste management systems in developing countries: A Brazilian case study.

PubMed

Ibáñez-Forés, Valeria; Bovea, María D; Coutinho-Nóbrega, Claudia; de Medeiros-García, Hozana R; Barreto-Lins, Raissa

2018-02-01

The aim of this study is to analyse the evolution of the municipal solid waste management system of João Pessoa (Brazil), which was one of the Brazilian pioneers cities in implementing door-to-door selective collection programmes, in order to analyse the effect of policy decisions adopted in last decade with regard to selective collection. To do it, this study focuses on analysing the evolution, from 2005 to 2015, of the environmental performance of the municipal solid waste management (MSWM) system implemented in different sorting units with selective collection programmes by applying the Life Cycle Assessment (LCA) methodology and using as a starting point data collected directly from the different stakeholders involved in the MSWM system. This article presents the temporal evolution of environmental indicators measuring the environmental performance of the MSWM system implemented in João Pessoa by sorting unit, for each stage of the life cycle of the waste (collection, classification, intermediate transports, recycling and landfilling), for each waste fraction and for each collection method (selective collection or mixed collection), with the aim of identifying the key aspects with the greatest environmental impact and their causes. Results show on one hand, that environmental behaviour of waste management in a door-to-door selective collection programme significantly improves the behaviour of the overall waste management system. Consequently, the potential to reduce the existing environmental impact based on citizens' increased participation in selective collection is evidenced, so the implementation of awareness-raising campaigns should be one of the main issues of the next policies on solid waste. On the other hand, increasing the amount of recyclable wastes collected selectively, implementing alternative methods for valorising the organic fraction (compost/biomethanization) and improving the efficiency of the transportation stage by means of optimizing

Fractionation of Hydrogen Isotopes by Sulfate- and Nitrate-Reducing Bacteria.

PubMed

Osburn, Magdalena R; Dawson, Katherine S; Fogel, Marilyn L; Sessions, Alex L

2016-01-01

Hydrogen atoms from water and food are incorporated into biomass during cellular metabolism and biosynthesis, fractionating the isotopes of hydrogen-protium and deuterium-that are recorded in biomolecules. While these fractionations are often relatively constant in plants, large variations in the magnitude of fractionation are observed for many heterotrophic microbes utilizing different central metabolic pathways. The correlation between metabolism and lipid δ(2)H provides a potential basis for reconstructing environmental and ecological parameters, but the calibration dataset has thus far been limited mainly to aerobes. Here we report on the hydrogen isotopic fractionations of lipids produced by nitrate-respiring and sulfate-reducing bacteria. We observe only small differences in fractionation between oxygen- and nitrate-respiring growth conditions, with a typical pattern of variation between substrates that is broadly consistent with previously described trends. In contrast, fractionation by sulfate-reducing bacteria does not vary significantly between different substrates, even when autotrophic and heterotrophic growth conditions are compared. This result is in marked contrast to previously published observations and has significant implications for the interpretation of environmental hydrogen isotope data. We evaluate these trends in light of metabolic gene content of each strain, growth rate, and potential flux and reservoir-size effects of cellular hydrogen, but find no single variable that can account for the differences between nitrate- and sulfate-respiring bacteria. The emerging picture of bacterial hydrogen isotope fractionation is therefore more complex than the simple correspondence between δ(2)H and metabolic pathway previously understood from aerobes. Despite the complexity, the large signals and rich variability of observed lipid δ(2)H suggest much potential as an environmental recorder of metabolism.

Bacteria versus selenium: A view from the inside out

USGS Publications Warehouse

Staicu, Lucian; Oremland, Ronald S.; Tobe, Ryuta; Mihara, Hisaaki

2017-01-01

Bacteria and selenium (Se) are closely interlinked as the element serves both essential nutrient requirements and energy generation functions. However, Se can also behave as a powerful toxicant for bacterial homeostasis. Conversely, bacteria play a tremendous role in the cycling of Se between different environmental compartments, and bacterial metabolism has been shown to participate to all valence state transformations undergone by Se in nature. Bacteria possess an extensive molecular repertoire for Se metabolism. At the end of the 1980s, a novel mode of anaerobic respiration based on Se oxyanions was experimentally documented for the first time. Following this discovery, specific enzymes capable of reducing Se oxyanions and harvesting energy were found in a number of anaerobic bacteria. The genes involved in the expression of these enzymes have later been identified and cloned. This iterative approach undertaken outside-in led to the understanding of the molecular mechanisms of Se transformations in bacteria. Based on the extensive knowledge accumulated over the years, we now have a full(er) view from the inside out, from DNA-encoding genes to enzymes and thermodynamics. Bacterial transformations of Se for assimilatory purposes have been the object of numerous studies predating the investigation of Se respiration. Remarkable contributions related to the understating of the molecular picture underlying seleno-amino acid biosynthesis are reviewed herein. Under certain circumstances, Se is a toxicant for bacterial metabolism and bacteria have evolved strategies to counteract this toxicity, most notably by the formation of elemental Se (nano)particles. Several biotechnological applications, such as the production of functional materials and the biofortification of crop species using Se-utilizing bacteria, are presented in this chapter.

Ecology and Biotechnology of Selenium-Respiring Bacteria

PubMed Central

2015-01-01

SUMMARY In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications. PMID:25631289

[Mutant prevention concentrations of antibacterial agents to ocular pathogenic bacteria].

PubMed

Liang, Qing-Feng; Wang, Zhi-Qun; Li, Ran; Luo, Shi-Yun; Deng, Shi-Jing; Sun, Xu-Guang

2009-01-01

To establish a method to measure mutant prevention concentration (MPC) in vitro, and to measure MPC of antibacterial agents for ocular bacteria caused keratitis. It was an experimental study. Forty strains of ocular bacteria were separated from cornea in Beijing Institute of Ophthalmology, which included 8 strains of Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Pseudomonas aeruginosa and Klebsiella pneumoniae respectively. The minimal inhibitory concentration (MIC) of the levofloxacin (LVF), ofloxacin (OFL), ciprofloxacin (CIP), norfloxacin (NFL), tobramycin (TOB) and chloromycetin (CHL) were determined by agar dilution method from National Committee of Clinical Laboratory Standard (NCCLS). The MPC were measured by accumulate-bacterial methods with bacterial population inoculated more than 1.2 x 10(10) colony forming units per milliliter with Mueller-Hinton broth and tryptic soy agar plate. With the software of SPSS 11.0, the datum such as the range of MIC, MPC, MIC90 and MPC90 were calculated, and the selection index (MPC90/ MI90) and mutant selection window (MSW) were obtained. The MI90 of LVF and TOB (4 mg/L) to Staphylococcus aureus strains were the lowest. CIP showed the lowest MIC90 (0.25 mg/L) to Pseudomonas aeruginosa among six kinds of antibacterial agents. The MIC90 of LVF to Staphylococcus epidermidis (256 mg/L), Streptococcus pneumoniae (1 mg/L) and Klebsiella pneumoniae (0.25 mg/L) were lower than other antibacterial agents. The MPC90, MSW and the MPC90/MIC90 of levofloxacin showed lower values compared with other antibacterial medicines. From all the datum, the MIC90 of CHL was the highest and the activity was the weakest. Although the activity of LVF was higher to every kind of bacteria, CIP had the highest activity antibacterial to Pseudomonas aeruginosa. The capacity of CHL and TOB was weaker than Quinolones for restricting resistant mutants on ocular bacteria. LVF had the strongest capacity for restricting resistant

Bacterial hybrid histidine kinases in plant-bacteria interactions.

PubMed

Borland, Stéphanie; Prigent-Combaret, Claire; Wisniewski-Dyé, Florence

2016-10-01

Two-component signal transduction systems are essential for many bacteria to maintain homeostasis and adapt to environmental changes. Two-component signal transduction systems typically involve a membrane-bound histidine kinase that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid histidine kinase (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra-fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere, where intricate plant-bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings on the mechanistic of their signalling properties. Recent insights into understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.

Biodegradation of Phenylmercuric Acetate by Mercury-Resistant Bacteria

PubMed Central

Nelson, J. D.; Blair, W.; Brinckman, F. E.; Colwell, R. R.; Iverson, W. P.

1973-01-01

Selected cultures of mercury-resistant bacteria degrade the fungicide-slimicide phenylmercuric acetate. By means of a closed system incorporating a flameless atomic absorption spectrophotometer and a vapor phase chromatograph, it was demonstrated that elemental mercury vapor and benzene were products of phenylmercuric acetate degradation. PMID:4584577

Efficacy of on-farm use of ultraviolet light for inactivation of bacteria in milk for calves.

PubMed

Gelsinger, S L; Heinrichs, A J; Jones, C M; Van Saun, R J; Wolfgang, D R; Burns, C M; Lysczek, H R

2014-05-01

Ultraviolet light is being employed for bacterial inactivation in milk for calves; however, limited evidence is available to support the claim that UV light effectively inactivates bacteria found in milk. Thus, the objective of this observational study was to investigate the efficacy of on-farm UV light treatment in reducing bacteria populations in waste milk used for feeding calves. Samples of nonsaleable milk were collected from 9 Pennsylvania herds, twice daily for 15 d, both before and after UV light treatment (n=60 samples per farm), and analyzed for standard plate count, coliforms, noncoliform, gram-negative bacteria, environmental and contagious streptococci, coagulase-negative staphylococci, Streptococcus agalactiae, Staphylococcus aureus count, and total solids percentage, and log reduction and percentage log reduction were calculated. Data were analyzed using the mixed procedure in SAS. In all bacteria types, samples collected after UV treatment contained significantly fewer bacteria compared with samples collected before UV treatment. Weighted least squares means for log reduction (percentage log reduction) were 1.34 (29%), 1.27 (58%), 1.48 (53%), 1.85 (55%), 1.37 (72%), 1.92 (63%), 1.07 (33%), and 1.67 (82%) for standard plate count, coliforms, noncoliform, gram-negative bacteria, environmental and contagious streptococci, Strep. agalactiae, coagulase-negative staphylococci, and Staph. aureus, respectively. A percentage log reduction greater than 50% was achieved in 6 of 8 bacteria types, and 43 and 94% of samples collected after UV treatment met recommended bacterial standards for milk for feeding calves. Based on these results, UV light treatment may be effective for some, but not all bacteria types found in nonsaleable waste milk. Thus, farmers should take into account the bacteria types that may need to be reduced when considering the purchase of a UV-treatment system. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc

Protist-facilitated transport of soil bacteria in an artificial soil micromodel

NASA Astrophysics Data System (ADS)

Rubinstein, R. L.; Cousens, V.; Gage, D. J.; Shor, L. M.

2013-12-01

Soil bacteria within the rhizosphere benefit plants by protecting roots from pathogens, producing growth factors, and improving nutrient availability. These effects can greatly improve overall plant health and increase crop yield, but as roots grow out from the tips they quickly outpace their bacterial partners. Some soil bacteria are motile and can chemotact towards root tips, but bacterial mobility in unsaturated soils is limited to interconnected hydrated pores. Mobility is further reduced by the tendency of soil bacteria to form biofilms. The introduction of protists to the rhizosphere has been shown to benefit plants, purportedly by selective grazing on harmful bacteria or release of nutrients otherwise sequestered in bacteria. We propose that an additional benefit to the presence of protists is the facilitated transport of beneficial bacteria along root systems. Using microfluidic devices designed to imitate narrow, fluid-filled channels in soil, we have shown that the distribution of bacteria through micro-channels is accelerated in the presence of protists. Furthermore, we have observed that even with predation effects, the bacteria remain viable and continue to reproduce for the duration of our experiments. These results expand upon our understanding of complex bio-physical interactions in the rhizosphere system, and may have important implications for agricultural practices.

Enhanced antiadhesive properties of chitosan/hyaluronic acid polyelectrolyte multilayers driven by thermal annealing: Low adherence for mammalian cells and selective decrease in adhesion for Gram-positive bacteria.

PubMed

Muzzio, Nicolás E; Pasquale, Miguel A; Diamanti, Eleftheria; Gregurec, Danijela; Moro, Marta Martinez; Azzaroni, Omar; Moya, Sergio E

2017-11-01

The development of antifouling coatings with restricted cell and bacteria adherence is fundamental for many biomedical applications. A strategy for the fabrication of antifouling coatings based on the layer-by-layer assembly and thermal annealing is presented. Polyelectrolyte multilayers (PEMs) assembled from chitosan and hyaluronic acid were thermally annealed in an oven at 37°C for 72h. The effect of annealing on the PEM properties and topography was studied by atomic force microscopy, ζ-potential, circular dichroism and contact angle measurements. Cell adherence on PEMs before and after annealing was evaluated by measuring the cell spreading area and aspect ratio for the A549 epithelial, BHK kidney fibroblast, C2C12 myoblast and MC-3T3-E1 osteoblast cell lines. Chitosan/hyaluronic acid PEMs show a low cell adherence that decreases with the thermal annealing, as observed from the reduction in the average cell spreading area and more rounded cell morphology. The adhesion of S. aureus (Gram-positive) and E. coli (Gram-negative) bacteria strains was quantified by optical microscopy, counting the number of colony-forming units and measuring the light scattering of bacteria suspension after detachment from the PEM surface. A 20% decrease in bacteria adhesion was selectively observed in the S. aureus strain after annealing. The changes in mammalian cell and bacteria adhesion correlate with the changes in topography of the chitosan/hyaluronic PEMs from a rough fibrillar 3D structure to a smoother and planar surface after thermal annealing. Copyright © 2017. Published by Elsevier B.V.

Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria.

PubMed

Adesoji, Ayodele T; Ogunjobi, Adeniyi A; Olatoye, Isaac O; Call, Douglas R; Douglas, Douglas R

2015-06-25

Antibiotic resistance genes [ARGs] in aquatic systems have drawn increasing attention they could be transferred horizontally to pathogenic bacteria. Water treatment plants (WTPs) are intended to provide quality and widely available water to the local populace they serve. However, WTPs in developing countries may not be dependable for clean water and they could serve as points of dissemination for antibiotic resistant bacteria. Only a few studies have investigated the occurrence of ARGs among these bacteria including tetracycline resistance genes in water distribution systems in Nigeria. Multi-drug resistant (MDR) bacteria, including resistance to tetracycline, were isolated from treated and untreated water distribution systems in southwest Nigeria. MDR bacteria were resistant to >3 classes of antibiotics based on break-point assays. Isolates were characterized using partial 16S rDNA sequencing and PCR assays for six tetracycline-resistance genes. Plasmid conjugation was evaluated using E. coli strain DH5α as the recipient strain. Out of the 105 bacteria, 85 (81 %) and 20 (19 %) were Gram- negative or Gram- positive, respectively. Twenty-nine isolates carried at least one of the targeted tetracycline resistance genes including strains of Aeromonas, Alcaligenes, Bacillus, Klebsiella, Leucobacter, Morganella, Proteus and a sequence matching a previously uncultured bacteria. Tet(A) was the most prevalent (16/29) followed by tet(E) (4/29) and tet30 (2/29). Tet(O) was not detected in any of the isolates. Tet(A) was mostly found with Alcaligenes strains (9/10) and a combination of more than one resistance gene was observed only amongst Alcaligenes strains [tet(A) + tet30 (2/10), tet(A) + tet(E) (3/10), tet(E) + tet(M) (1/10), tet(E) + tet30 (1/10)]. Tet(A) was transferred by conjugation for five Alcaligenes and two E. coli isolates. This study found a high prevalence of plasmid-encoded tet(A) among Alcaligenes isolates, raising the possibility that this

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mortimer, Monika; Petersen, Elijah; Buchholz, Bruce

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here in this paper, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstratemore » separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. Lastly, the optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation.« less

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

DOE PAGES

Mortimer, Monika; Petersen, Elijah; Buchholz, Bruce; ...

2016-10-12

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here in this paper, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstratemore » separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. Lastly, the optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation.« less

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria

PubMed Central

Yosef, Ido; Manor, Miriam; Kiro, Ruth

2015-01-01

The increasing threat of pathogen resistance to antibiotics requires the development of novel antimicrobial strategies. Here we present a proof of concept for a genetic strategy that aims to sensitize bacteria to antibiotics and selectively kill antibiotic-resistant bacteria. We use temperate phages to deliver a functional clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) system into the genome of antibiotic-resistant bacteria. The delivered CRISPR-Cas system destroys both antibiotic resistance-conferring plasmids and genetically modified lytic phages. This linkage between antibiotic sensitization and protection from lytic phages is a key feature of the strategy. It allows programming of lytic phages to kill only antibiotic-resistant bacteria while protecting antibiotic-sensitized bacteria. Phages designed according to this strategy may be used on hospital surfaces and hand sanitizers to facilitate replacement of antibiotic-resistant pathogens with sensitive ones. PMID:26060300

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria.

PubMed

Yosef, Ido; Manor, Miriam; Kiro, Ruth; Qimron, Udi

2015-06-09

The increasing threat of pathogen resistance to antibiotics requires the development of novel antimicrobial strategies. Here we present a proof of concept for a genetic strategy that aims to sensitize bacteria to antibiotics and selectively kill antibiotic-resistant bacteria. We use temperate phages to deliver a functional clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system into the genome of antibiotic-resistant bacteria. The delivered CRISPR-Cas system destroys both antibiotic resistance-conferring plasmids and genetically modified lytic phages. This linkage between antibiotic sensitization and protection from lytic phages is a key feature of the strategy. It allows programming of lytic phages to kill only antibiotic-resistant bacteria while protecting antibiotic-sensitized bacteria. Phages designed according to this strategy may be used on hospital surfaces and hand sanitizers to facilitate replacement of antibiotic-resistant pathogens with sensitive ones.

Lipidomics as an important key for the identification of beer-spoilage bacteria.

PubMed

Řezanka, T; Matoulková, D; Benada, O; Sigler, K

2015-06-01

Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was used for characterizing intact plasmalogen phospholipid molecules in beer-spoilage bacteria. Identification of intact plasmalogens was carried out using collision-induced dissociation and the presence of suitable marker molecular species, both qualitative and quantitative, was determined in samples containing the anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method had a limit of detection at 1 pg for the standard, i.e. 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and be linear in the range of four orders of magnitude from 2 pg to 20 ng. This technique was applied to intact plasmalogen extracts from the samples of contaminated and uncontaminated beer without derivatization and resulted in the identification of contamination of beer by Megasphaera and Pectinatus bacteria. The limit of detection was about 830 cells of anaerobic bacteria, i.e. bacteria containing natural cyclopropane plasmalogenes (c-p-19:0/15:0), which is the majority plasmalogen located in both Megasphaera and Pectinatus. The SIM ESI-MS method has been shown to be useful for the analysis of low concentration of plasmalogens in all biological samples, which were contaminated with anaerobic bacteria, e.g. juice, not only in beer. Significance and impact of the study: Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) using collision-induced dissociation was used to characterize intact plasmalogen phospholipid molecules in beer-spoilage anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method has a detection limit of 1 pg for the standard 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and is linear within four orders of magnitude (2 pg to 20 ng). The limit of detection was about 830 cells of bacteria containing natural cyclopropane plasmalogen (c-p-19:0/15:0). SIM ESI-MS method is useful for analyzing low

Variable selection with random forest: Balancing stability, performance, and interpretation in ecological and environmental modeling

EPA Science Inventory

Random forest (RF) is popular in ecological and environmental modeling, in part, because of its insensitivity to correlated predictors and resistance to overfitting. Although variable selection has been proposed to improve both performance and interpretation of RF models, it is u...

Distribution of multi-resistant Gram-negative versus Gram-positive bacteria in the hospital inanimate environment.

PubMed

Lemmen, S W; Häfner, H; Zolldann, D; Stanzel, S; Lütticken, R

2004-03-01

We prospectively studied the difference in detection rates of multi-resistant Gram-positive and multi-resistant Gram-negative bacteria in the inanimate environment of patients harbouring these organisms. Up to 20 different locations around 190 patients were surveyed. Fifty-four patients were infected or colonized with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant enterococci (VRE) and 136 with multi-resistant Gram-negative bacteria. The environmental detection rate for MRSA or VRE was 24.7% (174/705 samples) compared with 4.9% (89/1827 samples) for multi-resistant Gram-negative bacteria (P<0.001). Gram-positive bacteria were isolated more frequently than Gram-negatives from the hands of patients (P<0.001) and hospital personnel (P=0.1145). Environmental contamination did not differ between the intensive care units (ICUs) and the general wards (GWs), which is noteworthy because our ICUs are routinely disinfected twice a day, whereas GWs are cleaned just once a day with detergent. Current guidelines for the prevention of spread of multi-resistant bacteria in the hospital setting do not distinguish between Gram-positive and Gram-negative isolates. Our results suggest that the inanimate environment serves as a secondary source for MRSA and VRE, but less so for Gram-negative bacteria. Thus, strict contact isolation in a single room with complete barrier precautions is recommended for MRSA or VRE; however, for multi-resistant Gram-negative bacteria, contact isolation with barrier precautions for close contact but without a single room seems sufficient. This benefits not only the patients, but also the hospital by removing some of the strain placed on already over-stretched resources.

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments

PubMed Central

Finkelshtein, Alin; Roth, Dalit

2015-01-01

ABSTRACT Swarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacterium Paenibacillus vortex can collectively transport other microorganisms. Here we show that P. vortex can invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitive P. vortex used beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal. P. vortex transported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way. P. vortex displayed a bet-hedging strategy that promoted the colonization of nontoxic niches by P. vortex alone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications. PMID:25968641

Isolation and identification of chitinolytic bacteria of pohara river of South East Sulawesi and the optimization production of chitinase enzyme

NASA Astrophysics Data System (ADS)

Halimahtussadiyah, R.; Natsir, Muh.; Kurniawati, Desy; Utamy, Sukma Puspita

2017-03-01

Isolation and identification of chitinolytic bacteria from pohara river and optimation of chitinase enzyme production has been conducted. The aims of the study were isolation, characterize and optimaze of chitinase enzyme production. This study was carried out in three stages; isolation and selection of chitinolytic bacteria, characterization and identification of selected bacteria; optimization of the production of the enzyme (substrate concentration, temperature, and pH), and the determination of growth curve of T3 isolate. The chitinase activity assay was carried out using Schales method. The results of the screening obtained 6 isolates of potential bacteria of chitinolytic. The T3 isolate then was selected for the enzyme production, because it had the highest chitinolytic index of 22.31 mm. The morphological and biochemical observation showed that T3 isolate as a group of bacteria Aerobacter with Gram-negative nature, and shaped bacillus. The optimum condition for chitinase enzyme production was in chitin substrat concentration 0.06%, temperature of 30°C, and pH of 6.

The ability of selected plant essential oils to enhance the action of recommended antibiotics against pathogenic wound bacteria.

PubMed

Sienkiewicz, Monika; Łysakowska, Monika; Kowalczyk, Edward; Szymańska, Grażyna; Kochan, Ewa; Krukowska, Jolanta; Olszewski, Jurek; Zielińska-Bliźniewska, Hanna

2017-03-01

The aim of this work was to characterize the ability of essential oils to support antibiotics against pathogenic bacteria in wounds. Gram-positive and Gram-negative bacteria obtained from wound infections were identified according to standard microbiological methods. Essential oils were analysed by GC-FID-MS. The susceptibility of bacteria to antibiotics, essential oils and their combination was assessed using the disc-diffusion method. The Minimal Inhibitory Concentration and Minimum Bactericidal Concentration of the essential oils were established by the micro-dilution broth method. Although cinnamon, clove, thyme and lavender essential oils were found to have the greatest antibacterial activity when used alone, the greatest additive and synergistic effects against pathogenic wound bacteria in combination with recommended antibiotics were demonstrated by basil, clary sage and rosemary oils. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

Agar Underlay Method for Recovery of Sublethally Heat-Injured Bacteria

PubMed Central

Kang, D. H.; Siragusa, G. R.

1999-01-01

A method of recovering sublethally heat-injured bacteria was developed. The procedure (termed the agar underlay method) uses a nonselective agar underlaid with a selective medium. In a two-chambered petri dish, the Lutri plate (LP), a nonselective agar is inoculated with a population of sublethally heat-injured bacteria. After a 2-h repair incubation period, selective agar is added to the bottom chamber of the LP and incubated. By diffusing through the nonselective top agar, selective agents from the underlay medium impart selectivity to the system. By the agar underlay method, recovery rates of the heat-injured food-borne pathogens Escherichia coli O157:H7 and Salmonella typhimurium were not different (P > 0.05) from recovery rates determined with nonselective media. Sublethally heat-injured cells (60°C for 1.5 min in buffer or 80°C for 30 s on meat surfaces) grew and produced a typical colony morphology and color reaction when the agar underlay procedure was used with the appropriate respective selective agars. Unlike agar overlay methods for injury repair, the agar underlay procedure allows the typical selective-medium colony morphology to develop and allows colonies to be more easily picked for further characterization. Higher recovery rates of heat-injured fecal enterococci from bovine fecal samples and total coliforms from animal waste lagoons were obtained by the agar underlay method with selective agars than by direct plating on the respective selective media. PMID:10583985

Tracking spore-forming bacteria in food: from natural biodiversity to selection by processes.

PubMed

Postollec, Florence; Mathot, Anne-Gabrielle; Bernard, Muriel; Divanac'h, Marie-Laure; Pavan, Sonia; Sohier, Danièle

2012-08-01

Sporeforming bacteria are ubiquitous in the environment and exhibit a wide range of diversity leading to their natural prevalence in foodstuff. The state of the art of sporeformer prevalence in ingredients and food was investigated using a multiparametric PCR-based tool that enables simultaneous detection and identification of various genera and species mostly encountered in food, i.e., Alicyclobacillus, Anoxybacillus flavithermus, Bacillus, B. cereus group, B. licheniformis, B. pumilus, B. sporothermodurans, B. subtilis, Brevibacillus laterosporus, Clostridium, Geobacillus stearothermophilus, Moorella and Paenibacillus species. In addition, 16S rDNA sequencing was used to extend identification to other possibly present contaminants. A total of 90 food products, with or without visible trace of spoilage were analysed, i.e., 30 egg-based products, 30 milk and dairy products and 30 canned food and ingredients. Results indicated that most samples contained one or several of the targeted genera and species. For all three tested food categories, 30 to 40% of products were contaminated with both Bacillus and Clostridium. The percentage of contaminations associated with Clostridium or Bacillus represented 100% in raw materials, 72% in dehydrated ingredients and 80% in processed foods. In the last two product types, additional thermophilic contaminants were identified (A. flavithermus, Geobacillus spp., Thermoanaerobacterium spp. and Moorella spp.). These results suggest that selection, and therefore the observed (re)-emergence of unexpected sporeforming contaminants in food might be favoured by the use of given food ingredients and food processing technologies. Copyright © 2012 Elsevier B.V. All rights reserved.

Selection of antagonistic bacteria isolated from the Physalis peruviana rhizosphere against Fusarium oxysporum.

PubMed

Urrea, R; Cabezas, L; Sierra, R; Cárdenas, M; Restrepo, S; Jiménez, P

2011-09-01

Cape gooseberries (Physalis peruviana) have become increasingly important in Colombia for both domestic consumption and the international export market. Vascular wilting caused by Fusarium oxysporum is the most damaging disease to P. peruviana crops in Colombia. The control of this pathogen is mainly carried out by chemical and cultural practices, increasing production costs and generating resistance. Therefore, the objectives of this study were to test rhizobacteria isolates from P. peruviana rhizosphere against F. oxysporum under in vitro and in vivo conditions. Over 120 strains were isolated, and five were selected for their high inhibition of F. oxysporum growth and conidia production under in vitro conditions. These strains inhibited growth by 41-58% and reduced three- to fivefold conidia production. In the in vivo assays, all the tested isolates significantly reduced fungal pathogenicity in terms of virulence. Isolate B-3.4 was the most efficient in delaying the onset of the first symptoms. All isolates were identified as belonging to the genus Pseudomonas except for A-19 (Bacillus sp.). Our results confirmed that there are prospective rhizobacteria strains that can be used as biological control agents; some of them being able to inhibit in vitro F. oxysporum growth and sporulation. Incorporating these bacteria into biological control strategies for the disease that causes high economical losses in the second most exported fruit from Colombia would result in a reduced impact on environment and economy. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

PubMed Central

Sime-Ngando, Télesphore

2014-01-01

Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology. PMID:25104950

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

PubMed Central

2013-01-01

Background Guanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuable information can be acquired from amino acid composition data. To address this concern, in-depth analyses of the amino acid composition of the complete proteomes from 63 archaea, 270 bacteria, and 128 eukaryotes were performed. Results Principal component analysis of the amino acid matrices showed that the main contributors to proteomic architecture were genomic GC variation, phylogeny, and environmental influences. GC pressure drove positive selection on Ala, Arg, Gly, Pro, Trp, and Val, and adverse selection on Asn, Lys, Ile, Phe, and Tyr. The physico-chemical framework of the complete proteomes withstood GC pressure by frequency complementation of GC-dependent amino acid pairs with similar physico-chemical properties. Gln, His, Ser, and Val were responsible for phylogeny and their constituted components could differentiate archaea, bacteria, and eukaryotes. Environmental niche was also a significant factor in determining proteomic architecture, especially for archaea for which the main amino acids were Cys, Leu, and Thr. In archaea, hyperthermophiles, acidophiles, mesophiles, psychrophiles, and halophiles gathered successively along the environment-based principal component. Concordance between proteomic architecture and the genetic code was also related closely to genomic GC content, phylogeny, and lifestyles. Conclusions Large-scale analyses of the complete proteomes of a wide range of organisms suggested that amino acid composition retained the trace of GC variation, phylogeny, and environmental influences during evolution. The findings from this study will help in the development of a global understanding of proteome evolution, and even biological evolution. PMID:24088322

Environmental change disrupts communication and sexual selection in a stickleback population.

PubMed

Candolin, Ulrika; Tukiainen, Iina; Bertell, Elina

2016-04-01

Environmental change that disrupts communication during mate choice and alters sexual selection could influence population dynamics. Yet little is known about such long-term effects. We investigated experimentally the consequences that disrupted visual communication during mate choice has for the quantity and viability of offspring produced in a threespine stickleback population (Gasterosteus aculeatus). We further related the results to long-term monitoring of population dynamics in the field to determine if changes are apparent under natural conditions. The results show that impaired visual communication because of algal blooms reduces reliability of male visual signals as indicators of offspring survival during their first weeks of life. This relaxes sexual selection but has no effect on the number of offspring hatching, as most males have a high hatching success in turbid water. Despite eutrophication and high turbidity levels that interfere with communication during mate choice, the population has grown during recent decades. Large numbers of offspring hatching, combined with high variation in juvenile fitness, has probably shifted selection to later life history stages and maintained a viable population. Together with reduced cost of sexual selection and ongoing ecosystem changes caused by human activities, this could have promoted population growth. These results point to the complexity of ecosystems and the necessity to consider all influencing factors when attempting to understand impacts of human activities on populations.

Adhesion of Biodegradative Anaerobic Bacteria to Solid Surfaces

PubMed Central

van Schie, Paula M.; Fletcher, Madilyn

1999-01-01

In order to exploit the ability of anaerobic bacteria to degrade certain contaminants for bioremediation of polluted subsurface environments, we need to understand the mechanisms by which such bacteria partition between aqueous and solid phases, as well as the environmental conditions that influence partitioning. We studied four strictly anaerobic bacteria, Desulfomonile tiedjei, Syntrophomonas wolfei, Syntrophobacter wolinii, and Desulfovibrio sp. strain G11, which theoretically together can constitute a tetrachloroethylene- and trichloroethylene-dechlorinating consortium. Adhesion of these organisms was evaluated by microscopic determination of the numbers of cells that attached to glass coverslips exposed to cell suspensions under anaerobic conditions. We studied the effects of the growth phase of the organisms on adhesion, as well as the influence of electrostatic and hydrophobic properties of the substratum. Results indicate that S. wolfei adheres in considerably higher numbers to glass surfaces than the other three organisms. Starvation greatly decreases adhesion of S. wolfei and Desulfovibrio sp. strain G11 but seems to have less of an effect on the adhesion of the other bacteria. The presence of Fe3+ on the substratum, which would be electropositive, significantly increased the adhesion of S. wolfei, whereas the presence of silicon hydrophobic groups decreased the numbers of attached cells of all species. Measurements of transport of cells through hydrophobic-interaction and electrostatic-interaction columns indicated that all four species had negatively charged cell surfaces and that D. tiedjei and Desulfovibrio sp. strain G11 possessed some hydrophobic cell surface properties. These findings are an early step toward understanding the dynamic attachment of anaerobic bacteria in anoxic environments. PMID:10543826

Microtiter plate-based antibody microarrays for bacteria and toxins

USDA-ARS?s Scientific Manuscript database

Research has focused on the development of rapid biosensor-based, high-throughput, and multiplexed detection of pathogenic bacteria in foods. Specifically, antibody microarrays in 96-well microtiter plates have been generated for the purpose of selective detection of Shiga toxin-producing E. coli (...

Selection of Lactic Acid Bacteria with Probiotic Potential Isolated from the Fermentation Process of "Cupuaçu" (Theobroma grandiflorum).

PubMed

Ornellas, Roberta Maria Santos; Santos, Tiza Teles; Arcucio, Leonardo Borges; Sandes, Sávio Henrique Cicco; Oliveira, Mayara Messias; Dias, Cristiano Villela; de Carvalho Silva, Samuel; Uetanabaro, Ana Paula Trovatti; Vinderola, Gabriel; Nicoli, Jacques Robert

2017-01-01

In the present study, nine lactic acid bacteria isolated from the fermentation process of "cupuaçu" (Theobroma grandiflorum) were selected for probiotic use. In vitro (resistance to gastrointestinal environment, in vitro antagonism and co-aggregation with pathogens) and in vivo (intestinal colonization and ex vivo antagonism in germ-free mice, cumulative mortality, translocation to liver and spleen, histopathological examination of liver and ileum and mRNA cytokine gene expression during an experimental infection with S. Typhimurium) assays were used. Among the nine Lactobacillus strains isolated from the "cupuaçu" fermentation, L. plantarum 81 and L. plantarum 90 were selected as potential probiotics based on better results obtained in in vitro evaluations (production of diffusible inhibitory compounds and co-aggregation) as well as in vivo experiments (resistance to gastrointestinal environment, ex vivo antagonism, higher survival after enteropathogen challenge, lower hepatic translocation of enteropathogen, lower histopathological lesions in ileum and liver and anti-inflammatory pattern of immunological response). Concluding, L. plantarum 81 and L. plantarum 90 showed in vitro and in vivo capacities for probiotic use through different mechanisms of protection and its origin would allow an easier adaptation in an alimentary matrix for its administration.

The Use of Predatory Bacteria to Control Select Pathogens and Treat Respiratory Infections

DTIC Science & Technology

2015-04-13

Monnappa, A. K. & Mitchell, R. J. The dual probiotic and antibiotic nature of Bdellovibrio bacteriovorus. BMB Rep 45, 71-78, doi:10.5483/BMBRep...Perdigon, G. Gut immune stimulation by non pathogenic Gram(+) and Gram(-) bacteria. Comparison with a probiotic strain. Cytokine 41, 223-231, doi:10.1016

Characterization of radiation-resistant vegetative bacteria in beef.

PubMed

Welch, A B; Maxcy, R B

1975-08-01

Ground beef contains numerous microorganisms of various types. The commonly recognized bacteria are associated with current problems of spoilage. Irradiation, however, contributes a new factor through selective destruction of the microflora. The residual microorganisms surviving a nonsterilizing dose are predominantly gram-negative coccobacilli. Various classifications have been given, e.g., Moraxella, Acinetobacter, Achromobacter, etc. For a more detailed study of these radiation-resistant bacteria occurring in ground beef, an enrichment procedure was used for isolation. By means of morphological and biochemical tests, most of the isolates were found to be Moraxella, based on current classifications. The range of growth temperatures was from 2 to 50 C. These bacteria were relatively heat sensitive, e.g., D10 of 5.4 min at 70 C or less. The radiation resistance ranged from D10 values of 273 to 2,039 krad. Thus, some were more resistant than any presently recognized spores. A reference culture of Moraxella osloensis was irradiated under conditions comparable to the enrichment procedure used with the ground beef. The only apparent changes were in morphology and penicillin sensitivity. However, after a few subcultures these bacteria reverted to the characteristics of the parent strain. Thus, it is apparent that these isolates are a part of the normal flora of ground beef and not aberrant forms arising from the irradiation procedure. The significance, if any, of these bacteria is not presently recognized.

Stone-isolated carbonatogenic bacteria as inoculants in bioconsolidation treatments for historical limestone.

PubMed

Jroundi, Fadwa; Gómez-Suaga, Patricia; Jimenez-Lopez, Concepción; González-Muñoz, Maria Teresa; Fernandez-Vivas, Maria Antonia

2012-05-15

Stone consolidation treatments that use bacterial biomineralization are mainly based on two strategies: (1) the inoculation of a bacterial culture with proven carbonatogenic ability and/or (2) the application of a culture medium capable of activating those bacteria able to induce the formation of calcium carbonate, from amongst the bacterial community of the stone. While the second strategy has been demonstrated to be effective and, unlike first strategy, it does not introduce any exogenous microorganism into the stone, problems may arise when the bacterial community of the stone is altered, for instance by the use of biocides in the cleaning process. In this study we isolate bacteria that belong to the natural microbial community of the stone and which have proven biomineralization capabilities, with the aim of preparing an inoculum that may be used in stone consolidation treatments wherein the natural community of those stones is altered. With this aim, outdoor experiments were undertaken to activate and isolate bacteria that display high biomineralization capacity from altered calcarenite stone. Most of the bacteria precipitated calcium carbonate in the form of calcite. The selected bacteria were phylogenetically affiliated with members of Actinobacteria, Gamma-proteobacteria and Firmicutes. Furthermore, the capability of these selected carbonatogenic bacteria to consolidate altered calcarenite stone slabs was studied in in vitro experiments, both in the presence and the absence of Myxococcus xanthus, as a potential reinforcement for the bacterial biomineralization. Herein, Acinetobacter species, belonging to the microbial community of the stone, are proposed as powerful carbonatogenic bacteria that, inoculated under appropriate conditions, may be used as inoculum for calcareous stone conservation/consolidation in restoration interventions where the microbial community of the stone is altered. Copyright © 2012 Elsevier B.V. All rights reserved.

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

PubMed Central

Azarian, Taj; Ali, Afsar; Johnson, Judith A.; Mohr, David; Prosperi, Mattia; Veras, Nazle M.; Jubair, Mohammed; Strickland, Samantha L.; Rashid, Mohammad H.; Alam, Meer T.; Weppelmann, Thomas A.; Katz, Lee S.; Tarr, Cheryl L.; Colwell, Rita R.

2014-01-01

ABSTRACT Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. PMID:25538191

Ecology and biotechnology of selenium-respiring bacteria.

PubMed

Nancharaiah, Y V; Lens, P N L

2015-03-01

In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.

PubMed

Stark, Lucy; Giersch, Tina; Wünschiers, Röbbe

2014-10-01

Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome

PubMed Central

Hernandez-Sanabria, Emma; Slomka, Vera; Herrero, Esteban R.; Kerckhof, Frederiek-Maarten; Zaidel, Lynette; Teughels, Wim; Boon, Nico

2017-01-01

Understanding the driving forces behind the shifts in the ecological balance of the oral microbiota will become essential for the future management and treatment of periodontitis. As the use of competitive approaches for modulating bacterial outgrowth is unexplored in the oral ecosystem, our study aimed to investigate both the associations among groups of functional compounds and the impact of individual substrates on selected members of the oral microbiome. We employed the Phenotype Microarray high-throughput technology to analyse the microbial cellular phenotypes of 15 oral bacteria. Multivariate statistical analysis was used to detect respiratory activity triggers and to assess similar metabolic activities. Carbon and nitrogen were relevant for the respiration of health-associated bacteria, explaining competitive interactions when grown in biofilms. Carbon, nitrogen, and peptides tended to decrease the respiratory activity of all pathobionts, but not significantly. None of the evaluated compounds significantly increased activity of pathobionts at both 24 and 48 h. Additionally, metabolite requirements of pathobionts were dissimilar, suggesting that collective modulation of their respiratory activity may be challenging. Flow cytometry indicated that the metabolic activity detected in the Biolog plates may not be a direct result of the number of bacterial cells. In addition, damage to the cell membrane may not influence overall respiratory activity. Our methodology confirmed previously reported competitive and collaborative interactions among bacterial groups, which could be used either as marker of health status or as targets for modulation of the oral environment. PMID:28638806

Ethylene-producing bacteria that ripen fruit.

PubMed

Digiacomo, Fabio; Girelli, Gabriele; Aor, Bruno; Marchioretti, Caterina; Pedrotti, Michele; Perli, Thomas; Tonon, Emil; Valentini, Viola; Avi, Damiano; Ferrentino, Giovanna; Dorigato, Andrea; Torre, Paola; Jousson, Olivier; Mansy, Sheref S; Del Bianco, Cristina

2014-12-19

Ethylene is a plant hormone widely used to ripen fruit. However, the synthesis, handling, and storage of ethylene are environmentally harmful and dangerous. We engineered E. coli to produce ethylene through the activity of the ethylene-forming enzyme (EFE) from Pseudomonas syringae. EFE converts a citric acid cycle intermediate, 2-oxoglutarate, to ethylene in a single step. The production of ethylene was placed under the control of arabinose and blue light responsive regulatory systems. The resulting bacteria were capable of accelerating the ripening of tomatoes, kiwifruit, and apples.

Characteristic Assessment of Diesel-degrading Bacteria Immobilized on Natural Organic Carriers in Marine Environment: the Degradation Activity and Nutrient.

PubMed

Xue, Jianliang; Wu, Yanan; Liu, Zhixiu; Li, Menglu; Sun, Xiyu; Wang, Huajun; Liu, Bing

2017-08-17

Oil spill has led to severe environmental and ecological problems. Due to the harsh environmental conditions, the bioremediation technology is not successfully used to remedy the oil spill in marine environment. In this study, immobilization technology was used to immobilize bacteria on natural organic carriers (i.e., wood chips and maize straw). The higher surface area of in wood chips leads to larger biomass density (0.0242 gVSS/g) than that of maize straw of 0.0097 gVSS/g carrier. Compared with biodegradation efficiency of free bacteria (44.79%), the immobilized bacteria on wood chips and maize straw reached to 73.39% and 52.28%, respectively. The high biological activity of the immobilized bacteria can be also explained by nutrients, such as TN (total nitrogen) and TP (total phosphorus), released from wood chips and maize straw, which was 8.83 mg/g and 5.53 mg/g, 0.0624 mg/g and 0.0099 mg/g, respectively.

Indigenous soil bacteria and low moisture may limit but allow faecal bacteria to multiply and become a minor population in tropical soils

USGS Publications Warehouse

Byappanahalli, M.; Fujioka, R.

2004-01-01

The soil environment in Hawaii is generally characterised as sub-optimal but permissive to support the in situ growth of E. coli and enterococci. However, soil desiccation and competition for nutrients by major indigenous soil microflora have been identified as potential factors that could limit a rapid and continual growth of faecal indicator bacteria in this soil environment. Despite these limitations, the genetic capacities of E. coli and enterococci are robust enough to enable these bacteria to become established as minor populations of Hawaii's soil microflora. Although the concentrations of E. coli and enterococci may have represented a fraction of the total soil microbiota, their presence in this habitat was very significant, for two important reasons: (a) soil was a major environmental source of E. coli and enterococci, and (b) the elevated counts of these bacteria in streams that routinely exceeded the EPA standards were due to run-off from soil. As a result, E. coli and enterococci were inadequate indicators to measure the degree of faecal contamination and potential presence of sewage-borne pathogens in Hawaiian streams. ?? IWA Publishing 2004.

Ciprofloxacin residue and antibiotic-resistant biofilm bacteria in hospital effluent.

PubMed

Ory, Jérôme; Bricheux, Geneviève; Togola, Anne; Bonnet, Jean Louis; Donnadieu-Bernard, Florence; Nakusi, Laurence; Forestier, Christiane; Traore, Ousmane

2016-07-01

Discharge of antimicrobial residues and resistant bacteria in hospital effluents is supposed to have strong impacts on the spread of antibiotic resistant bacteria in the environment. This study aimed to characterize the effluents of the Gabriel Montpied teaching hospital, Clermont-Ferrand, France, by simultaneously measuring the concentration of ciprofloxacin and of biological indicators resistant to this molecule in biofilms formed in the hospital effluent and by comparing these data to ciprofloxacin consumption and resistant bacterial isolates of the hospital. Determination of the measured environmental concentration of ciprofloxacin by spot sampling and polar organic chemical integrative (POCIS) sampling over 2 weeks, and comparison with predicted environmental concentrations produced a hazard quotient >1, indicating a potential ecotoxicological risk. A negative impact was also observed with whole hospital effluent samples using the Tetrahymena pyriformis biological model. During the same period, biofilms were formed within the hospital effluent, and analysis of ciprofloxacin-resistant isolates indicated that Gamma-Proteobacteria were numerous, predominantly Aeromonadaceae (69.56%) and Enterobacteriaceae (22.61%). Among the 115 isolates collected, plasmid-mediated fluoroquinolone-resistant genes were detected, with mostly aac(6')-lb-cr and qnrS. In addition, 60% of the isolates were resistant to up to six antibiotics, including molecules mostly used in the hospital (aminosides and third-generation cephalosporins). In parallel, 1247 bacteria isolated from hospitalized patients and resistant to at least one of the fluoroquinolones were collected. Only 5 of the 14 species identified in the effluent biofilm were also found in the clinical isolates, but PFGE typing of the Gram-negative isolates found in both compartments showed there was no clonality among the strains. Altogether, these data confirm the role of hospital loads as sources of pollution for wastewater

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

Bacteria transport simulation using apex model in the toenepi watershed, New Zealand

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy/Environmental eXtender (APEX) model is a distributed, continuous, daily-timestep small watershed-scale hydrologic and water quality model. In this study, the newly developed fecal-derived bacteria fate and transport subroutine was applied and validated using APEX model. The ...

Lead absorption mechanisms in bacteria as strategies for lead bioremediation.

PubMed

Tiquia-Arashiro, Sonia M

2018-05-08

Bacteria exhibit a number of metabolism-dependent and metabolism-independent processes for the uptake and accumulation of toxic metals. The removal of these metals from environmental sources such as soil, sludge, and wastewaters using microbe-based technologies provide an alternative for their recovery and remediation. Lead (Pb) is a pervasive metal in the environment that adversely affects all living organisms. Many aspects of metal-microbe interactions remain unexploited in biotechnology and further development and application is necessary, particularly to the problem of Pb release into the environment. Thus, this review provides a synopsis of the most important bacterial phenotypes and biochemical attributes that are instrumental in lead bioremediation, along with what is known of their genetic background that can be exploited or improved through genetic engineering. This review also highlights the potential of Pb-resistant bacteria in bringing about detoxification of Pb-contaminated terrestrial and aquatic systems in a highly sustainable and environmental friendly manner, and the existing challenges that still lie in the path to in situ and large-scale bioremediation.

Quorum quenching is an antivirulence strategy employed by endophytic bacteria.

PubMed

Kusari, Parijat; Kusari, Souvik; Lamshöft, Marc; Sezgin, Selahaddin; Spiteller, Michael; Kayser, Oliver

2014-08-01

Bacteria predominantly use quorum sensing to regulate a plethora of physiological activities such as cell-cell crosstalk, mutualism, virulence, competence, biofilm formation, and antibiotic resistance. In this study, we investigated how certain potent endophytic bacteria harbored in Cannabis sativa L. plants use quorum quenching as an antivirulence strategy to disrupt the cell-to-cell quorum sensing signals in the biosensor strain, Chromobacterium violaceum. We used a combination of high-performance liquid chromatography high-resolution mass spectrometry (HPLC-ESI-HRMS(n)) and matrix-assisted laser desorption ionization imaging high-resolution mass spectrometry (MALDI-imaging-HRMS) to first quantify and visualize the spatial distribution of the quorum sensing molecules in the biosensor strain, C. violaceum. We then showed, both quantitatively and visually in high spatial resolution, how selected endophytic bacteria of C. sativa can selectively and differentially quench the quorum sensing molecules of C. violaceum. This study provides fundamental insights into the antivirulence strategies used by endophytes in order to survive in their ecological niches. Such defense mechanisms are evolved in order to thwart the plethora of pathogens invading associated host plants in a manner that prevents the pathogens from developing resistance against the plant/endophyte bioactive secondary metabolites. This work also provides evidence towards utilizing endophytes as tools for biological control of bacterial phytopathogens. In continuation, such insights would even afford new concepts and strategies in the future for combating drug resistant bacteria by quorum-inhibiting clinical therapies.

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum▿

PubMed Central

Ettwig, Katharina F.; van Alen, Theo; van de Pas-Schoonen, Katinka T.; Jetten, Mike S. M.; Strous, Marc

2009-01-01

Anaerobic methane oxidation coupled to denitrification was recently assigned to bacteria belonging to the uncultured phylum NC10. In this study, we incubated sediment from a eutrophic ditch harboring a diverse community of NC10 bacteria in a bioreactor with a constant supply of methane and nitrite. After 6 months, fluorescence in situ hybridization showed that NC10 bacteria dominated the resulting population. The enrichment culture oxidized methane and reduced nitrite to dinitrogen gas. We assessed NC10 phylum diversity in the inoculum and the enrichment culture, compiled the sequences currently available for this bacterial phylum, and showed that of the initial diversity, only members of one subgroup had been enriched. The growth of this subgroup was monitored by quantitative PCR and correlated to nitrite-reducing activity and the total biomass of the culture. Together, the results indicate that the enriched subgroup of NC10 bacteria is responsible for anaerobic methane oxidation coupled to nitrite reduction. Due to methodological limitations (a strong bias against NC10 bacteria in 16S rRNA gene clone libraries and inhibition by commonly used stopper material) the environmental distribution and importance of these bacteria could be largely underestimated at present. PMID:19329658

[Screening endophytic bacteria against plant-parasitic nematodes].

PubMed

Peng, Shuang; Yan, Shuzhen; Chen, Shuanglin

2011-03-01

Plant-parasite nematode is one of the most important pathogens in plant. Our objective is to screen endophytic bacteria against plant-parasitic nematodes from plant. Endophytic bacteria were isolated and screened by testing their metabolite against Bursaphelenchus xylophilus in vitro. Those strains inhibiting B. xylophilus were selected to culture in liquid medium and fermentation conditions were optimized by orthogonal test. The stability of the antinematode substances was evaluated by various. In addition, four strains were identified by 16SrDNA sequence analysis. In total 13 strains of endophytic bacteria secreting antinematode metabolite were isolated from 6 species of plant. The supernatant of the fermentation broth of these endophytic bacteria gave 100% mortality of nematodes after treated as the follows: 1 ml each was mixed with 0.2 ml of the suspension of nematodes (2000 nematodes/ml) then incubated at 250C for 24 h, some of which could led to leakage or dissolution of nematodes. Among them, four strains, BCM2, SZ5, CCM7 and DP1, showed stronger activity than others. The supernatants diluted three times also gave not less than 95% mortality after 24 h treatment, and those from DP1 and SZ5 even gave 100% mortality. The fermentation conditions of the four strains were optimized and the antinematode activity grew up four times after optimization. The antinematode substances of these strains were found stable when treated with protease or heating or stored at 4 degrees C after 100 days, while instable when treated with acid or alkali. DP1 and CCM7 were identified to be Bacillus subtilis, while SZ5 and BCM2 to be Bacillus cereus. Endophytic bacteria secreting antinematode metabolite were found in economic crops. The metabolite of some strains showed strong and stable antinematode activity. Our results indicate the real potential of biocontrol by endophytic bacteria.

In-vitro effect of edta-tris-lysozyme solutions on selected pathogenic bacteria.

PubMed

Wooley, R E; Blue, J L

1975-02-01

The in-vitro effect of EDTA-Tris-lysozyme solution on 16 pathogenic bacteria of medical or veterinary importance was determined. Marked decreases in bacterial count occurred with Pseudomonas aeruginosa, Escherichia coli, Moraxella osloensis and Campylobacter fetus, and smaller decreses with Salmonella typhimurium, Shigella boydii, Aeromonas hydrophila, proteus mirabilis, Listeria monocytogenes and Erysipelothrix insidiosa. The test solution had no effect on Klebsiella ozaenae, Brucella canis, Cornynebacterium pyogenes, Coryne, renale, Streptococcus equi and staphylococcus aureus.

Environmental History Modulates Arabidopsis Pattern-Triggered Immunity in a HISTONE ACETYLTRANSFERASE1-Dependent Manner.

PubMed

Singh, Prashant; Yekondi, Shweta; Chen, Po-Wen; Tsai, Chia-Hong; Yu, Chun-Wei; Wu, Keqiang; Zimmerli, Laurent

2014-06-01

In nature, plants are exposed to a fluctuating environment, and individuals exposed to contrasting environmental factors develop different environmental histories. Whether different environmental histories alter plant responses to a current stress remains elusive. Here, we show that environmental history modulates the plant response to microbial pathogens. Arabidopsis thaliana plants exposed to repetitive heat, cold, or salt stress were more resistant to virulent bacteria than Arabidopsis grown in a more stable environment. By contrast, long-term exposure to heat, cold, or exposure to high concentrations of NaCl did not provide enhanced protection against bacteria. Enhanced resistance occurred with priming of Arabidopsis pattern-triggered immunity (PTI)-responsive genes and the potentiation of PTI-mediated callose deposition. In repetitively stress-challenged Arabidopsis, PTI-responsive genes showed enrichment for epigenetic marks associated with transcriptional activation. Upon bacterial infection, enrichment of RNA polymerase II at primed PTI marker genes was observed in environmentally challenged Arabidopsis. Finally, repetitively stress-challenged histone acetyltransferase1-1 (hac1-1) mutants failed to demonstrate enhanced resistance to bacteria, priming of PTI, and increased open chromatin states. These findings reveal that environmental history shapes the plant response to bacteria through the development of a HAC1-dependent epigenetic mark characteristic of a primed PTI response, demonstrating a mechanistic link between the primed state in plants and epigenetics. © 2014 American Society of Plant Biologists. All rights reserved.

Bacteria transport simulation using APEX model in the Toenepi watershed, New Zealand

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy/Environmental eXtender (APEX) model is a distributed, continuous, daily-time step small watershed-scale hydrologic and water quality model. In this study, the newly developed fecal-derived bacteria fate and transport subroutine was applied and evalated using APEX model. The e...

Intrinsic, adaptive and acquired antimicrobial resistance in Gram-negative bacteria.

PubMed

Arzanlou, Mohsen; Chai, Wern Chern; Venter, Henrietta

2017-02-28

Gram-negative bacteria are responsible for a large proportion of antimicrobial-resistant infections in humans and animals. Among this class of bacteria are also some of the most successful environmental organisms. Part of this success is their adaptability to a variety of different niches, their intrinsic resistance to antimicrobial drugs and their ability to rapidly acquire resistance mechanisms. These mechanisms of resistance are not exclusive and the interplay of several mechanisms causes high levels of resistance. In this review, we explore the molecular mechanisms underlying resistance in Gram-negative organisms and how these different mechanisms enable them to survive many different stress conditions. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

The impact of bacteria of circulating water on apatite-nepheline ore flotation.

PubMed

Evdokimova, G A; Gershenkop, A Sh; Fokina, N V

2012-01-01

A new phenomenon has been identified and studied-the impact of bacteria on the benefication process of non-sulphide ores using circulating water supply-a case study of apatite-nepheline ore. It is shown that bacteria deteriorate the floatability of apatite due to their interaction with active centres of calcium-containing minerals and intense flocculation, resulting in a decrease of the flotation process selectivity thus deteriorating the quality of concentrate. Based on the comparative analysis of primary sequences of 16S rRNA genes, there have been identified dominating bacteria species, recovered from the circulating water used at apatite-nepheline concentrating mills, and their phylogenetic position has been determined. All the bacteria were related to γ-Proteobacteria, including the Acinetobacter species, Pseudomonas alcaliphila, Ps. plecoglossicida, Stenotrophomonas rhizophila. A method of non-sulphide ores flotation has been developed with consideration of the bacterial factor. It consists in use of small concentrations of sodium hypochlorite, which inhibits the development of bacteria in the flotation of apatite-nepheline ores.

Resistance to Antibiotics, Biocides, Preservatives and Metals in Bacteria Isolated from Seafoods: Co-Selection of Strains Resistant or Tolerant to Different Classes of Compounds

PubMed Central

Romero, José L.; Grande Burgos, María J.; Pérez-Pulido, Rubén; Gálvez, Antonio; Lucas, Rosario

2017-01-01

Multi-drug resistant bacteria (particularly those producing extended-spectrum β-lactamases) have become a major health concern. The continued exposure to antibiotics, biocides, chemical preservatives, and metals in different settings such as the food chain or in the environment may result in development of multiple resistance or co-resistance. The aim of the present study was to determine multiple resistances (biocides, antibiotics, chemical preservatives, phenolic compounds, and metals) in bacterial isolates from seafoods. A 75.86% of the 87 isolates studied were resistant to at least one antibiotic or one biocide, and 6.90% were multiply resistant to at least three biocides and at least three antibiotics. Significant (P < 0.05) moderate or strong positive correlations were detected between tolerances to biocides, between antibiotics, and between antibiotics with biocides and other antimicrobials. A sub-set of 30 isolates selected according to antimicrobial resistance profile and food type were identified by 16S rDNA sequencing and tested for copper and zinc tolerance. Then, the genetic determinants for biocide and metal tolerance and antibiotic resistance were investigated. The selected isolates were identified as Pseudomonas (63.33%), Acinetobacter (13.33%), Aeromonas (13.33%), Shewanella, Proteus and Listeria (one isolate each). Antibiotic resistance determinants detected included sul1 (43.33% of tested isolates), sul2 (6.66%), blaTEM (16.66%), blaCTX−M (16.66%), blaPSE (10.00%), blaIMP (3.33%), blaNDM−1 (3.33%), floR (16.66%), aadA1 (20.0%), and aac(6′)-Ib (16.66%). The only biocide resistance determinant detected among the selected isolates was qacEΔ1 (10.00%). A 23.30 of the selected isolates were able to grow on media containing 32 mM copper sulfate, and 46.60% on 8 mM zinc chloride. The metal resistance genes pcoA/copA, pcoR, and chrB were detected in 36.66, 6.66, and 13.33% of selected isolates, respectively. Twelve isolates tested positive for

Investigation of diverse bacteria in cloud water at Mt. Tai, China.

PubMed

Xu, Caihong; Wei, Min; Chen, Jianmin; Sui, Xiao; Zhu, Chao; Li, Jiarong; Zheng, Lulu; Sui, Guodong; Li, Weijun; Wang, Wenxing; Zhang, Qingzhu; Mellouki, Abdelwahid

2017-02-15

Bacteria are abundant in atmospheric water phase with the potential to influence atmospheric processes and human health, yet relatively little information is known about the bacterial characteristics at high altitudes. Here we investigated the bacterial community by high throughput sequencing in 24 cloud water samples collected from September 26 to October 31, at the summit of Mt. Tai (36°15' N, 117°06' E, 1534m a.s.l) in China. Diverse bacterial population were identified and the gram-negative bacteria contributed the majority of total bacteria including Proteobacteria (81.6%) and Bacteroidetes (3.9%), followed by gram-positive bacteria Firmicutes (7.1%) and Actinobacteria (2.3%). These gram-negative taxa mainly inhabited in leaf-surface and cold environments. Meanwhile bacteria involved in the cloud condensation nuclei and ice nuclei formation were observed such as Sphingomonas (6.7%), Pseudomonas (4.1%), and Bacillus (1.1%). In addition, Sphingmonas was more active than that in daytime and participated in the cloud chemistry process. Meanwhile O 3 and SO 2 critically contributed to the variation of bacterial community. It is the first report on the bacterial community structure of cloud water over Asian area. Our results can serve as an important reference for environmental scientists, and biologists. Copyright © 2016. Published by Elsevier B.V.

Antigenotoxic activity of lactic acid bacteria, prebiotics, and products of their fermentation against selected mutagens.

PubMed

Nowak, Adriana; Śliżewska, Katarzyna; Otlewska, Anna

2015-12-01

Dietary components such as lactic acid bacteria (LAB) and prebiotics can modulate the intestinal microbiota and are thought to be involved in the reduction of colorectal cancer risk. The presented study measured, using the comet assay, the antigenotoxic activity of both probiotic and non-probiotic LAB, as well as some prebiotics and the end-products of their fermentation, against fecal water (FW). The production of short chain fatty acids by the bacteria was quantified using HPLC. Seven out of the ten tested viable strains significantly decreased DNA damage induced by FW. The most effective of them were Lactobacillus mucosae 0988 and Bifidobacterium animalis ssp. lactis Bb-12, leading to a 76% and 80% decrease in genotoxicity, respectively. The end-products of fermentation of seven prebiotics by Lactobacillus casei DN 114-001 exhibited the strongest antigenotoxic activity against FW, with fermented inulin reducing genotoxicity by 75%. Among the tested bacteria, this strain produced the highest amounts of butyrate in the process of prebiotic fermentation, and especially from resistant dextrin (4.09 μM/mL). Fermented resistant dextrin improved DNA repair by 78% in cells pre-treated with 6.8 μM methylnitronitrosoguanidine (MNNG). Fermented inulin induced stronger DNA repair in cells pre-treated with mutagens (FW, 25 μM hydrogen peroxide, or MNNG) than non-fermented inulin, and the efficiency of DNA repair after 120 min of incubation decreased by 71%, 50% and 70%, respectively. The different degrees of genotoxicity inhibition observed for the various combinations of bacteria and prebiotics suggest that this effect may be attributable to carbohydrate type, SCFA yield, and the ratio of the end-products of prebiotic fermentation. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluation of indigenous potent mushroom growth promoting bacteria (MGPB) on Agaricus bisporus production.

PubMed

Zarenejad, F; Yakhchali, B; Rasooli, I

2012-01-01

Mushrooms such as Agaricus bisporus, are cultivated for food worldwide. Fruit body initiation in Agaricus bisporus is a phase change from the vegetative to the reproductive stage which depends on the presence of a casing layer with particular physical, chemical and microbiological properties. The phase change is achieved practically by environmental manipulation and the presence of naturally occurring bacteria such as Pseuodomonas putida. In this study, 274 individual bacterial isolates were collected by screening the casing layer of 14 edible mushroom farms. The isolates were analysed with respect to biochemical properties, organic and inorganic phosphate solubilization, production of siderophore and growth in the presence of volatile compound of 1-octen-3-ol. It was found that approximately 97% of the strains were able to grow in the presence of 1-octen-3-ol and 36% were able to solubilize phosphorus. Among the isolates, 23 strains were selected as potent mushroom growth promoting bacteria (MGPB) for inoculation of the casing layer. Field experiments using these strains showed various promoting effects on production of mushroom. Finally, 2 strains (strains Bt4 and Ps7) showing the highest increase in A. bisporus production, were characterized as Pseuodomonas putida by molecular methods and identified as the best suited growth promoting inoculants for application in production farms for increasing the mushroom yield.

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics

PubMed Central

Anderson, Rika E.; Sogin, Mitchell L.; Baross, John A.

2014-01-01

The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities. PMID:25279954

Heterotrophic bacteria in soils of Larsemann Oasis of East Antarctica

NASA Astrophysics Data System (ADS)

Churilin, Nikita; Soina, Vera

2015-04-01

Antarctic soils. Primitive soils and permafrost layer have a great unevenness in the number of cultivated and potentially viable cells in different horizons. This phenomenon is characteristic for habitats with stable and alternating negative temperatures that can be attributed to the irregular migration of cells during freezing and heterogeneity of microbial populations along the depth of dormancy. One of the identified features was the lack of correlation with the organic content. SEM study of microbial communities in native Antarctic soils revealed the presence of biofilms, which can play an important role in weathering of rocks and primary soil formation, by forming organic horizon and protecting cells from environmental impact. Biofilms can also influence on distribution of bacterial cells in forming soils. Growth regulators (indoleacetic acid, wheat germ agglutinin, alkylhydroxybenzenes, pyruvate Na and serotonin) were used in experiments on the growth reactivation using soil samples with low number of microorganisms. The results obtained by this analysis can be used for further research to develop methods of the most complete selection of viable bacteria from Antarctic soils. We also determined the physiological condition of bacterial populations and their maximum specific growth rate. This method determines the functional (trophic) diversity of microbial communities and the maximum specific growth rate that reflects the environmental strategy of bacterial growth. In spite of the extreme conditions, a variety of physiological and metabolic willingness to consume polymers hydrolytic bacterial associations of endolithic soil is highest in the surface horizon and sharply decreases in the mineral horizon.

In vitro and in vivo inoculation of four endophytic bacteria on Lycopersicon esculentum.

PubMed

Botta, Anna Lucia; Santacecilia, Alessandra; Ercole, Claudia; Cacchio, Paola; Del Gallo, Maddalena

2013-09-25

Four bacteria selected on the basis of their capability of fixing atmospheric nitrogen, stimulating plant-growth, and protecting the host plant from pathogens - Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, Burkholderia ambifaria - were inoculated on tomato seeds either singularly, in couple and in a four bacteria mixer. Aim of this research was to evaluate: (1) effect of single and mixed cultures on the inoculated plant - plant growth, dry weight, root length and surface, number of leaves, among others; (2) colonization and interactions of the bacteria inside the host plant; (3) localization inside the host of single bacterial strains marked with the gusA reporter gene. The results obtained indicate that all selected microbial strains have colonized Lycopersicon esculentum but in a different way, depending on the single species. A. brasilense, G. diazotrophicus inoculated in vitro singularly and together were the best plant colonizers. In vivo essays, instead, B. ambifaria and the four-bacteria mixer gave the best results. It was possible to localize both A. brasilense and H. seropedicae inside the plant by the gusA reporter gene. The bacterial strains occur along the root axis from the apical zone until to the basal stem, on the shoot from the base up to the leaves. The four bacteria actively colonize tomato seeds and establish an endophytic community inside the plant. This review gives new information about colonization processes, in particular how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilizers or biocontrol agents. Copyright © 2013 Elsevier B.V. All rights reserved.

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing.

PubMed

Pumphrey, Graham M; Ranchou-Peyruse, Anthony; Spain, Jim C

2011-07-01

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

Relationship between antibiotic- and disinfectant-resistance profiles in bacteria harvested from tap water.

PubMed

Khan, Sadia; Beattie, Tara K; Knapp, Charles W

2016-06-01

Chlorination is commonly used to control levels of bacteria in drinking water; however, viable bacteria may remain due to chlorine resistance. What is concerning is that surviving bacteria, due to co-selection factors, may also have increased resistance to common antibiotics. This would pose a public health risk as it could link resistant bacteria in the natural environment to human population. Here, we investigated the relationship between chlorine- and antibiotic-resistances by harvesting 148 surviving bacteria from chlorinated drinking-water systems and compared their susceptibilities against chlorine disinfectants and antibiotics. Twenty-two genera were isolated, including members of Paenibacillus, Burkholderia, Escherichia, Sphingomonas and Dermacoccus species. Weak (but significant) correlations were found between chlorine-tolerance and minimum inhibitory concentrations against the antibiotics tetracycline, sulfamethoxazole and amoxicillin, but not against ciprofloxacin; this suggest that chlorine-tolerant bacteria are more likely to also be antibiotic resistant. Further, antibiotic-resistant bacteria survived longer than antibiotic-sensitive organisms when exposed to free chlorine in a contact-time assay; however, there were little differences in susceptibility when exposed to monochloramine. Irrespective of antibiotic-resistance, spore-forming bacteria had higher tolerance against disinfection compounds. The presence of chlorine-resistant bacteria surviving in drinking-water systems may carry additional risk of antibiotic resistance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Alternative methodology for isolation of biosurfactant-producing bacteria.

PubMed

Krepsky, N; Da Silva, F S; Fontana, L F; Crapez, M A C

2007-02-01

Wide biosurfactant application on biorremediation is limited by its high production cost. The search for cheaper biossurfactant production alternatives has guided our study. The use of selective media containing sucrose (10 g x L(-1)) and Arabian Light oil (2 g x L(-1)) as carbon sources showed to be effective to screen and maintain biosurfactant-producing consortia isolated from mangrove hydrocarbon-contaminated sediment. The biosurfactant production was assayed by kerosene, gasoline and Arabian Light Emulsification activity and the bacterial growth curve was determined by bacterial quantification. The parameters analyzed for biosurfactant production were the growth curve, salinity concentration, flask shape and oxygenation. All bacteria consortia screened were able to emulsify the petroleum derivatives tested. Biosurfactant production increased according to the incubation time; however the type of emulsification (non-aqueous phase or aqueous phase) did not change with time but with the compound tested. The methodology was able to isolate biosurfactant-producing consortia from superficial mangrove sediment contaminated by petroleum hydrocarbons and was recommended for selection of biosurfactant producing bacteria in tropical countries with low financial resources.

Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking.

PubMed

Ernebjerg, Morten; Kishony, Roy

2012-03-01

Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.

Antimicrobial copper alloys decreased bacteria on stethoscope surfaces.

PubMed

Schmidt, Michael G; Tuuri, Rachel E; Dharsee, Arif; Attaway, Hubert H; Fairey, Sarah E; Borg, Keith T; Salgado, Cassandra D; Hirsch, Bruce E

2017-06-01

Stethoscopes may serve as vehicles for transmission of bacteria among patients. The aim of this study was to assess the efficacy of antimicrobial copper surfaces to reduce the bacterial concentration associated with stethoscope surfaces. A structured prospective trial involving 21 health care providers was conducted at a pediatric emergency division (ED) (n = 14) and an adult medical intensive care unit located in tertiary care facilities (n = 7). Four surfaces common to a stethoscope and a facsimile instrument fabricated from U.S. Environmental Protection Agency-registered antimicrobial copper alloys (AMCus) were assessed for total aerobic colony counts (ACCs), methicillin-resistant Staphylococcus aureus, gram-negative bacteria, and vancomycin-resistant enterococci for 90 days. The mean ACCs collectively recovered from all stethoscope surfaces fabricated from the AMCus were found to carry significantly lower concentrations of bacteria (pediatric ED, 11.7 vs 127.1 colony forming units [CFU]/cm 2 , P < .00001) than their control equivalents. This observation was independent of health care provider or infection control practices. Absence of recovery of bacteria from the AMCu surfaces (66.3%) was significantly higher (P < .00001) than the control surfaces (22.4%). The urethane rim common to the stethoscopes was the most heavily burdened surface; mean concentrations exceeded the health care-associated infection acquisition concentration (5 CFU/cm 2 ) by at least 25×, supporting that the stethoscope warrants consideration in plans mitigating microbial cross-transmission during patient care. Stethoscope surfaces fabricated with AMCus were consistently found to harbor fewer bacteria. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Molecular Fingerprint and Dominant Environmental Factors of Nitrite-Dependent Anaerobic Methane-Oxidizing Bacteria in Sediments from the Yellow River Estuary, China.

PubMed

Yan, Pengze; Li, Mingcong; Wei, Guangshan; Li, Han; Gao, Zheng

2015-01-01

Nitrite-dependent anaerobic methane oxidation (n-damo) is performed by "Candidatus Methylomirabilis oxyfera" (M. oxyfera), which connects the carbon and nitrogen global nutrient cycles. In the present study, M. oxyfera-like bacteria sequences were successfully recovered from Yellow River Estuary sediments using specific primers for 16S rRNA and pmoA genes. A M. oxyfera-like sequences analysis based on the 16S rRNA gene revealed greater diversity compared with the pmoA gene; the 16S rRNA gene sequences retrieved from the Yellow River Estuary sediments belong to groups A as well as B and were mainly found in freshwater habitats. Quantitative PCR showed that 16S rRNA gene abundance varied from 9.28±0.11×10(3) to 2.10±0.13×10(5) copies g(-1) (dry weight), and the pmoA gene abundance ranged from 8.63±0.50×10(3) to 1.83±0.18×10(5) copies g(-1) (dry weight). A correlation analysis showed that the total organic carbon (TOC) and ammonium (NH4(+)) as well as the ratio of total phosphorus to total nitrogen (TP/TN) influenced the M. oxyfera-like bacteria distribution in the Yellow River Estuary sediments. These findings will aid in understanding the n-damo bacterial distribution pattern as well as their correlation with surrounding environmental factors in temperate estuarine ecosystems.

A novel method for single bacteria identification by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Schultz, Emmanuelle; Simon, Anne-Catherine; Strola, Samy Andrea; Perenon, Rémi; Espagnon, Isabelle; Allier, Cédric; Claustre, Patricia; Jary, Dorothée.; Dinten, Jean-Marc

2014-03-01

In this paper we present results on single bacteria rapid identification obtained with a low-cost and compact Raman spectrometer. At present, we demonstrate that a 1 minute procedure, including the localization of single bacterium, is sufficient to acquire comprehensive Raman spectrum in the range of 600 to 3300 cm-1. Localization and detection of single bacteria is performed by means of lensfree imaging over a large field of view of 24 mm2. An excitation source of 532 nm and 30 mW illuminates single bacteria to collect Raman signal into a Tornado Spectral Systems prototype spectrometer (HTVS technology). The acquisition time to record a single bacterium spectrum is as low as 10 s owing to the high light throughput of this spectrometer. The spectra processing features different steps for cosmic spikes removal, background subtraction, and gain normalization to correct the residual inducted fluorescence and substrate fluctuations. This allows obtaining a fine chemical fingerprint analysis. We have recorded a total of 1200 spectra over 7 bacterial species (E. coli, Bacillus species, S. epidermis, M. luteus, S. marcescens). The analysis of this database results in a high classification score of almost 90 %. Hence we can conclude that our setup enables automatic recognition of bacteria species among 7 different species. The speed and the sensitivity (<30 minutes for localization and spectra collection of 30 single bacteria) of our Raman spectrometer pave the way for high-throughput and non-destructive real-time bacteria identification assays. This compact and low-cost technology can benefit biomedical, clinical diagnostic and environmental applications.

Use of Selected Lactic Acid Bacteria and Quinoa Flour for Manufacturing Novel Yogurt-Like Beverages.

PubMed

Lorusso, Anna; Coda, Rossana; Montemurro, Marco; Rizzello, Carlo Giuseppe

2018-04-01

This study aimed at investigating the suitability of quinoa for making yogurt-like beverages. After the selection of the adequate technological parameters, the fermentation was carried out by using different lactic acid bacteria strains: a probiotic ( Lactobacillus rhamnosus SP1), an exopolysaccharides (EPS)-producing ( Weissella confusa DSM 20194), and one isolated from quinoa ( Lactobacillus plantarum T6B10). During the 20 h of fermentation, W. confusa caused the highest viscosity increase. All the strains had improved concentration of free amino acids and γ-Aminobutyric acid (GABA), polyphenols availability, antioxidant activity (up to 54%), and protein digestibility. The nutritional index (NI) was the highest when L. rhamnosus SP1 was used. The starch hydrolysis index in vitro ranged from 52 to 60. During storage at 4 °C, viscosity and water holding capacity decreased with the exception of the beverage fermented with W. confusa , while all the nutritional characteristics remained stable or slightly increased. Sensory analyses showed that beverages had good textural and organoleptic profiles. Besides the well-known positive properties of the raw matrix, fermentation allowed the obtainment of beverages with different features. Due to the nutritional and functional characteristics conferred to the quinoa beverages, the use of the probiotic and EPS-producing strains showed adequate potential for the industrial application.

Use of Selected Lactic Acid Bacteria and Quinoa Flour for Manufacturing Novel Yogurt-Like Beverages

PubMed Central

Lorusso, Anna; Montemurro, Marco; Rizzello, Carlo Giuseppe

2018-01-01

This study aimed at investigating the suitability of quinoa for making yogurt-like beverages. After the selection of the adequate technological parameters, the fermentation was carried out by using different lactic acid bacteria strains: a probiotic (Lactobacillus rhamnosus SP1), an exopolysaccharides (EPS)-producing (Weissella confusa DSM 20194), and one isolated from quinoa (Lactobacillus plantarum T6B10). During the 20 h of fermentation, W. confusa caused the highest viscosity increase. All the strains had improved concentration of free amino acids and γ-Aminobutyric acid (GABA), polyphenols availability, antioxidant activity (up to 54%), and protein digestibility. The nutritional index (NI) was the highest when L. rhamnosus SP1 was used. The starch hydrolysis index in vitro ranged from 52 to 60. During storage at 4 °C, viscosity and water holding capacity decreased with the exception of the beverage fermented with W. confusa, while all the nutritional characteristics remained stable or slightly increased. Sensory analyses showed that beverages had good textural and organoleptic profiles. Besides the well-known positive properties of the raw matrix, fermentation allowed the obtainment of beverages with different features. Due to the nutritional and functional characteristics conferred to the quinoa beverages, the use of the probiotic and EPS-producing strains showed adequate potential for the industrial application. PMID:29614769