Living bacteria in silica gels

NASA Astrophysics Data System (ADS)

Nassif, Nadine; Bouvet, Odile; Noelle Rager, Marie; Roux, Cécile; Coradin, Thibaud; Livage, Jacques

2002-09-01

The encapsulation of enzymes within silica gels has been extensively studied during the past decade for the design of biosensors and bioreactors. Yeast spores and bacteria have also been recently immobilized within silica gels where they retain their enzymatic activity, but the problem of the long-term viability of whole cells in an inorganic matrix has never been fully addressed. It is a real challenge for the development of sol-gel processes. Generic tests have been performed to check the viability of Escherichia coli bacteria in silica gels. Surprisingly, more bacteria remain culturable in the gel than in an aqueous suspension. The metabolic activity of the bacteria towards glycolysis decreases slowly, but half of the bacteria are still viable after one month. When confined within a mineral environment, bacteria do not form colonies. The exchange of chemical signals between isolated bacteria rather than aggregates can then be studied, a point that could be very important for 'quorum sensing'.

Agarolytic culturable bacteria associated with three antarctic subtidal macroalgae.

PubMed

Sánchez Hinojosa, Verónica; Asenjo, Joel; Leiva, Sergio

2018-05-21

Bacterial communities of Antarctic marine macroalgae remain largely underexplored in terms of diversity and biotechnological applications. In this study, three Antarctic subtidal macroalgae (Himantothallus grandifolius, Pantoneura plocamioides and Plocamium cartilagineum), two of them endemic of Antarctica, were investigated as a source for isolation of agar-degrading bacteria. A total of 21 epiphytic isolates showed agarolytic activity at low temperature on agar plates containing agar as the sole carbon source. 16S rRNA identification showed that the agar-degrading bacteria belonged to the genera Cellulophaga, Colwellia, Lacinutrix, Olleya, Paraglaciecola, Pseudoalteromonas and Winogradskyella. The agarase enzyme from a potential new species of the genus Olleya was selected for further purification. The enzyme was purified from the culture supernatant of Olleya sp. HG G5.3 by ammonium sulfate precipitation and ion-exchange chromatography. Molecular weight of the agarase was estimated to be 38 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The purified enzyme exhibited activity at 4 °C, retaining > 50% of its maximum activity at this temperature. This is the first study reporting the phylogeny of agar-degrading bacteria isolated from Antarctic subtidal macroalgae and the results suggest the huge potential of Antarctic algae-associated bacteria as a source of cold-active hydrolytic enzymes of biotechnological interest.

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria.

PubMed

Thorpe, Harry A; Bayliss, Sion C; Sheppard, Samuel K; Feil, Edward J

2018-04-01

The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences. To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

The origin of human milk bacteria: is there a bacterial entero-mammary pathway during late pregnancy and lactation?

PubMed

Rodríguez, Juan M

2014-11-01

Human milk is a source of bacteria to the infant gut; however, the origin of milk bacteria, as well as their impact on neonatal gut microbiota establishment, remains largely unknown. In the past years, results provided by different research groups suggest that certain bacteria from the maternal gastrointestinal tract could translocate through a mechanism involving mononuclear immune cells, migrate to the mammary glands via an endogenous cellular route (the bacterial entero-mammary pathway), and subsequently colonize the gastrointestinal tract of the breast-fed neonate. If such findings are confirmed in the future, we could exert a positive influence on infant health by modulating the maternal gut microbiota. © 2014 American Society for Nutrition.

Survival of soil bacteria during prolonged desiccation.

NASA Technical Reports Server (NTRS)

Chen, M.; Alexander, M.

1973-01-01

A determination was made of the kinds and numbers of bacteria surviving when two soils were maintained in the laboratory under dry conditions for more than half a year. Certain non-spore-forming bacteria were found to survive in the dry condition for long periods. A higher percentage of drought-tolerant than drought-sensitive bacteria was able to grow at low water activities. When they were grown in media with high salt concentrations, bacteria generally became more tolerant of prolonged drought and they persisted longer. The percent of cells in a bacterial population that remained viable when exposed to drought stress varied with the stage of growth.

Ice-Nucleating Bacteria

NASA Astrophysics Data System (ADS)

Obata, Hitoshi

Since the discovery of ice-nucleating bacteria in 1974 by Maki et al., a large number of studies on the biological characteristics, ice-nucleating substance, ice nucleation gene and frost damage etc. of the bacteria have been carried out. Ice-nucleating bacteria can cause the freezing of water at relatively warm temperature (-2.3°C). Tween 20 was good substrates for ice-nucleating activity of Pseudomonas fluorescens KUIN-1. Major fatty acids of Isolate (Pseudomonas fluorescens) W-11 grown at 30°C were palmitic, cis-9-hexadecenoic and cis-11-octadecenoic which amounted to 90% of the total fatty acids. Sequence analysis shows that an ice nucleation gene from Pseudomonas fluorescens is related to the gene of Pseudomonas syringae.

Sexually transmitted bacteria affect female cloacal assemblages in a wild bird

USGS Publications Warehouse

White, Joël; Mirleau, Pascal; Danchin, Etienne; Mulard, Hervé; Hatch, Scott A.; Heeb, Phillipp; Wagner, Richard H.

2010-01-01

Sexual transmission is an important mode of disease propagation, yet its mechanisms remain largely unknown in wild populations. Birds comprise an important model for studying sexually transmitted microbes because their cloaca provides a potential for both gastrointestinal pathogens and endosymbionts to become incorporated into ejaculates. We experimentally demonstrate in a wild population of kittiwakes (Rissa tridactyla) that bacteria are transmitted during copulation and affect the composition and diversity of female bacterial communities. We used an anti-insemination device attached to males in combination with a molecular technique (automated ribosomal intergenic spacer analysis) that describes bacterial communities. After inseminations were experimentally blocked, the cloacal communities of mates became increasingly dissimilar. Moreover, female cloacal diversity decreased and the extinction of mate-shared bacteria increased, indicating that female cloacal assemblages revert to their pre-copulatory state and that the cloaca comprises a resilient microbial ecosystem.

Effect of dietary copper sulfate, Aureo SP250, or clinoptilolite on ureolytic bacteria found in the pig large intestine.

PubMed Central

Varel, V H; Robinson, I M; Pond, W G

1987-01-01

The predominant ureolytic bacteria in the pig large intestine were determined while growing pigs were fed a basal diet or basal diet plus copper sulfate, Aureo SP250, or clinoptilolite. Fecal samples were collected from four pigs fed each diet at 3, 9, and 14 weeks and analyzed for total colony counts and percent ureolytic bacteria. Fecal urease activity, ammonia nitrogen, and identity of the ureolytic bacteria were determined at 14 weeks. Copper sulfate and Aureo SP250 reduced the number of ureolytic organisms, with a marked decrease occurring in the Streptococcus spp., which made up 74% of the ureolytic isolates from the pigs on the basal diet. Other ureolytic species detected at lower concentrations were Staphylococcus spp., Selenomonas ruminantium, Bacteroides multiacidus, and Eubacterium limosum. Copper sulfate also reduced fecal urease activity (P less than 0.10). Fecal ammonia concentrations were not different between pigs fed the various diets. These data suggest that the streptococci are the most numerous ureolytic species in the pig intestinal tract and are significantly reduced by copper sulfate and Aureo SP250; however, only copper sulfate reduced intestinal urease activity. PMID:2823707

Dominant oceanic bacteria secure phosphate using a large extracellular buffer

PubMed Central

Zubkov, Mikhail V.; Martin, Adrian P.; Hartmann, Manuela; Grob, Carolina; Scanlan, David J.

2015-01-01

The ubiquitous SAR11 and Prochlorococcus bacteria manage to maintain a sufficient supply of phosphate in phosphate-poor surface waters of the North Atlantic subtropical gyre. Furthermore, it seems that their phosphate uptake may counter-intuitively be lower in more productive tropical waters, as if their cellular demand for phosphate decreases there. By flow sorting 33P-phosphate-pulsed 32P-phosphate-chased cells, we demonstrate that both Prochlorococcus and SAR11 cells exploit an extracellular buffer of labile phosphate up to 5–40 times larger than the amount of phosphate required to replicate their chromosomes. Mathematical modelling is shown to support this conclusion. The fuller the buffer the slower the cellular uptake of phosphate, to the point that in phosphate-replete tropical waters, cells can saturate their buffer and their phosphate uptake becomes marginal. Hence, buffer stocking is a generic, growth-securing adaptation for SAR11 and Prochlorococcus bacteria, which lack internal reserves to reduce their dependency on bioavailable ambient phosphate. PMID:26198420

Phage-bacteria infection networks: From nestedness to modularity

NASA Astrophysics Data System (ADS)

Flores, Cesar O.; Valverde, Sergi; Weitz, Joshua S.

2013-03-01

Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we re-evaluated 38 prior studies and demonstrated that phage-bacteria infection networks tend to be statistically nested in small scale communities (Flores et al 2011). Nestedness is consistent with a hierarchy of infection and resistance within phages and bacteria, respectively. However, we predicted that at large scales, phage-bacteria infection networks should be typified by a modular structure. We evaluate and confirm this hypothesis using the most extensive study of phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-infections were evaluated between 215 marine phages and 286 marine bacteria. We develop a novel multi-scale network analysis and find that the Moebus and Nattkemper (1981) study, is highly modular (at the whole network scale), yet also exhibits nestedness and modularity at the within-module scale. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. CFG acknowledges the support of CONACyT Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and acknowledges the support of the James S. McDonnell Foundation

Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria.

PubMed

Perera, Manosha; Al-Hebshi, Nezar Noor; Speicher, David J; Perera, Irosha; Johnson, Newell W

2016-01-01

Oral cancer, primarily oral squamous cell carcinoma (OSCC), continues to be a major global health problem with high incidence and low survival rates. While the major risk factors for this malignancy, mostly lifestyle related, have been identified, around 15% of oral cancer cases remain unexplained. In light of evidence implicating bacteria in the aetiology of some cancer types, several epidemiological studies have been conducted in the last decade, employing methodologies ranging from traditional culture techniques to 16S rRNA metagenomics, to assess the possible role of bacteria in OSCC. While these studies have demonstrated differences in microbial composition between cancerous and healthy tissues, they have failed to agree on specific bacteria or patterns of oral microbial dysbiosis to implicate in OSCC. On the contrary, some oral taxa, particularly Porphyromonas gingivalis and Fusobacterium nucleatum, show strong oral carcinogenic potential in vitro and in animal studies. Bacteria are thought to contribute to oral carcinogenesis via inhibition of apoptosis, activation of cell proliferation, promotion of cellular invasion, induction of chronic inflammation, and production of carcinogens. This narrative review provides a critical analysis of and an update on the association between bacteria and oral carcinogenesis and the possible mechanisms underlying it.

3D printing of bacteria into functional complex materials.

PubMed

Schaffner, Manuel; Rühs, Patrick A; Coulter, Fergal; Kilcher, Samuel; Studart, André R

2017-12-01

Despite recent advances to control the spatial composition and dynamic functionalities of bacteria embedded in materials, bacterial localization into complex three-dimensional (3D) geometries remains a major challenge. We demonstrate a 3D printing approach to create bacteria-derived functional materials by combining the natural diverse metabolism of bacteria with the shape design freedom of additive manufacturing. To achieve this, we embedded bacteria in a biocompatible and functionalized 3D printing ink and printed two types of "living materials" capable of degrading pollutants and of producing medically relevant bacterial cellulose. With this versatile bacteria-printing platform, complex materials displaying spatially specific compositions, geometry, and properties not accessed by standard technologies can be assembled from bottom up for new biotechnological and biomedical applications.

3D printing of bacteria into functional complex materials

PubMed Central

Schaffner, Manuel; Rühs, Patrick A.; Coulter, Fergal; Kilcher, Samuel; Studart, André R.

2017-01-01

Despite recent advances to control the spatial composition and dynamic functionalities of bacteria embedded in materials, bacterial localization into complex three-dimensional (3D) geometries remains a major challenge. We demonstrate a 3D printing approach to create bacteria-derived functional materials by combining the natural diverse metabolism of bacteria with the shape design freedom of additive manufacturing. To achieve this, we embedded bacteria in a biocompatible and functionalized 3D printing ink and printed two types of “living materials” capable of degrading pollutants and of producing medically relevant bacterial cellulose. With this versatile bacteria-printing platform, complex materials displaying spatially specific compositions, geometry, and properties not accessed by standard technologies can be assembled from bottom up for new biotechnological and biomedical applications. PMID:29214219

Interactions between Diatoms and Bacteria

PubMed Central

Amin, Shady A.; Parker, Micaela S.

2012-01-01

Summary: Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans. PMID:22933565

The complete general secretory pathway in gram-negative bacteria.

PubMed Central

Pugsley, A P

1993-01-01

The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins. PMID:8096622

Effects of symbiotic bacteria on chemical sensitivity of Daphnia magna.

PubMed

Manakul, Patcharaporn; Peerakietkhajorn, Saranya; Matsuura, Tomoaki; Kato, Yasuhiko; Watanabe, Hajime

2017-07-01

The crustacean zooplankton Daphnia magna has been widely used for chemical toxicity tests. Although abiotic factors have been well documented in ecotoxicological test protocols, biotic factors that may affect the sensitivity to chemical compounds remain limited. Recently, we identified symbiotic bacteria that are critical for the growth and reproduction of D. magna. The presence of symbiotic bacteria on Daphnia raised the question as to whether these bacteria have a positive or negative effect on toxicity tests. In order to evaluate the effects of symbiotic bacteria on toxicity tests, bacteria-free Daphnia were prepared, and their chemical sensitivities were compared with that of Daphnia with symbiotic bacteria based on an acute immobilization test. The Daphnia with symbiotic bacteria showed higher chemical resistance to nonylphenol, fenoxycarb, and pentachlorophenol than bacteria-free Daphnia. These results suggested potential roles of symbiotic bacteria in the chemical resistance of its host Daphnia. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tissue-Associated “Candidatus Mycoplasma corallicola” and Filamentous Bacteria on the Cold-Water Coral Lophelia pertusa (Scleractinia)▿ †

PubMed Central

Neulinger, Sven C.; Gärtner, Andrea; Järnegren, Johanna; Ludvigsen, Martin; Lochte, Karin; Dullo, Wolf-Christian

2009-01-01

The cold-water coral Lophelia pertusa (Scleractinia, Caryophylliidae) is a key species in the formation of cold-water reefs, which are among the most diverse deep-sea ecosystems. It occurs in two color varieties: white and red. Bacterial communities associated with Lophelia have been investigated in recent years, but the role of the associated bacteria remains largely obscure. This study uses catalyzed reporter deposition fluorescence in situ hybridization to detect the in situ location of specific bacterial groups on coral specimens from the Trondheimsfjord (Norway). Two tissue-associated groups were identified: (i) bacteria on the host's tentacle ectoderm, “Candidatus Mycoplasma corallicola,” are flasklike, pointed cells and (ii) endoderm-associated bona fide TM7 bacteria form long filaments in the gastral cavity. These tissue-bound bacteria were found in all coral specimens from the Trondheimsfjord, indicating a closer relationship with the coral compared to bacterial assemblages present in coral mucus and gastric fluid. PMID:19114511

Mineral remains of early life on Earth? On Mars?

USGS Publications Warehouse

Iberall, Robbins E.; Iberall, A.S.

1991-01-01

The oldest sedimentary rocks on Earth, the 3.8-Ga Isua Iron-Formation in southwestern Greenland, are metamorphosed past the point where organic-walled fossils would remain. Acid residues and thin sections of these rocks reveal ferric microstructures that have filamentous, hollow rod, and spherical shapes not characteristic of crystalline minerals. Instead, they resemble ferric-coated remains of bacteria. Because there are no earlier sedimentary rocks to study on Earth, it may be necessary to expand the search elsewhere in the solar system for clues to any biotic precursors or other types of early life. A study of morphologies of iron oxide minerals collected in the southern highlands during a Mars sample return mission may therefore help to fill in important gaps in the history of Earth's earliest biosphere. -from Authors

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin

PubMed Central

Sharrar, Allison M.; Flood, Beverly E.; Bailey, Jake V.; Jones, Daniel S.; Biddanda, Bopaiah A.; Ruberg, Steven A.; Marcus, Daniel N.; Dick, Gregory J.

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

PubMed

Sharrar, Allison M; Flood, Beverly E; Bailey, Jake V; Jones, Daniel S; Biddanda, Bopaiah A; Ruberg, Steven A; Marcus, Daniel N; Dick, Gregory J

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H 2 -based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H 2 oxidation via Ni-Fe hydrogenases, and the use of O 2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction ( sat, apr , and dsr ) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate

Gastric spiral bacteria in small felids.

PubMed

Kinsel, M J; Kovarik, P; Murnane, R D

1998-06-01

Nine small cats, including one bobcat (Felis rufus), one Pallas cat (F. manul), one Canada lynx (F. lynx canadensis), two fishing cats (F. viverrina), two margays (F. wiedii), and two sand cats (F. margarita), necropsied between June 1995 and March 1997 had large numbers of gastric spiral bacteria, whereas five large cats, including one African lion (Panthera leo), two snow leopards (P. uncia), one Siberian tiger (P. tigris altaica), and one jaguar (P. onca), necropsied during the same period had none. All of the spiral organisms from the nine small cats were histologically and ultrastructurally similar. Histologically, the spiral bacteria were 5-14 microm long with five to nine coils per organism and were located both extracellularly within gastric glands and surface mucus, and intracellularly in parietal cells. Spiral bacteria in gastric mucosal scrapings from the Canada lynx, one fishing cat, and the two sand cats were gram negative and had corkscrewlike to tumbling motility when viewed with phase contrast microscopy. The bacteria were 0.5-0.7 microm wide, with a periodicity of 0.65-1.1 microm in all cats. Bipolar sheathed flagella were occasionally observed, and no periplasmic fibrils were seen. The bacteria were extracellular in parietal cell canaliculi and intracellular within parietal cells. Culture of mucosal scrapings from the Canada lynx and sand cats was unsuccessful. Based on morphology, motility, and cellular tropism, the bacteria were probably Helicobacter-like organisms. Although the two margays had moderate lymphoplasmacytic gastritis, the other cats lacked or had only mild gastric lymphoid infiltrates, suggesting that these organisms are either commensals or opportunistic pathogens.

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.

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.

Biochemistry, physiology and biotechnology of sulfate-reducing bacteria.

PubMed

Barton, Larry L; Fauque, Guy D

2009-01-01

Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The

Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria

PubMed Central

Perera, Manosha; Al-hebshi, Nezar Noor; Speicher, David J.; Perera, Irosha; Johnson, Newell W.

2016-01-01

Oral cancer, primarily oral squamous cell carcinoma (OSCC), continues to be a major global health problem with high incidence and low survival rates. While the major risk factors for this malignancy, mostly lifestyle related, have been identified, around 15% of oral cancer cases remain unexplained. In light of evidence implicating bacteria in the aetiology of some cancer types, several epidemiological studies have been conducted in the last decade, employing methodologies ranging from traditional culture techniques to 16S rRNA metagenomics, to assess the possible role of bacteria in OSCC. While these studies have demonstrated differences in microbial composition between cancerous and healthy tissues, they have failed to agree on specific bacteria or patterns of oral microbial dysbiosis to implicate in OSCC. On the contrary, some oral taxa, particularly Porphyromonas gingivalis and Fusobacterium nucleatum, show strong oral carcinogenic potential in vitro and in animal studies. Bacteria are thought to contribute to oral carcinogenesis via inhibition of apoptosis, activation of cell proliferation, promotion of cellular invasion, induction of chronic inflammation, and production of carcinogens. This narrative review provides a critical analysis of and an update on the association between bacteria and oral carcinogenesis and the possible mechanisms underlying it. PMID:27677454

Identification of Mucosa-Invading and Intravascular Bacteria in Feline Small Intestinal Lymphoma.

PubMed

Hoehne, S N; McDonough, S P; Rishniw, M; Simpson, K W

2017-03-01

Persistent bacterial infections of the gastrointestinal mucosa are causally linked to gastric carcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma in people and laboratory animals. We examined the relationship of mucosa-associated bacteria to alimentary lymphoma in cats. Intestinal biopsies from 50 cats with alimentary lymphoma (small cell, n = 33; large cell, n = 17) and 38 controls without lymphoma (normal to minimal change on histopathology, n = 18; lymphocytic-plasmacytic enteritis, n = 20) were evaluated. The number and spatial distribution of bacteria (ie, in luminal cellular debris, villus-associated mucus, adherent to epithelium, mucosal invasion, intravascular, or serosal) were determined by fluorescence in situ hybridization with the eubacterial probe EUB-338. Mucosa-invasive bacteria were more frequently observed in cats with large cell lymphoma (82%, P ≤ .001) than in cats with small cell lymphoma (18%), normal to minimal change on histopathology, and lymphocytic-plasmacytic enteritis (3%). Intravascular bacteria were observed solely in large cell lymphoma (29%), and serosal colonization was more common in cats with large cell lymphoma (57%) than with small cell lymphoma (11%, P ≤ .01), normal to minimal change (8%, P ≤ .01), and lymphocytic-plasmacytic enteritis (6%, P ≤ .001). The high frequency of invasive bacteria within blood vessels and serosa of cats with large cell lymphoma may account for the sepsis-related complications associated with large cell lymphoma and inform clinical management. Further studies are required to determine the role of intramucosal bacteria in the etiopathogenesis of feline alimentary lymphoma.

Elasto-inertial microfluidics for bacteria separation from whole blood for sepsis diagnostics.

PubMed

Faridi, Muhammad Asim; Ramachandraiah, Harisha; Banerjee, Indradumna; Ardabili, Sahar; Zelenin, Sergey; Russom, Aman

2017-01-04

Bloodstream infections (BSI) remain a major challenge with high mortality rate, with an incidence that is increasing worldwide. Early treatment with appropriate therapy can reduce BSI-related morbidity and mortality. However, despite recent progress in molecular based assays, complex sample preparation steps have become critical roadblock for a greater expansion of molecular assays. Here, we report a size based, label-free, bacteria separation from whole blood using elasto-inertial microfluidics. In elasto-inertial microfluidics, the viscoelastic flow enables size based migration of blood cells into a non-Newtonian solution, while smaller bacteria remain in the streamline of the blood sample entrance and can be separated. We first optimized the flow conditions using particles, and show continuous separation of 5 μm particles from 2 μm at a yield of 95% for 5 µm particle and 93% for 2 µm particles at respective outlets. Next, bacteria were continuously separated at an efficiency of 76% from undiluted whole blood sample. We demonstrate separation of bacteria from undiluted while blood using elasto-inertial microfluidics. The label-free, passive bacteria preparation method has a great potential for downstream phenotypic and molecular analysis of bacteria.

Aerosol pH buffering in the southeastern US: Fine particles remain highly acidic despite large reductions in sulfate

NASA Astrophysics Data System (ADS)

Weber, R. J.; Guo, H.; Russell, A. G.; Nenes, A.

2015-12-01

pH is a critical aerosol property that impacts many atmospheric processes, including biogenic secondary organic aerosol formation, gas-particle phase partitioning, and mineral dust or redox metal mobilization. Particle pH has also been linked to adverse health effects. Using a comprehensive data set from the Southern Oxidant and Aerosol Study (SOAS) as the basis for thermodynamic modeling, we have shown that particles are currently highly acidic in the southeastern US, with pH between 0 and 2. Sulfate and ammonium are the main acid-base components that determine particle pH in this region, however they have different sources and their concentrations are changing. Over 15 years of network data show that sulfur dioxide emission reductions have resulted in a roughly 70 percent decrease in sulfate, whereas ammonia emissions, mainly link to agricultural activities, have been largely steady, as have gas phase ammonia concentrations. This has led to the view that particles are becoming more neutralized. However, sensitivity analysis, based on thermodynamic modeling, to changing sulfate concentrations indicates that particles have remained highly acidic over the past decade, despite the large reductions in sulfate. Furthermore, anticipated continued reductions of sulfate and relatively constant ammonia emissions into the future will not significantly change particle pH until sulfate drops to clean continental background levels. The result reshapes our expectation of future particle pH and implies that atmospheric processes and adverse health effects linked to particle acidity will remain unchanged for some time into the future.

Relationship between serologic markers of periodontal bacteria and metabolic syndrome and its components.

PubMed

Shrestha, Deepika; Choi, Youn-Hee; Zhang, Jiajia; Hazlett, Linda J; Merchant, Anwar T

2015-03-01

Periodontitis is a result of a complex biologic alteration of the periodontal microenvironment and a distributional shift of key periodontal pathogens. Metabolic syndrome (MetS), a complex cluster of cardiovascular risk factors, has been linked to periodontal diseases; however, the contribution of periodontal bacteria to systemic conditions remains unclear. The study population comprised 7,848 United States adults who participated in an interview, underwent a clinical oral-health examination, and had serum immunoglobulin G titers measured against 19 periodontal bacteria as part of the third National Health and Nutritional Examination Survey. The z-score antibody titers were clustered into four mutually exclusive groups and named after Socransky's classification of periodontal bacteria (Orange-Red, Red-Green, Yellow-Orange, and Orange-Blue). Survey logistic regression was used to investigate the independent associations between the cluster scores, and MetS and each component, including hypertension, hypertriglyceridemia, low high-density lipoprotein cholesterol, central obesity, and elevated fasting glucose. The Orange-Red cluster score (that included Porphyromonas gingivalis and Prevotella spp.) was positively associated (odds ratio [OR] = 1.067, 95% confidence interval [CI] = 1.02 to 1.12) and the Orange-Blue cluster score (which included Actinomyces naeslundii and Eubacterium nodatum) was inversely associated (OR = 0.93, 95% CI = 0.88 to 0.97) with elevated fasting glucose (≥ 110 mg/dL) after adjustment for clusters and potential confounders. Neither MetS nor its other remaining MetS components were associated with a particular cluster score. The associations between specific antibody clusters (Orange-Red and Orange-Blue) against periodontal bacteria and elevated plasma glucose were in qualitatively opposite directions after multivariable adjustment in a large, adult population. The periodontal bacterial profile was not found to be associated with metabolic

EFFECT OF AEROSOLIZATION ON CULTURABILITY AND VIABILITY OF GRAM-NEGATIVE BACTERIA

EPA Science Inventory

Estimations of the bacterial content of air can be more easily made now than a decade ago, with colony formation the method of choice for enumeration of airborne bacteria.However, plate counts are subject to error because bacteria exposed to the air may remain viable yet lose the...

ON THE RELATION OF BACTERIA TO SO-CALLED "CHEMICAL PNEUMONIA"

PubMed Central

Koontz, A. R.; Allen, M. S.

1929-01-01

The question of a causal relation of the bacteria in gassed lungs to the pneumonia present cannot be regarded as decided. It may be said that: 1. The appearance of gassed lungs with pneumonia is very similar to the pneumonia of known bacterial origin. 2. In a few cases the type of pneumonia found coincides with the reported cases of so-called "chemical pneumonia," which is characterized by a preponderance of epithelial cells in the exudate. 3. Gassed lungs are not sterile but show highly varying numbers of bacteria. 4. The bacteria are not intracellular and are not present in large numbers in the majority of cases. The arguments for and against a causal relationship between the bacteria and the pneumonia may be summed up as follows: 1. Against a Causal Relationship a. The early appearance of pneumonia after gassing. b. The occurrence of pneumonia with very small numbers of bacteria present. c. The fact that very few bacteria are engulfed by leucocytes in gassed lungs, whereas large numbers are present in the non-gassed pneumonias and are conspicuously intracellular. 2. In Favor of a Causal Relationship a. The presence of bacteria in any numbers. b. The picture of broncho-pneumonia presented is similar to broncho-pneumonia of known bacterial origin. c. Pneumonias characterized by large numbers of epithelial cells in the exudate (so-called "chemical pneumonia") occur in animals that were never gassed or subjected to other irritating substances in any way. PMID:19869606

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments.

PubMed

Heir, Even; Møretrø, Trond; Simensen, Andreas; Langsrud, Solveig

2018-06-20

Interactions and competition between resident bacteria in food processing environments could affect their ability to survive, grow and persist in microhabitats and niches in the food industry. In this study, the competitive ability of L. monocytogenes strains grown together in separate culture mixes with other L. monocytogenes (L. mono mix), L. innocua (Listeria mix), Gram-negative bacteria (Gram- mix) and with a multigenera mix (Listeria + Gram- mix) was investigated in biofilms on stainless steel and in suspensions at 12 °C. The mixed cultures included resident bacteria from processing surfaces in meat and salmon industry represented by L. monocytogenes (n = 6), L. innocua (n = 5) and Gram-negative bacteria (n = 6; Acinetobacter sp., Pseudomonas fragi, Pseudomonas fluorescens, Serratia liquefaciens, Stenotrophomonas maltophilia). Despite hampered in growth in mixed cultures, L. monocytogenes established in biofilms with counts at day nine between 7.3 and 9.0 log per coupon with the lowest counts in the Listeria + G- mix that was dominated by Pseudomonas. Specific L. innocua inhibited growth of L. monocytogenes strains differently; inhibition that was further enhanced by the background Gram-negative microbiota. In these multispecies and multibacteria cultures, the growth competitive effects lead to the dominance of a strong competitor L. monocytogenes strain that was only slightly inhibited by L. innocua and showed strong competitive abilities in mixed cultures with resident Gram-negative bacteria. The results indicates complex patterns of bacterial interactions and L. monocytogenes inhibition in the multibacteria cultures that only partially depend on cell contact and likely involve various antagonistic and bacterial tolerance mechanisms. The study indicates large variations among L. monocytogenes in their competitiveness under multibacterial culture conditions that should be considered in further studies towards understanding of L

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling.

PubMed

Cui, Li; Yang, Kai; Li, Hong-Zhe; Zhang, Han; Su, Jian-Qiang; Paraskevaidi, Maria; Martin, Francis L; Ren, Bin; Zhu, Yong-Guan

2018-04-17

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N 2 ) to bioavailable N essential for all forms of life. N 2 -fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15 N 2 stable isotope probing (SIP) was developed to discern N 2 -fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N 2 -fixing bacteria), along with a marked 15 N 2 -induced Cyt c band shift, generated a highly distinguishable biomarker for N 2 fixation. 15 N 2 -induced shift was consistent well with 15 N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N 2 -fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus 15 N 2 percentage allowed quantification of N 2 fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large European prospective cohort study.

PubMed

Michaud, Dominique S; Izard, Jacques; Wilhelm-Benartzi, Charlotte S; You, Doo-Ho; Grote, Verena A; Tjønneland, Anne; Dahm, Christina C; Overvad, Kim; Jenab, Mazda; Fedirko, Veronika; Boutron-Ruault, Marie Christine; Clavel-Chapelon, Françoise; Racine, Antoine; Kaaks, Rudolf; Boeing, Heiner; Foerster, Jana; Trichopoulou, Antonia; Lagiou, Pagona; Trichopoulos, Dimitrios; Sacerdote, Carlotta; Sieri, Sabina; Palli, Domenico; Tumino, Rosario; Panico, Salvatore; Siersema, Peter D; Peeters, Petra H M; Lund, Eiliv; Barricarte, Aurelio; Huerta, José-María; Molina-Montes, Esther; Dorronsoro, Miren; Quirós, J Ramón; Duell, Eric J; Ye, Weimin; Sund, Malin; Lindkvist, Björn; Johansen, Dorthe; Khaw, Kay-Tee; Wareham, Nick; Travis, Ruth C; Vineis, Paolo; Bueno-de-Mesquita, H Bas; Riboli, Elio

2013-12-01

Examine the relationship between antibodies to 25 oral bacteria and pancreatic cancer risk in a prospective cohort study. We measured antibodies to oral bacteria in prediagnosis blood samples from 405 pancreatic cancer cases and 416 matched controls, nested within the European Prospective Investigation into Cancer and Nutrition study. Analyses were conducted using conditional logistic regression and additionally adjusted for smoking status and body mass index. Individuals with high levels of antibodies against Porphyromonas gingivalis ATTC 53978, a pathogenic periodontal bacteria, had a twofold higher risk of pancreatic cancer than individuals with lower levels of these antibodies (OR 2.14; 95% CI 1.05 to 4.36; >200 ng/ml vs ≤200 ng/ml). To explore the association with commensal (non-pathogenic) oral bacteria, we performed a cluster analysis and identified two groups of individuals, based on their antibody profiles. A cluster with overall higher levels of antibodies had a 45% lower risk of pancreatic cancer than a cluster with overall lower levels of antibodies (OR 0.55; 95% CI 0.36 to 0.83). Periodontal disease might increase the risk for pancreatic cancer. Moreover, increased levels of antibodies against specific commensal oral bacteria, which can inhibit growth of pathogenic bacteria, might reduce the risk of pancreatic cancer. Studies are needed to determine whether oral bacteria have direct effects on pancreatic cancer pathogenesis or serve as markers of the immune response.

Buoyant densities of phototrophic sulfur bacteria and cyanobacteria

NASA Technical Reports Server (NTRS)

Guerrero, R.

1985-01-01

The buoyant densities of bacterial cells are greatly influenced by the accumulation of intracellular reserve material. The buoyant density of phototrophic bacteria that are planktonic is of particular interest, since these organisms must remain in the photic zone of the water column for optimal growth. Separation of cells by their buoyant density may also be of use in separating and identifying organisms from a natural population. The bacteria used were obtained from pure cultures, enrichments, or samples taken directly from the environment.

Swarming bacteria migrate by Lévy Walk

NASA Astrophysics Data System (ADS)

Ariel, Gil; Rabani, Amit; Benisty, Sivan; Partridge, Jonathan D.; Harshey, Rasika M.; Be'Er, Avraham

2015-09-01

Individual swimming bacteria are known to bias their random trajectories in search of food and to optimize survival. The motion of bacteria within a swarm, wherein they migrate as a collective group over a solid surface, is fundamentally different as typical bacterial swarms show large-scale swirling and streaming motions involving millions to billions of cells. Here by tracking trajectories of fluorescently labelled individuals within such dense swarms, we find that the bacteria are performing super-diffusion, consistent with Lévy walks. Lévy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Lévy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought.

Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

PubMed

Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

2011-12-01

Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

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

Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large European prospective cohort study

PubMed Central

Michaud, Dominique S.; Izard, Jacques; Wilhelm-Benartzi, Charlotte S.; You, Doo-Ho; Grote, Verena A; Tjønneland, Anne; Dahm, Christina C.; Overvad, Kim; Jenab, Mazda; Fedirko, Veronika; Boutron-Ruault, Marie Christine; Clavel-Chapelon, Françoise; Racine, Antoine; Kaaks, Rudolf; Boeing, Heiner; Foerster, Jana; Trichopoulou, Antonia; Lagiou, Pagona; Trichopoulos, Dimitrios; Sacerdote, Carlotta; Sieri, Sabina; Palli, Domenico; Tumino, Rosario; Panico, Salvatore; Siersema, Peter; Peeters, Petra HM; Lund, Eiliv; Barricarte, Aurelio; Huerta, José-María; Molina-Montes, Esther; Dorronsoro, Miren; Quirós, J. Ramón; Duell, Eric J.; Ye, Weimin; Sund, Malin; Lindkvist, Björn; Johansen, Dorthe; Khaw, Kay-Tee; Wareham, Nick; Travis, Ruth C.; Vineis, Paolo; Bueno-de-Mesquita, H. Bas; Riboli, Elio

2013-01-01

Objective Examine the relationship between antibodies to 25 oral bacteria and pancreatic cancer risk in a prospective cohort study. Design We measured antibodies to oral bacteria in prediagnosis blood samples from 405 pancreatic cancer cases and 416 matched controls, nested within the European Prospective Investigation into Cancer and Nutrition study (EPIC). Analyses were conducted using conditional logistic regression and additionally adjusted for smoking status and body mass index. Results Individuals with high levels of antibodies against Porphyromonas gingivalis ATTC 53978, a pathogenic periodontal bacteria, had a 2-fold higher risk of pancreatic cancer than individuals lower levels of these antibodies (odds ratio [OR], 2.14; 95% confidence interval [CI], 1.05–4.36; >200 ng/ml vs ≤200 ng/ml). To explore the association with commensal (non-pathogenic) oral bacteria, we performed a cluster analysis and identified 2 groups of individuals, based on their antibody profiles. A cluster with overall higher levels of antibodies had a 45% lower risk of pancreatic cancer than a cluster with overall lower levels of antibodies (OR, 0.55; 95% CI, 0.36–0.83). Conclusion Periodontal disease might increase the risk for pancreatic cancer. Moreover, increased levels of antibodies against specific commensal oral bacteria, which can inhibit growth of pathogenic bacteria, might reduce the risk of pancreatic cancer. Studies are needed to determine whether oral bacteria have direct effects on pancreatic cancer pathogenesis or serve as markers of the immune response. PMID:22990306

Competitive interactions between sponge-associated bacteria.

PubMed

Esteves, Ana I S; Cullen, Alescia; Thomas, Torsten

2017-03-01

The diversity of the microbial communities associated with marine sponges has been extensively studied, but their functioning and interactions within the sponge holobiont are only recently being appreciated. Sponge-associated microorganisms are known for the production of a range of inhibitory metabolites with biotechnological application, but the ecological role that these compounds remains elusive. In this work, we explore the competitive interactions between cultivated sponge-associated bacteria to inspect whether bacteria that produce antimicrobial activities are able to inhibit potentially pathogenic bacteria. We isolated a Bacillus sp. bacterium with sponge-degrading activity, which likely has a negative impact on the host. This bacterium, along with other sponge isolates from the same genus, was found to be inhibited by a subpopulation of closely related sponge-derived Pseudovibrio spp. In some Pseudovibrio strains, these inhibitory activities were correlated with the genetic capacity to produce polyketides, such as erythronolide. Our observations suggest that antagonistic activities likely influence the composition of the sponge microbiome, including the abundance of bacteria that can be harmful to the host. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacteria foraging in turbulent waters

NASA Astrophysics Data System (ADS)

Taylor, John; Tang, Wenbo; Stocker, Roman

2009-11-01

Marine bacteria are the Ocean's recyclers, contributing to as much as 50% of the productivity of the marine food web. Bacteria forage on patches of dissolved nutrients using chemotaxis, the ability to swim up chemical gradients. As turbulence is ubiquitous in the Ocean, it is important to understand how turbulent flow conditions affect bacterial foraging. We used three-dimensional, isotropic direct numerical simulations coupled with a bacterial transport equation to address this problem. After the flow is continuously forced until it reaches a steady state, microscale nutrient patches are injected into the turbulent flow, and stirring produces thin nutrient filaments. Two populations of bacteria compete against each other: one population is motile and chemotactic (`active'), the other is non-motile (`passive'). The distribution of both populations is initially uniform. Chemotaxis allows active bacteria to cluster near the center of the nutrient filaments, increasing their nutrient uptake relative to passive bacteria. Increasing the turbulence intensity increases the short-term chemotactic advantage by quickly producing large gradients in the nutrient concentration, but also leads to rapid mixing of the nutrient field, which makes the chemotactic advantage short-lived. The results suggest that the evolutionary advantage of chemotaxis, based on the increase in nutrient uptake relative to the energetic cost of swimming, strongly depends on the turbulence level.

Background culturable bacteria aerosol in two large public buildings using HVAC filters as long term, passive, high-volume air samplers.

PubMed

Stanley, Nicholas J; Kuehn, Thomas H; Kim, Seung Won; Raynor, Peter C; Anantharaman, Senthilvelan; Ramakrishnan, M A; Goyal, Sagar M

2008-04-01

Background culturable bacteria aerosols were collected and identified in two large public buildings located in Minneapolis, Minnesota and Seattle, Washington over a period of 5 months and 3 months, respectively. The installed particulate air filters in the ventilation systems were used as the aerosol sampling devices at each location. Both pre and final filters were collected from four air handing units at each site to determine the influence of location within the building, time of year, geographical location and difference between indoor and outdoor air. Sections of each loaded filter were eluted with 10 ml of phosphate buffered saline (PBS). The resulting solutions were cultured on blood agar plates and incubated for 24 h at 36 degrees C. Various types of growth media were then used for subculturing, followed by categorization using a BioLog MicroStation (Biolog, Hayward, CA, USA) and manual observation. Environmental parameters were gathered near each filter by the embedded on-site environmental monitoring systems to determine the effect of temperature, humidity and air flow. Thirty nine different species of bacteria were identified, 17 found only in Minneapolis and 5 only in Seattle. The hardy spore-forming genus Bacillus was the most commonly identified and showed the highest concentrations. A significant decrease in the number of species and their concentration occurred in the Minneapolis air handling unit supplying 100% outdoor air in winter, however no significant correlations between bacteria concentration and environmental parameters were found.

Bacteria as a new model system for aging studies: investigations using light microscopy.

PubMed

Ackermann, Martin

2008-04-01

Aging-the decline in an individual's condition over time-is at the center of an active research field in medicine and biology. Some very basic questions have, however, remained unresolved, the most fundamental being: do all organisms age? Or are there organisms that would continue to live forever if not killed by external forces? For a long time it was believed that aging only affected organisms such as animals, plants, and fungi. Bacteria, in contrast, were assumed to be potentially immortal and until recently this assertion remained untested. We used phase-contrast microscopy (on an Olympus BX61) to follow individual bacterial cells over many divisions to prove that some bacteria show a distinction between an aging mother cell and a rejuvenated daughter, and that these bacteria thus age. This indicates that aging is a more fundamental property of organisms than was previously assumed. Bacteria can now be used as very simple model system for investigating why and how organisms age.

Synthesis of bacteria promoted reduced graphene oxide-nickel sulfide networks for advanced supercapacitors.

PubMed

Zhang, Haiming; Yu, Xinzhi; Guo, Di; Qu, Baihua; Zhang, Ming; Li, Qiuhong; Wang, Taihong

2013-08-14

Supercapacitors with potential high power are useful and have attracted much attention recently. Graphene-based composites have been demonstrated to be promising electrode materials for supercapacitors with enhanced properties. To improve the performance of graphene-based composites further and realize their synthesis with large scale, we report a green approach to synthesize bacteria-reduced graphene oxide-nickel sulfide (BGNS) networks. By using Bacillus subtilis as spacers, we deposited reduced graphene oxide/Ni3S2 nanoparticle composites with submillimeter pores directly onto substrate by a binder-free electrostatic spray approach to form BGNS networks. Their electrochemical capacitor performance was evaluated. Compared with stacked reduced graphene oxide-nickel sulfide (GNS) prepared without the aid of bacteria, BGNS with unique nm-μm structure exhibited a higher specific capacitance of about 1424 F g(-1) at a current density of 0.75 A g(-1). About 67.5% of the capacitance was retained as the current density increased from 0.75 to 15 A g(-1). At a current density of 75 A g(-1), a specific capacitance of 406 F g(-1) could still remain. The results indicate that the reduced graphene oxide-nickel sulfide network promoted by bacteria is a promising electrode material for supercapacitors.

Bioenergetics of photoheterotrophic bacteria in the oceans.

PubMed

Kirchman, David L; Hanson, Thomas E

2013-04-01

Photoheterotrophic microbes, such as proteorhodopsin (PR)-based phototrophic (PRP) and aerobic anoxygenic phototrophic (AAP) bacteria, are well known to be abundant in the oceans, potentially playing unique roles in biogeochemical cycles. However, the contribution of phototrophy to the energy requirements of these bacteria has not been quantitatively examined to date. To better understand the implications of photoheterophy in the oceans, we calculated energy benefits and costs of phototrophy and compared net benefits with maintenance costs. Benefits depend on the number of photosynthetic units (PSUs), absorption cross-section area of each PSU as function of wavelength, the in situ light quality, and the energy yield per absorbed photon. For costs we considered the energy required for the synthesis of pigments, amino acids and proteins in each PSU. Our calculations indicate that AAP bacteria harvest more light energy than do PRP bacteria, but the costs of phototrophy are much higher for AAP bacteria. Still, the net energy gained by AAP bacteria is often sufficient to meet maintenance costs, while that is not the case for PRP bacteria except with high light intensities and large numbers of proteorhodopsin molecules per cell. The low costs and simplicity of PR-based phototrophy explain the high abundance of proteorhodopsin genes in the oceans. However, even for AAP bacteria, the net energy yield of phototrophy is apparently too low to influence the distribution of photoheterotrophic bacteria among various marine systems. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Histopathology and culturable bacteria associated with "big belly" and "skin nodule" syndromes in ornamental Siamese fighting fish, Betta splendens.

PubMed

Dong, H T; Senapin, S; Phiwsaiya, K; Techatanakitarnan, C; Dokladda, K; Ruenwongsa, P; Panijpan, B

2018-06-02

The Siamese fighting fish (Betta splendens) is one of the popular aquarium ornamental fish in the global trade. Large numbers of ornamental fish farmed in central Thailand suffered from two common syndromes; preliminarily named skin nodule syndrome (SNS) and big belly syndrome (BBS): they showed noticeable clinical signs of abnormal appearances resulting in depressed saleability. Since very few specifics are known about causative agents of these syndromes, this study aimed at investigating histopathological features and culturable bacteria associated with these fish infected in the process of farming. Histopathologically, SNS fish consistently exhibited necrosis and severe melanization in the muscles and multiple internal organs. Whereas BBS fish exhibited either typical granulomas or tissue damage associated with acid-fast stained bacteria and Gram negative bacteria, respectively. Six different Gram negative bacterial species were recovered from BBS fish while 23 bacterial species belonging to 14 genera were recovered from fish suffering from SNS. Most of the culturable bacteria are new to betta fish and some of them are known to be marine bacteria, suggesting possible entry route via a contaminated live feed, commercial Artemia shrimp. The true causative agents of these syndromes remain unclear. However, histopathological changes and existence of a wide range of bacteria associated with the naturally diseased fish suggest involvement of multiple bacterial infections. Copyright © 2018 Elsevier Ltd. All rights reserved.

Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.

PubMed

Yang, Shan; Sun, Wei; Zhang, Fengli; Li, Zhiyong

2013-10-01

To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.

Large-Scale 13C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose

PubMed Central

Klingner, Arne; Bartsch, Annekathrin; Dogs, Marco; Wagner-Döbler, Irene; Jahn, Dieter; Simon, Meinhard; Brinkhoff, Thorsten; Becker, Judith

2015-01-01

Marine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia of the Bacteriodetes phylum. We used 13C isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all strains studied use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the terrestrial model strains studied, which preferentially used the EMP pathway yielding high levels of ATP. Strains using the ED pathway exhibited a more robust resistance against the oxidative stress typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The marine bacteria studied did not specifically rely on a distinct anaplerotic route, but the carboxylation of phosphoenolpyruvate (PEP) or pyruvate for fueling of the tricarboxylic acid (TCA) cycle was evenly distributed. The marine isolates studied belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems. PMID:25616803

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

PubMed Central

Knief, Claudia

2015-01-01

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

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

Cd(II) Sorption on Montmorillonite-Humic acid-Bacteria Composites

PubMed Central

Du, Huihui; Chen, Wenli; Cai, Peng; Rong, Xingmin; Dai, Ke; Peacock, Caroline L.; Huang, Qiaoyun

2016-01-01

Soil components (e.g., clays, bacteria and humic substances) are known to produce mineral-organic composites in natural systems. Herein, batch sorption isotherms, isothermal titration calorimetry (ITC), and Cd K-edge EXAFS spectroscopy were applied to investigate the binding characteristics of Cd on montmorillonite(Mont)-humic acid(HA)-bacteria composites. Additive sorption and non-additive Cd(II) sorption behaviour is observed for the binary Mont-bacteria and ternary Mont-HA-bacteria composite, respectively. Specifically, in the ternary composite, the coexistence of HA and bacteria inhibits Cd adsorption, suggesting a “blocking effect” between humic acid and bacterial cells. Large positive entropies (68.1 ~ 114.4 J/mol/K), and linear combination fitting of the EXAFS spectra for Cd adsorbed onto Mont-bacteria and Mont-HA-bacteria composites, demonstrate that Cd is mostly bound to bacterial surface functional groups by forming inner-sphere complexes. All our results together support the assertion that there is a degree of site masking in the ternary clay mineral-humic acid-bacteria composite. Because of this, in the ternary composite, Cd preferentially binds to the higher affinity components-i.e., the bacteria. PMID:26792640

Multidrug resistance in enteric and other gram-negative bacteria.

PubMed

George, A M

1996-05-15

In Gram-negative bacteria, multidrug resistance is a term that is used to describe mechanisms of resistance by chromosomal genes that are activated by induction or mutation caused by the stress of exposure to antibiotics in natural and clinical environments. Unlike plasmid-borne resistance genes, there is no alteration or degradation of drugs or need for genetic transfer. Exposure to a single drug leads to cross-resistance to many other structurally and functionally unrelated drugs. The only mechanism identified for multidrug resistance in bacteria is drug efflux by membrane transporters, even though many of these transporters remain to be identified. The enteric bacteria exhibit mostly complex multidrug resistance systems which are often regulated by operons or regulons. The purpose of this review is to survey molecular mechanisms of multidrug resistance in enteric and other Gram-negative bacteria, and to speculate on the origins and natural physiological functions of the genes involved.

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria

PubMed Central

Gilbert, Rosalind A.; Kelly, William J.; Altermann, Eric; Leahy, Sinead C.; Minchin, Catherine; Ouwerkerk, Diane; Klieve, Athol V.

2017-01-01

The rumen is known to harbor dense populations of bacteriophages (phages) predicted to be capable of infecting a diverse range of rumen bacteria. While bacterial genome sequencing projects are revealing the presence of phages which can integrate their DNA into the genome of their host to form stable, lysogenic associations, little is known of the genetics of phages which utilize lytic replication. These phages infect and replicate within the host, culminating in host lysis, and the release of progeny phage particles. While lytic phages for rumen bacteria have been previously isolated, their genomes have remained largely uncharacterized. Here we report the first complete genome sequences of lytic phage isolates specifically infecting three genera of rumen bacteria: Bacteroides, Ruminococcus, and Streptococcus. All phages were classified within the viral order Caudovirales and include two phage morphotypes, representative of the Siphoviridae and Podoviridae families. The phage genomes displayed modular organization and conserved viral genes were identified which enabled further classification and determination of closest phage relatives. Co-examination of bacterial host genomes led to the identification of several genes responsible for modulating phage:host interactions, including CRISPR/Cas elements and restriction-modification phage defense systems. These findings provide new genetic information and insights into how lytic phages may interact with bacteria of the rumen microbiome. PMID:29259581

Role of dissolved organic carbon upon re-entrainment and surface properties of aquifer bacteria and bacteria-sized microspheres during subsurface transport (Invited)

NASA Astrophysics Data System (ADS)

Harvey, R. W.; Metge, D. W.; Mohanram, A.; Gao, X.; Chorover, J.

2010-12-01

Susceptibilities for in-situ re-entrainment of attached 0.2 and 1.0 μm (diameter) microspheres and groundwater bacteria (Pseudomonas stuzeri and uncultured, native bacteria) were assessed during transport studies involving an organically contaminated, sandy aquifer in Cape Cod, MA. Aquifer sediments between pairs of injection and sampling wells were initially loaded with fluorescently labeled, carboxylated microspheres and bacteria that had been stained with the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole. In response to subsequent hydrodynamic perturbations and injections of deionized water (ionic strength reduction), anionic surfactants (77 μM linear alkylbenzene sulfonates, LAS) and non-ionic surfactant (76 μM polyoxyethylene sorbitan monooleate, Tween 80), differing patterns of re-entrainment were evident for the two colloids. Injections of anionic surfactant and deionized water were the most efficient in causing detachment of the highly hydrophilic and negatively charged microspheres, but largely ineffective in causing re-entrainment of bacteria. In contrast, the nonionic surfactant was highly effective in re-entraining bacteria, but not microspheres. The hydrophobicities and zeta potentials of the indigenous bacteria were highly sensitive to modest concentration changes (0.6 to 1.3 mg L-1) in groundwater dissolved organic carbon (DOC), whereas the microspheres were largely unaffected. The most hydrophilic and negatively charged bacterial community was isolated from groundwater having the lowest DOC. FTIR spectra indicated that the community from the lowest DOC groundwater also had the highest average density of surface carboxyl groups. This indicates that DOC may have a biological effect on native bacteria resulting in changes to surface structures or changes in the makeup of the bacterial community.

Phototrophic bacteria and their role in the biogeochemical sulfur cycle

NASA Technical Reports Server (NTRS)

Trueper, H. G.

1985-01-01

An essential step that cannot be bypassed in the biogeochemical cycle of sulfur today is dissimilatory sulfate reduction by anaerobic bacteria. The enormous amounts of sulfides produced by these are oxidized again either anaerobically by phototrophic bacteria or aerobically by thiobacilli and large chemotrophic bacteria (Beggiatoa, Thiovulum, etc.). Phototrophic bacteria use sulfide, sulfur, thiosulfate, and sulfite as electron donors for photosynthesis. The most obvious intermediate in their oxidative sulfur metabolism is a long chain polysulfide that appears as so called sulfur globules either inside (Chromatiaceae) or outside (Ectothiorhodospiraceae, Chlorobiaceae, and some of the Rhodospirillaceae) the cells. The assimilation of sulfur compounds in phototrophic bacteria is in principle identical with that of nonphototrophic bacteria. However, the Chlorobiaceae and some of the Chromatiaceae and Rhodospirillaceae, unable to reduce sulfate, rely upon reduced sulfur for biosynthetic purposes.

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 ...

Impact of chemical oxidation on indigenous bacteria and mobilization of nutrients and subsequent bioremediation of crude oil-contaminated soil.

PubMed

Xu, Jinlan; Deng, Xin; Cui, Yiwei; Kong, Fanxing

2016-12-15

Fenton pre-oxidation provides nutrients to promote bioremediation. However, the effects of the indigenous bacteria that remain following Fenton oxidation on nutrient mobilization and subsequent bioremediation remain unclear. Experiments were performed with inoculation with native bacteria and foreign bacteria or without inoculation after four regimens of stepwise pre-oxidations. The effects of the indigenous bacteria remaining after stepwise oxidation on nutrient mobilization and subsequent bioremediation over 80 days were investigated. After stepwise Fenton pre-oxidation at a low H 2 O 2 concentration (225×4), the remaining indigenous bacterial populations reached their peak (4.8±0.17×10 6 CFU/g), the nutrients were mobilized rapidly, and the subsequent bioremediation of crude oil was improved (biodegradation efficiency of 35%). However, after stepwise Fenton pre-oxidation at a high H 2 O 2 concentration (450×4), only 3.6±0.16×10 3 CFU/g of indigenous bacteria remained, and the indigenous bacteria that degrade C 15 -C 30 alkanes were inhibited. The nutrient mobilization was then highly limited, and only 19% of total petroleum hydrocarbon was degraded. Furthermore, the recovery period after the low H 2 O 2 concentration stepwise Fenton pre-oxidation (225×4) was less than 20 days, which was 20-30 days shorter than with the other pre-oxidation treatments. Therefore, stepwise Fenton pre-oxidation at a low H 2 O 2 concentration protects indigenous bacterial populations and improves the nutrient mobilization and subsequent bioremediation. Copyright © 2016 Elsevier B.V. All rights reserved.

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine.

PubMed

Louis, Petra; Flint, Harry J

2009-05-01

Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria.

PubMed

Jiang, Tony T; Shao, Tzu-Yu; Ang, W X Gladys; Kinder, Jeremy M; Turner, Lucien H; Pham, Giang; Whitt, Jordan; Alenghat, Theresa; Way, Sing Sing

2017-12-13

Commensal intestinal microbes are collectively beneficial in preventing local tissue injury and augmenting systemic antimicrobial immunity. However, given the near-exclusive focus on bacterial species in establishing these protective benefits, the contributions of other types of commensal microbes remain poorly defined. Here, we show that commensal fungi can functionally replace intestinal bacteria by conferring protection against injury to mucosal tissues and positively calibrating the responsiveness of circulating immune cells. Susceptibility to colitis and influenza A virus infection occurring upon commensal bacteria eradication is efficiently overturned by mono-colonization with either Candida albicans or Saccharomyces cerevisiae. The protective benefits of commensal fungi are mediated by mannans, a highly conserved component of fungal cell walls, since intestinal stimulation with this moiety alone overrides disease susceptibility in mice depleted of commensal bacteria. Thus, commensal enteric fungi safeguard local and systemic immunity by providing tonic microbial stimulation that can functionally replace intestinal bacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacteriocins active against multi-resistant gram negative bacteria implicated in nosocomial infections.

PubMed

Ghodhbane, Hanen; Elaidi, Sabrine; Sabatier, Jean-Marc; Achour, Sami; Benhmida, Jeannette; Regaya, Imed

2015-01-01

Multiresistant Gram-negative bacteria are the prime mover of nosocomial infections. Some are naturally resistant to antibiotics, their genetic makes them insensitive to certain families of antibiotics and they transmit these resistors to their offspring. Moreover, when bacteria are subjected to antibiotics, they eventually develop resistance against drugs to which they were previously sensitive. In recent years, many bacteriocins active against gram-negative bacteria have been identified proving their efficacy in treating infections. While further investigation remains necessary before the possibilities for bacteriocins in clinical practice can be described more fully, this review provides an overview of bacteriocins acting on the most common infectious gram negative bacteria (Klebsiella, Acinetobacter, Pseudomonas aeruginosa and E. coli).

Envisaging bacteria as phage targets

PubMed Central

Abedon, Stephen T.

2011-01-01

It can be difficult to appreciate just how small bacteria and phages are or how large, in comparison, the volumes that they occupy. A single milliliter, for example, can represent to a phage what would be, with proper scaling, an “ocean” to you and me. Here I illustrate, using more easily visualized macroscopic examples, the difficulties that a phage, as a randomly diffusing particle, can have in locating bacteria to infect. I conclude by restating the truism that the rate of phage adsorption to a given target bacterium is a function of phage density, that is, titer, in combination with the degree of bacterial susceptibility to adsorption by an encountering phage. PMID:23616932

Heterotrophic bacteria in an air-handling system.

PubMed Central

Hugenholtz, P; Fuerst, J A

1992-01-01

Heterotrophic bacteria from structural surfaces, drain pan water, and the airstream of a well-maintained air-handling system with no reported building-related illness were enumerated. Visually the system appeared clean, but large populations of bacteria were found on the fin surface of the supply-side cooling coils (10(5) to 10(6) CFU cm-2), in drain pan water (10(5) to 10(7) CFU ml-1), and in the sump water of the evaporative condenser (10(5) CFU ml-1). Representative bacterial colony types recovered from heterotrophic plate count cultures on R2A medium were identified to the genus level. Budding bacteria belonging to the genus Blastobacter dominated the supply surface of the coil fins, the drain pan water, and the postcoil air. These data and independent scanning electron microscopy indicated that a resident population of predominantly Blastobacter bacteria was present as a biofilm on the supply-side cooling coil fins. Images PMID:1476435

Heterotrophic bacteria in an air-handling system.

PubMed

Hugenholtz, P; Fuerst, J A

1992-12-01

Heterotrophic bacteria from structural surfaces, drain pan water, and the airstream of a well-maintained air-handling system with no reported building-related illness were enumerated. Visually the system appeared clean, but large populations of bacteria were found on the fin surface of the supply-side cooling coils (10(5) to 10(6) CFU cm-2), in drain pan water (10(5) to 10(7) CFU ml-1), and in the sump water of the evaporative condenser (10(5) CFU ml-1). Representative bacterial colony types recovered from heterotrophic plate count cultures on R2A medium were identified to the genus level. Budding bacteria belonging to the genus Blastobacter dominated the supply surface of the coil fins, the drain pan water, and the postcoil air. These data and independent scanning electron microscopy indicated that a resident population of predominantly Blastobacter bacteria was present as a biofilm on the supply-side cooling coil fins.

Manipulating Genetic Material in Bacteria

NASA Technical Reports Server (NTRS)

1998-01-01

Lisa Crawford, a graduate research assistant from the University of Toledo, works with Laurel Karr of Marshall Space Flight Center (MSFC) in the molecular biology laboratory. They are donducting genetic manipulation of bacteria and yeast for the production of large amount of desired protein. Photo credit: NASA/Marshall Space Flight Center (MSFC)

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting.

PubMed

Wang, Tingting; Cheng, Lijun; Zhang, Wenhao; Xu, Xiuhong; Meng, Qingxin; Sun, Xuewei; Liu, Huajing; Li, Hongtao; Sun, Yu

2017-07-28

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene ( hzo ) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between 2.13 × 10 5 and 1.15 × 10 6 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.

Symbiotic bacteria enable olive fly larvae to overcome host defences

PubMed Central

Ben-Yosef, Michael; Pasternak, Zohar; Jurkevitch, Edouard; Yuval, Boaz

2015-01-01

Ripe fruit offer readily available nutrients for many animals, including fruit fly larvae (Diptera: Tephritidae) and their associated rot-inducing bacteria. Yet, during most of their ontogeny, fruit remain chemically defended and effectively suppress herbivores and pathogens by high levels of secondary metabolites. Olive flies (Bactrocera oleae) are uniquely able to develop in unripe olives. Unlike other frugivorous tephritids, the larvae maintain bacteria confined within their midgut caeca. We examined the interaction between larvae, their associated bacteria, and fruit chemical defence, hypothesizing that bacterial contribution to larval development is contingent on the phenology of fruit defensive chemistry. We demonstrate that larvae require their natural complement of bacteria (Candidatus Erwinia dacicola: Enterobacteriaceae) in order to develop in unripe olives. Conversely, when feeding on ripe fruit, larval development proceeds independently of these bacteria. Our experiments suggest that bacteria counteract the inhibitory effect of oleuropein—the principal phenolic glycoside in unripe olives. In light of these results, we suggest that the unique symbiosis in olive flies, compared with other frugivorous tephritids, is understood by considering the relationship between the fly, bacteria and fruit chemistry. When applied in an evolutionary context, this approach may also point out the forces which shaped symbioses across the Tephritidae. PMID:26587275

The aerobic activity of metronidazole against anaerobic bacteria.

PubMed

Dione, Niokhor; Khelaifia, Saber; Lagier, Jean-Christophe; Raoult, Didier

2015-05-01

Recently, the aerobic growth of strictly anaerobic bacteria was demonstrated using antioxidants. Metronidazole is frequently used to treat infections caused by anaerobic bacteria; however, to date its antibacterial activity was only tested in anaerobic conditions. Here we aerobically tested using antioxidants the in vitro activities of metronidazole, gentamicin, doxycycline and imipenem against 10 common anaerobic and aerobic bacteria. In vitro susceptibility testing was performed by the disk diffusion method, and minimum inhibitory concentrations (MICs) were determined by Etest. Aerobic culture of the bacteria was performed at 37°C using Schaedler agar medium supplemented with 1mg/mL ascorbic acid and 0.1mg/mL glutathione; the pH was adjusted to 7.2 by 10M KOH. Growth of anaerobic bacteria cultured aerobically using antioxidants was inhibited by metronidazole after 72h of incubation at 37°C, with a mean inhibition diameter of 37.76mm and an MIC of 1μg/mL; however, strains remained non-sensitive to gentamicin. No growth inhibition of aerobic bacteria was observed after 24h of incubation at 37°C with metronidazole; however, inhibition was observed with doxycycline and imipenem used as controls. These results indicate that bacterial sensitivity to metronidazole is not related to the oxygen tension but is a result of the sensitivity of the micro-organism. In future, both culture and antibiotic susceptibility testing of strictly anaerobic bacteria will be performed in an aerobic atmosphere using antioxidants in clinical microbiology laboratories. Copyright © 2015 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Chemical signaling between plants and plant-pathogenic bacteria.

PubMed

Venturi, Vittorio; Fuqua, Clay

2013-01-01

Studies of chemical signaling between plants and bacteria in the past have been largely confined to two models: the rhizobial-legume symbiotic association and pathogenesis between agrobacteria and their host plants. Recent studies are beginning to provide evidence that many plant-associated bacteria undergo chemical signaling with the plant host via low-molecular-weight compounds. Plant-produced compounds interact with bacterial regulatory proteins that then affect gene expression. Similarly, bacterial quorum-sensing signals result in a range of functional responses in plants. This review attempts to highlight current knowledge in chemical signaling that takes place between pathogenic bacteria and plants. This chemical communication between plant and bacteria, also referred to as interkingdom signaling, will likely become a major research field in the future, as it allows the design of specific strategies to create plants that are resistant to plant pathogens.

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

Psychobiotics and the Manipulation of Bacteria-Gut-Brain Signals.

PubMed

Sarkar, Amar; Lehto, Soili M; Harty, Siobhán; Dinan, Timothy G; Cryan, John F; Burnet, Philip W J

2016-11-01

Psychobiotics were previously defined as live bacteria (probiotics) which, when ingested, confer mental health benefits through interactions with commensal gut bacteria. We expand this definition to encompass prebiotics, which enhance the growth of beneficial gut bacteria. We review probiotic and prebiotic effects on emotional, cognitive, systemic, and neural variables relevant to health and disease. We discuss gut-brain signalling mechanisms enabling psychobiotic effects, such as metabolite production. Overall, knowledge of how the microbiome responds to exogenous influence remains limited. We tabulate several important research questions and issues, exploration of which will generate both mechanistic insights and facilitate future psychobiotic development. We suggest the definition of psychobiotics be expanded beyond probiotics and prebiotics to include other means of influencing the microbiome. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Spatio-temporal patterns of bacteria caused by collective motion

NASA Astrophysics Data System (ADS)

Kitsunezaki, So

2006-04-01

In incubation experiments on bacterial colonies of Proteus mirabilis, collective motion of bacteria is found to generate macroscopic turbulent patterns on the surface of agar media. We propose a mathematical model to describe the time evolution of the positional and directional distributions of motile bacteria in such systems, and investigate this model both numerically and analytically. It is shown that as the average density of bacteria increases, nonuniform swarming patterns emerge from a uniform stationary state. For a sufficient large density, we find that spiral patterns are caused by interactions between the local bacteria densities and the rotational mode of the collective motion. Unidirectional spiral patterns similar to those observed in experiments appear in the case in which the equilibrium directional distribution is asymmetric.

[Spectrum and susceptibility of preoperative conjunctival bacteria].

PubMed

Fernández-Rubio, M E; Cuesta-Rodríguez, T; Urcelay-Segura, J L; Cortés-Valdés, C

2013-12-01

To describe the conjunctival bacterial spectrum of our patients undergoing intraocular surgery and their antibiotic sensitivity during the study period. A retrospective study of preoperative conjunctival culture of patients consecutively scheduled for intraocular surgery from 21 February 2011 to 1 April 2013. Specimens were directly seeded onto blood-agar and MacConkey-agar (aerobiosis incubation, 2 days), and on chocolate-agar (6% CO2 incubation, 7 days). The identified bacteria were divided into 3 groups according to their origin; the bacteria susceptibility tests were performed on those more pathogenic and on some of the less pathogenic when more than 5 colonies were isolated. The sensitivity of the exigent growing bacteria was obtained with disk diffusion technique, and for of the non-exigent bacteria by determining their minimum inhibitory concentration. The Epidat 3.1 program was used for statistical calculations. A total of 13,203 bacteria were identified in 6,051 cultures, with 88.7% being typical colonizers of conjunctiva (group 1), 8.8% typical of airways (group 2), and the remaining 2.5% of undetermined origin (group 3). 530 cultures (8.8%) were sterile. The sensitivity of group 1 was: 99% vancomycin, 95% rifampicin, 87% chloramphenicol, 76% tetracycline. Levels of co-trimoxazole, aminoglycosides, quinolones, β-lactams and macrolides decreased since 2007. The group 2 was very sensitive to chloramphenicol, cefuroxime, rifampicin, ciprofloxacin and amoxicillin/clavulanate. In group 3, to levofloxacin 93%, ciprofloxacin 89%, tobramycin 76%, but ceftazidime 53% and cefuroxime 29% decreased. None of the tested antibiotics could eradicate all possible conjunctival bacteria. Bacteria living permanently on the conjunctiva (group 1) have achieved higher resistance than the eventual colonizers. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

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.

Bacteria in decomposing wood and their interactions with wood-decay fungi.

PubMed

Johnston, Sarah R; Boddy, Lynne; Weightman, Andrew J

2016-11-01

The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods.

PubMed

Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian

2015-03-01

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Lactic acid bacteria in the quality improvement and depreciation of wine.

PubMed

Lonvaud-Funel, A

1999-01-01

The winemaking process includes two main steps: lactic acid bacteria are responsible for the malolactic fermentation which follows the alcoholic fermentation by yeasts. Both types of microorganisms are present on grapes and on cellar equipment. Yeasts are better adapted to growth in grape must than lactic acid bacteria, so the alcoholic fermentation starts quickly. In must, up to ten lactic acid bacteria species can be identified. They belong to the Lactobacillus, Pediococcus, Leuconostoc and Oenococcus genera. Throughout alcoholic fermentation, a natural selection occurs and finally the dominant species is O. oeni, due to interactions between yeasts and bacteria and between bacteria themselves. After bacterial growth, when the population is over 10(6) CFU/ml, malolactic transformation is the obvious change in wine composition. However, many other substrates can be metabolized. Some like remaining sugars and citric acid are always assimilated by lactic acid bacteria, thus providing them with energy and carbon. Other substrates such as some amino acids may be used following pathways restricted to strains carrying the adequate enzymes. Some strains can also produce exopolysaccharides. All these transformations greatly influence the sensory and hygienic quality of wine. Malic acid transformation is encouraged because it induces deacidification. Diacetyl produced from citric acid is also helpful to some extent. Sensory analyses show that many other reactions change the aromas and make malolactic fermentation beneficial, but they are as yet unknown. On the contrary, an excess of acetic acid, the synthesis of glucane, biogenic amines and precursors of ethylcarbamate are undesirable. Fortunately, lactic acid bacteria normally multiply in dry wines; moreover some of these activities are not widespread. Moreover, the most striking trait of wine lactic acid bacteria is their capacity to adapt to a hostile environment. The mechanisms for this are not yet completely elucidated

Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm

PubMed Central

Chu, Chia-Ching; Spencer, Joseph L.; Curzi, Matías J.; Zavala, Jorge A.; Seufferheld, Manfredo J.

2013-01-01

Insects are constantly adapting to human-driven landscape changes; however, the roles of their gut microbiota in these processes remain largely unknown. The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) (Coleoptera: Chrysomelidae) is a major corn pest that has been controlled via annual rotation between corn (Zea mays) and nonhost soybean (Glycine max) in the United States. This practice selected for a “rotation-resistant” variant (RR-WCR) with reduced ovipositional fidelity to cornfields. When in soybean fields, RR-WCRs also exhibit an elevated tolerance of antiherbivory defenses (i.e., cysteine protease inhibitors) expressed in soybean foliage. Here we show that gut bacterial microbiota is an important factor facilitating this corn specialist’s (WCR's) physiological adaptation to brief soybean herbivory. Comparisons of gut microbiota between RR- and wild-type WCR (WT-WCR) revealed concomitant shifts in bacterial community structure with host adaptation to soybean diets. Antibiotic suppression of gut bacteria significantly reduced RR-WCR tolerance of soybean herbivory to the level of WT-WCR, whereas WT-WCR were unaffected. Our findings demonstrate that gut bacteria help to facilitate rapid adaptation of insects in managed ecosystems. PMID:23798396

Spatio-Temporal Patterns in Colonies of Rod-Shaped Bacteria

NASA Astrophysics Data System (ADS)

Kitsunezaki, S.

In incubation experiments of bacterial colonies of Proteus Mirabilis, macroscopic spatio-temporal patterns, such as turbulent and unidirectional spiral patterns, appear in colonies. Considering only kinetic propeties of rod-shaped bacteria, we propose a phenomenological model for the directional and positional distributions. As the average density increases, homogeneous states bifurcate sub-critically into nonuniform states exhibiting localized collective motion, and spiral patterns appear for sufficiently large density. These patterns result from interactions between the local bacteria densities and the order parameter representing collective motion. Our model can be described by reduced equations using a perturbative method for large density. The unidirectionality of sprial rotation is also discussed.

Rapid method for determination of antimicrobial susceptibilities pattern of urinary bacteria

NASA Technical Reports Server (NTRS)

Picciolo, G. L.; Chapelle, E. W.; Barza, M. J.; Weinstein, L.; Tuttle, S. A.; Vellend, H.

1975-01-01

Method determines bacterial sensitivity to antimicrobial agents by measuring level of adenosine triphosphate remaining in the bacteria. Light emitted during reaction of sample with a mixture of luciferase and luciferin is measured.

Sulphur bacteria mediated formation of Palaeoproterozoic phosphorites

NASA Astrophysics Data System (ADS)

Joosu, Lauri; Lepland, Aivo; Kirsimäe, Kalle

2014-05-01

Modern phosphorite formation is typically associated with high productivity in upwelling areas where apatite (Ca-phosphate) precipitation is mediated by sulphur oxidising bacteria [1]. They inhabit the oxic/anoxic interface within the upper few centimetres of sediment column, accumulating phosphate in their cells under oxic conditions and releasing it rapidly when conditions become anoxic. Sulphur bacteria are known to live in close association with a consortium of anaerobic methane oxidising archaea and syntrophic sulphate-reducing bacteria. Paleoproterozoic, c. 2.0 Ga Zaonega Formation in Karelia, Russia contains several P-rich intervals in the upper part of 1500 m thick succession of organic-rich sedimentary rocks interlayered with mafic tuffs and lavas. Apatite in these P-rich intervals forms impure laminae, lenses and round-oval nodules which diameters typically range from 300 to 1000 μm. Individual apatite particles in P-rich laminae and nodules commonly occur as cylinders that are 1-8 μm long and have diameters of 0.5-4 μm. Cross-sections of best preserved cylindrical apatite particles reveal a thin outer rim whereas the internal parts consist of small anhedral elongated crystallites, intergrown with carbonaceous material. During recrystallization the outer rim thickens towards interior and cylinders may attain hexagonal crystal habit, but their size and shape remains largely unchanged [2]. The sizes of Zaonega nodules are similar to giant sulphide-oxidising bacteria known from modern and ancient settings [3, 4]. Individual apatite cylinders and aggregates have shapes and sizes similar to the methanotrophic archaea that inhabit microbial mats in modern seep/vent areas where they operate in close associations with sulphur-oxidising microbial communities [5]. Seep/vent influence during the Zaonega phosphogenesis is indicated by variable, though positive Eu anomaly, expected in magmatically active sedimentary environment experiencing several lava flows

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review.

PubMed

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

PubMed Central

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

PubMed Central

Delmotte, Nathanaël; Knief, Claudia; Chaffron, Samuel; Innerebner, Gerd; Roschitzki, Bernd; Schlapbach, Ralph; von Mering, Christian; Vorholt, Julia A.

2009-01-01

Aerial plant surfaces represent the largest biological interface on Earth and provide essential services as sites of carbon dioxide fixation, molecular oxygen release, and primary biomass production. Rather than existing as axenic organisms, plants are colonized by microorganisms that affect both their health and growth. To gain insight into the physiology of phyllosphere bacteria under in situ conditions, we performed a culture-independent analysis of the microbiota associated with leaves of soybean, clover, and Arabidopsis thaliana plants using a metaproteogenomic approach. We found a high consistency of the communities on the 3 different plant species, both with respect to the predominant community members (including the alphaproteobacterial genera Sphingomonas and Methylo bacterium) and with respect to their proteomes. Observed known proteins of Methylobacterium were to a large extent related to the ability of these bacteria to use methanol as a source of carbon and energy. A remarkably high expression of various TonB-dependent receptors was observed for Sphingomonas. Because these outer membrane proteins are involved in transport processes of various carbohydrates, a particularly large substrate utilization pattern for Sphingomonads can be assumed to occur in the phyllosphere. These adaptations at the genus level can be expected to contribute to the success and coexistence of these 2 taxa on plant leaves. We anticipate that our results will form the basis for the identification of unique traits of phyllosphere bacteria, and for uncovering previously unrecorded mechanisms of bacteria-plant and bacteria-bacteria relationships. PMID:19805315

Coral symbiotic algae calcify ex hospite in partnership with bacteria.

PubMed

Frommlet, Jörg C; Sousa, Maria L; Alves, Artur; Vieira, Sandra I; Suggett, David J; Serôdio, João

2015-05-12

Dinoflagellates of the genus Symbiodinium are commonly recognized as invertebrate endosymbionts that are of central importance for the functioning of coral reef ecosystems. However, the endosymbiotic phase within Symbiodinium life history is inherently tied to a more cryptic free-living (ex hospite) phase that remains largely unexplored. Here we show that free-living Symbiodinium spp. in culture commonly form calcifying bacterial-algal communities that produce aragonitic spherulites and encase the dinoflagellates as endolithic cells. This process is driven by Symbiodinium photosynthesis but occurs only in partnership with bacteria. Our findings not only place dinoflagellates on the map of microbial-algal organomineralization processes but also point toward an endolithic phase in the Symbiodinium life history, a phenomenon that may provide new perspectives on the biology and ecology of Symbiodinium spp. and the evolutionary history of the coral-dinoflagellate symbiosis.

Guidelines for the recognition of cemetery remains in Greece.

PubMed

Eliopoulos, Constantine; Moraitis, Konstantinos; Reyes, Federico; Spiliopoulou, Chara; Manolis, Sotiris

2011-06-01

Forensic pathologists frequently consult anthropologists for the identification of skeletonized human remains. These remains may be the result of criminal activity or remains that were unearthed because of erosion, or during construction projects. In some cases, human remains that had been previously buried in a cemetery may be the subject of a forensic investigation. Early recognition of cemetery remains prevents unnecessary efforts and conserves precious resources. One of the key characteristics of cemetery remains is the presence of embalmed tissue. However, there are countries where embalming is not a common practice, and other clues must be sought for identifying previously buried remains. Current funerary customs in Greece and, in particular, the tradition of exhumations result in a large number of misplaced human remains. The present study presents examples of cemetery remains from Greece and offers guidelines for recognizing changes on skeletal remains that may be indicative of a cemetery origin. Location of discovery, condition of the remains, and the types of associated artifacts are all factors that aid forensic anthropologists in identifying cemetery remains.

Vibrio bacteria in raw oysters: managing risks to human health.

PubMed

Froelich, Brett A; Noble, Rachel T

2016-03-05

The human-pathogenic marine bacteria Vibrio vulnificus and V. parahaemolyticus are strongly correlated with water temperature, with concentrations increasing as waters warm seasonally. Both of these bacteria can be concentrated in filter-feeding shellfish, especially oysters. Because oysters are often consumed raw, this exposes people to large doses of potentially harmful bacteria. Various models are used to predict the abundance of these bacteria in oysters, which guide shellfish harvest policy meant to reduce human health risk. Vibrio abundance and behaviour varies from site to site, suggesting that location-specific studies are needed to establish targeted risk reduction strategies. Moreover, virulence potential, rather than simple abundance, should be also be included in future modeling efforts. © 2016 The Author(s).

Cecum Lymph Node Dendritic Cells Harbor Slow-Growing Bacteria Phenotypically Tolerant to Antibiotic Treatment

PubMed Central

Dolowschiak, Tamas; Wotzka, Sandra Y.; Lengefeld, Jette; Slack, Emma; Grant, Andrew J.; Ackermann, Martin; Hardt, Wolf-Dietrich

2014-01-01

In vivo, antibiotics are often much less efficient than ex vivo and relapses can occur. The reasons for poor in vivo activity are still not completely understood. We have studied the fluoroquinolone antibiotic ciprofloxacin in an animal model for complicated Salmonellosis. High-dose ciprofloxacin treatment efficiently reduced pathogen loads in feces and most organs. However, the cecum draining lymph node (cLN), the gut tissue, and the spleen retained surviving bacteria. In cLN, approximately 10%–20% of the bacteria remained viable. These phenotypically tolerant bacteria lodged mostly within CD103+CX3CR1−CD11c+ dendritic cells, remained genetically susceptible to ciprofloxacin, were sufficient to reinitiate infection after the end of the therapy, and displayed an extremely slow growth rate, as shown by mathematical analysis of infections with mixed inocula and segregative plasmid experiments. The slow growth was sufficient to explain recalcitrance to antibiotics treatment. Therefore, slow-growing antibiotic-tolerant bacteria lodged within dendritic cells can explain poor in vivo antibiotic activity and relapse. Administration of LPS or CpG, known elicitors of innate immune defense, reduced the loads of tolerant bacteria. Thus, manipulating innate immunity may augment the in vivo activity of antibiotics. PMID:24558351

[Antimicrobial therapy in severe infections with multidrug-resistant Gram-negative bacterias].

PubMed

Duszyńska, Wiesława

2010-01-01

Multidrug-resistant Gram-negative bacteria pose a serious and rapidly emerging threat to patients in healthcare settings, and are especially prevalent and problematic in intensive therapy units. Recently, the emergence of pandrug-resistance in Gram-negative bacteria poses additional concerns. This review examines the clinical impact and epidemiology of multidrug-resistant Gram-negative bacteria as a cause of increased morbidity and mortality among ITU patients. Beta-lactamases, cephalosporinases and carbapenemases play the most important role in resistance to antibiotics. Despite the tendency to increased resistance, carbapenems administered by continuous infusion remain the most effective drugs in severe sepsis. Drug concentration monitoring, albeit rarely used in practice, is necessary to ensure an effective therapeutic effect.

Asymmetric cellular memory in bacteria exposed to antibiotics.

PubMed

Mathis, Roland; Ackermann, Martin

2017-03-09

The ability to form a cellular memory and use it for cellular decision-making could help bacteria to cope with recurrent stress conditions. We analyzed whether bacteria would form a cellular memory specifically if past events are predictive of future conditions. We worked with the asymmetrically dividing bacterium Caulobacter crescentus where past events are expected to only be informative for one of the two cells emerging from division, the sessile cell that remains in the same microenvironment and does not migrate. Time-resolved analysis of individual cells revealed that past exposure to low levels of antibiotics increases tolerance to future exposure for the sessile but not for the motile cell. Using computer simulations, we found that such an asymmetry in cellular memory could be an evolutionary response to situations where the two cells emerging from division will experience different future conditions. Our results raise the question whether bacteria can evolve the ability to form and use cellular memory conditionally in situations where it is beneficial.

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

PubMed Central

Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori; Hisada, Takayoshi; Nishijima, Miyuki

2014-01-01

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (±20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples. PMID:25144201

DLVO, hydrophobic, capillary and hydrodynamic forces acting on bacteria at solid-air-water interfaces: Their relative impact on bacteria deposition mechanisms in unsaturated porous media.

PubMed

Bai, Hongjuan; Cochet, Nelly; Pauss, André; Lamy, Edvina

2017-02-01

Experimental and modeling studies were performed to investigate bacteria deposition behavior in unsaturated porous media. The coupled effect of different forces, acting on bacteria at solid-air-water interfaces and their relative importance on bacteria deposition mechanisms was explored by calculating Derjaguin-Landau-Verwey-Overbeek (DLVO) and non-DLVO interactions such as hydrophobic, capillary and hydrodynamic forces. Negatively charged non-motile bacteria and quartz sands were used in packed column experiments. The breakthrough curves and retention profiles of bacteria were simulated using the modified Mobile-IMmobile (MIM) model, to identify physico-chemical attachment or physical straining mechanisms involved in bacteria retention. These results indicated that both mechanisms might occur in both sand. However, the attachment was found to be a reversible process, because attachment coefficients were similar to those of detachment. DLVO calculations supported these results: the primary minimum did not exist, suggesting no permanent retention of bacteria to solid-water and air-water interfaces. Calculated hydrodynamic and resisting torques predicted that bacteria detachment in the secondary minimum might occur. The capillary potential energy was greater than DLVO, hydrophobic and hydrodynamic potential energies, suggesting that film straining by capillary forces might largely govern bacteria deposition under unsaturated conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Virus-Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences.

PubMed

Moore, Matthew D; Jaykus, Lee-Ann

2018-02-02

Eukaryotic virus-bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus-bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus-bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus-bacteria interactions would likely result in numerous discoveries and beneficial applications.

Contamination pathways of spore-forming bacteria in a vegetable cannery.

PubMed

Durand, Loïc; Planchon, Stella; Guinebretiere, Marie-Hélène; André, Stéphane; Carlin, Frédéric; Remize, Fabienne

2015-06-02

Spoilage of low-acid canned food during prolonged storage at high temperatures is caused by heat resistant thermophilic spores of strict or facultative bacteria. Here, we performed a bacterial survey over two consecutive years on the processing line of a French company manufacturing canned mixed green peas and carrots. In total, 341 samples were collected, including raw vegetables, green peas and carrots at different steps of processing, cover brine, and process environment samples. Thermophilic and highly-heat-resistant thermophilic spores growing anaerobically were counted. During vegetable preparation, anaerobic spore counts were significantly decreased, and tended to remain unchanged further downstream in the process. Large variation of spore levels in products immediately before the sterilization process could be explained by occasionally high spore levels on surfaces and in debris of vegetable combined with long residence times in conditions suitable for growth and sporulation. Vegetable processing was also associated with an increase in the prevalence of highly-heat-resistant species, probably due to cross-contamination of peas via blanching water. Geobacillus stearothermophilus M13-PCR genotypic profiling on 112 isolates determined 23 profile-types and confirmed process-driven cross-contamination. Taken together, these findings clarify the scheme of contamination pathway by thermophilic spore-forming bacteria in a vegetable cannery. Copyright © 2015 Elsevier B.V. All rights reserved.

Differential Attraction of Malaria Mosquitoes to Volatile Blends Produced by Human Skin Bacteria

PubMed Central

Verhulst, Niels O.; Andriessen, Rob; Groenhagen, Ulrike; Bukovinszkiné Kiss, Gabriella; Schulz, Stefan; Takken, Willem; van Loon, Joop J. A.; Schraa, Gosse; Smallegange, Renate C.

2010-01-01

The malaria mosquito Anopheles gambiae sensu stricto is mainly guided by human odour components to find its blood host. Skin bacteria play an important role in the production of human body odour and when grown in vitro, skin bacteria produce volatiles that are attractive to A. gambiae. The role of single skin bacterial species in the production of volatiles that mediate the host-seeking behaviour of mosquitoes has remained largely unknown and is the subject of the present study. Headspace samples were taken to identify volatiles that mediate this behaviour. These volatiles could be used as mosquito attractants or repellents. Five commonly occurring species of skin bacteria were tested in an olfactometer for the production of volatiles that attract A. gambiae. Odour blends produced by some bacterial species were more attractive than blends produced by other species. In contrast to odours from the other bacterial species tested, odours produced by Pseudomonas aeruginosa were not attractive to A. gambiae. Headspace analysis of bacterial volatiles in combination with behavioural assays led to the identification of six compounds that elicited a behavioural effect in A. gambiae. Our results provide, to our knowledge, the first evidence for a role of selected bacterial species, common on the human skin, in determining the attractiveness of humans to malaria mosquitoes. This information will be used in the further development of a blend of semiochemicals for the manipulation of mosquito behaviour. PMID:21209854

Bovine Intestinal Bacteria Inactivate and Degrade Ceftiofur and Ceftriaxone with Multiple β-Lactamases▿

PubMed Central

Wagner, R. Doug; Johnson, Shemedia J.; Cerniglia, Carl E.; Erickson, Bruce D.

2011-01-01

The veterinary cephalosporin drug ceftiofur is rapidly degraded in the bovine intestinal tract. A cylinder-plate assay was used to detect microbiologically active ceftiofur, and high-performance liquid chromatography-mass spectrometry analysis was used to quantify the amount of ceftiofur remaining after incubation with bovine intestinal anaerobic bacteria, which were isolated from colon contents or feces from 8 cattle. Ninety-six percent of the isolates were able to inactivate ceftiofur to some degree, and 54% actually degraded the drug. None of 9 fungal isolates inactivated or degraded ceftiofur. Facultative and obligate anaerobic bacterial species that inactivated or degraded ceftiofur were identified with Vitek and Biolog systems, respectively. A subset of ceftiofur degraders also degraded the chemically similar drug ceftriaxone. Most of the species of bacteria that degraded ceftiofur belonged to the genera Bacillus and Bacteroides. PCR analysis of bacterial DNA detected specific β-lactamase genes. Bacillus cereus and B. mycoides isolates produced extended-spectrum β-lactamases and metallo-β-lactamases. Seven isolates of Bacteroides spp. produced multiple β-lactamases, including possibly CepA, and metallo-β-lactamases. Isolates of Eubacterium biforme, Bifidobacterium breve, and several Clostridium spp. also produced ceftiofur-degrading β-lactamases. An agar gel overlay technique on isoelectric focusing separations of bacterial lysates showed that β-lactamase enzymes were sufficient to degrade ceftiofur. These results suggest that ceftiofur is inactivated nonenzymatically and degraded enzymatically by multiple β-lactamases from bacteria in the large intestines of cattle. PMID:21876048

Bovine intestinal bacteria inactivate and degrade ceftiofur and ceftriaxone with multiple beta-lactamases.

PubMed

Wagner, R Doug; Johnson, Shemedia J; Cerniglia, Carl E; Erickson, Bruce D

2011-11-01

The veterinary cephalosporin drug ceftiofur is rapidly degraded in the bovine intestinal tract. A cylinder-plate assay was used to detect microbiologically active ceftiofur, and high-performance liquid chromatography-mass spectrometry analysis was used to quantify the amount of ceftiofur remaining after incubation with bovine intestinal anaerobic bacteria, which were isolated from colon contents or feces from 8 cattle. Ninety-six percent of the isolates were able to inactivate ceftiofur to some degree, and 54% actually degraded the drug. None of 9 fungal isolates inactivated or degraded ceftiofur. Facultative and obligate anaerobic bacterial species that inactivated or degraded ceftiofur were identified with Vitek and Biolog systems, respectively. A subset of ceftiofur degraders also degraded the chemically similar drug ceftriaxone. Most of the species of bacteria that degraded ceftiofur belonged to the genera Bacillus and Bacteroides. PCR analysis of bacterial DNA detected specific β-lactamase genes. Bacillus cereus and B. mycoides isolates produced extended-spectrum β-lactamases and metallo-β-lactamases. Seven isolates of Bacteroides spp. produced multiple β-lactamases, including possibly CepA, and metallo-β-lactamases. Isolates of Eubacterium biforme, Bifidobacterium breve, and several Clostridium spp. also produced ceftiofur-degrading β-lactamases. An agar gel overlay technique on isoelectric focusing separations of bacterial lysates showed that β-lactamase enzymes were sufficient to degrade ceftiofur. These results suggest that ceftiofur is inactivated nonenzymatically and degraded enzymatically by multiple β-lactamases from bacteria in the large intestines of cattle.

Endosymbiotic calcifying bacteria across sponge species and oceans

NASA Astrophysics Data System (ADS)

Garate, Leire; Sureda, Jan; Agell, Gemma; Uriz, Maria J.

2017-03-01

From an evolutionary point of view, sponges are ideal targets to study marine symbioses as they are the most ancient living metazoans and harbour highly diverse microbial communities. A recently discovered association between the sponge Hemimycale columella and an intracellular bacterium that generates large amounts of calcite spherules has prompted speculation on the possible role of intracellular bacteria in the evolution of the skeleton in early animals. To gain insight into this purportedly ancestral symbiosis, we investigated the presence of symbiotic bacteria in Mediterranean and Caribbean sponges. We found four new calcibacteria OTUs belonging to the SAR116 in two orders (Poecilosclerida and Clionaida) and three families of Demospongiae, two additional OTUs in cnidarians and one more in seawater (at 98.5% similarity). Using a calcibacteria targeted probe and CARD-FISH, we also found calcibacteria in Spirophorida and Suberitida and proved that the calcifying bacteria accumulated at the sponge periphery, forming a skeletal cortex, analogous to that of siliceous microscleres in other demosponges. Bacteria-mediated skeletonization is spread in a range of phylogenetically distant species and thus the purported implication of bacteria in skeleton formation and evolution of early animals gains relevance.

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

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.

TNF-alpha and antibodies to periodontal bacteria discriminate between Alzheimer's disease patients and normal subjects.

PubMed

Kamer, Angela R; Craig, Ronald G; Pirraglia, Elizabeth; Dasanayake, Ananda P; Norman, Robert G; Boylan, Robert J; Nehorayoff, Andrea; Glodzik, Lidia; Brys, Miroslaw; de Leon, Mony J

2009-11-30

The associations of inflammation/immune responses with clinical presentations of Alzheimer's disease (AD) remain unclear. We hypothesized that TNF-alpha and elevated antibodies to periodontal bacteria would be greater in AD compared to normal controls (NL) and their combination would aid clinical diagnosis of AD. Plasma TNF-alpha and antibodies against periodontal bacteria were elevated in AD patients compared with NL and independently associated with AD. The number of positive IgG to periodontal bacteria incremented the TNF-alpha classification of clinical AD and NL. This study shows that TNF-alpha and elevated numbers of antibodies against periodontal bacteria associate with AD and contribute to the AD diagnosis.

Design of a large-scale femtoliter droplet array for single-cell analysis of drug-tolerant and drug-resistant bacteria.

PubMed

Iino, Ryota; Matsumoto, Yoshimi; Nishino, Kunihiko; Yamaguchi, Akihito; Noji, Hiroyuki

2013-01-01

Single-cell analysis is a powerful method to assess the heterogeneity among individual cells, enabling the identification of very rare cells with properties that differ from those of the majority. In this Methods Article, we describe the use of a large-scale femtoliter droplet array to enclose, isolate, and analyze individual bacterial cells. As a first example, we describe the single-cell detection of drug-tolerant persisters of Pseudomonas aeruginosa treated with the antibiotic carbenicillin. As a second example, this method was applied to the single-cell evaluation of drug efflux activity, which causes acquired antibiotic resistance of bacteria. The activity of the MexAB-OprM multidrug efflux pump system from Pseudomonas aeruginosa was expressed in Escherichia coli and the effect of an inhibitor D13-9001 were assessed at the single cell level.

Silver enhances antibiotic activity against gram-negative bacteria.

PubMed

Morones-Ramirez, J Ruben; Winkler, Jonathan A; Spina, Catherine S; Collins, James J

2013-06-19

A declining pipeline of clinically useful antibiotics has made it imperative to develop more effective antimicrobial therapies, particularly against difficult-to-treat Gram-negative pathogens. Silver has been used as an antimicrobial since antiquity, yet its mechanism of action remains unclear. We show that silver disrupts multiple bacterial cellular processes, including disulfide bond formation, metabolism, and iron homeostasis. These changes lead to increased production of reactive oxygen species and increased membrane permeability of Gram-negative bacteria that can potentiate the activity of a broad range of antibiotics against Gram-negative bacteria in different metabolic states, as well as restore antibiotic susceptibility to a resistant bacterial strain. We show both in vitro and in a mouse model of urinary tract infection that the ability of silver to induce oxidative stress can be harnessed to potentiate antibiotic activity. Additionally, we demonstrate in vitro and in two different mouse models of peritonitis that silver sensitizes Gram-negative bacteria to the Gram-positive-specific antibiotic vancomycin, thereby expanding the antibacterial spectrum of this drug. Finally, we used silver and antibiotic combinations in vitro to eradicate bacterial persister cells, and show both in vitro and in a mouse biofilm infection model that silver can enhance antibacterial action against bacteria that produce biofilms. This work shows that silver can be used to enhance the action of existing antibiotics against Gram-negative bacteria, thus strengthening the antibiotic arsenal for fighting bacterial infections.

Micro-motors: A motile bacteria based system for liposome cargo transport.

PubMed

Dogra, Navneet; Izadi, Hadi; Vanderlick, T Kyle

2016-07-05

Biological micro-motors (microorganisms) have potential applications in energy utilization and nanotechnology. However, harnessing the power generated by such motors to execute desired work is extremely difficult. Here, we employ the power of motile bacteria to transport small, large, and giant unilamellar vesicles (SUVs, LUVs, and GUVs). Furthermore, we demonstrate bacteria-bilayer interactions by probing glycolipids inside the model membrane scaffold. Fluorescence Resonance Energy Transfer (FRET) spectroscopic and microscopic methods were utilized for understanding these interactions. We found that motile bacteria could successfully propel SUVs and LUVs with a velocity of 28 μm s(-1) and 13 μm s(-1), respectively. GUVs, however, displayed Brownian motion and could not be propelled by attached bacteria. Bacterial velocity decreased with the larger loaded cargo, which agrees with our calculations of loaded bacteria swimming at low Reynolds number.

Pathogenesis of pigment gallstones in Western societies: the central role of bacteria.

PubMed

Stewart, Lygia; Oesterle, Adair L; Erdan, Ihsan; Griffiss, J MacLeod; Way, Lawrence W

2002-01-01

Bacteria are traditionally accorded a greater role in pigment gallstone formation in Eastern populations. Stone color is thought to predict the presence of bacteria; that is, black stones (Western predominant) are supposedly sterile and brown stones (Eastern predominant) contain bacteria. We previously reported that, regardless of appearance, most pigment gallstones contain bacteria. This study examined, in a large Western population (370 patients), the incidence, appearance, and chemical composition of pigment stones, and the characteristics of gallstone bacteria. One hundred eighty-six pigment stones were obtained aseptically. Bacteria were detected by means of scanning electron microscopy and gallstone culture. Chemical composition was determined by infrared spectroscopy. Bacteria were tested for slime and beta-glucuronidase production. Seventy-three percent of pigment stones contained bacteria. Choledocholithiasis was associated with gallstone bacteria. Ca-bilirubinate was present in all pigment stones. Ca-palmitate was characteristic of infected stones, and more than 75% Ca-carbonate was characteristic of sterile stones. Neither chemical composition nor stone appearance predicted the presence of bacteria. Ninety-five percent and 67% of infected pigment stones contained bacteria that produced slime and beta-glucuronidase, respectively. Most pigment stones contained bacteria that produced beta-glucuronidase, slime, and phospholipase, factors that facilitate stone formation. Thus bacteria have a major role in Western pigment gallstone formation. Furthermore, gallstone color did not predict composition or bacterial presence.

Rapid and automated enumeration of viable bacteria in compost using a micro-colony auto counting system.

PubMed

Wang, Xiaodan; Yamaguchi, Nobuyasu; Someya, Takashi; Nasu, Masao

2007-10-01

The micro-colony method was used to enumerate viable bacteria in composts. Cells were vacuum-filtered onto polycarbonate filters and incubated for 18 h on LB medium at 37 degrees C. Bacteria on the filters were stained with SYBR Green II, and enumerated using a newly developed micro-colony auto counting system which can automatically count micro-colonies on half the area of the filter within 90 s. A large number of bacteria in samples retained physiological activity and formed micro-colonies within 18 h, whereas most could not form large colonies on conventional media within 1 week. The results showed that this convenient technique can enumerate viable bacteria in compost rapidly for its efficient quality control.

UV-absorbing bacteria in coral mucus and their response to simulated temperature elevations

NASA Astrophysics Data System (ADS)

Ravindran, J.; Kannapiran, E.; Manikandan, B.; Francis, K.; Arora, Shruti; Karunya, E.; Kumar, Amit; Singh, S. K.; Jose, Jiya

2013-12-01

Reef-building corals encompass various strategies to defend against harmful ultraviolet (UV) radiation. Coral mucus contains UV-absorbing compounds and has rich prokaryotic diversity associated with it. In this study, we isolated and characterized the UV-absorbing bacteria from the mucus of the corals Porites lutea and Acropora hyacinthus during the pre-summer and summer seasons. A total of 17 UV-absorbing bacteria were isolated and sequenced. The UV-absorbing bacteria showed UV absorption at wavelengths ranging from λ max = 333 nm to λ min = 208 nm. Analysis of the DNA sequences revealed that the majority of the UV-absorbing bacteria belonged to the family Firmicutes and the remaining belonged to the family Proteobacteria (class Gammaproteobacteria). Comparison of the sequences with the curated database yielded four distinct bacterial groups belonging to the genus Bacillus, Staphylococcus, Salinicoccus and Vibrio. The absorption peaks for the UV-absorbing bacteria shifted to the UV-A range (320-400 nm) when they were incubated at higher temperatures. Deciphering the complex relationship between corals and their associated bacteria will help us to understand their adaptive strategies to various stresses.

Carbonate crystals precipitated by freshwater bacteria and their use as a limestone consolidant.

PubMed

Zamarreño, Dania V; Inkpen, Robert; May, Eric

2009-09-01

Bacterial carbonate precipitation is known to be a natural phenomenon associated with a wide range of bacterial species. Recently, the ability of bacteria to produce carbonates has been studied for its value in the conservation of limestone monuments and concrete. This paper describes investigations of carbonate crystals precipitated by freshwater bacteria by means of histological (Loeffler's methylene blue and alcian blue-periodic acid-Schiff stain) and fluorescence (CTC [5-cyano-2,3-ditolyl tetrazolium chloride]) stains, determination of cell viability inside carbonate crystals, and pore size reduction in limestone by image analysis. Carbonate crystals were found to be composed of bacteria embedded in a matrix of neutral and acid polysaccharides. Cell viability inside the carbonate crystals decreased with time. On stone, bacteria were found to form carbonate crystals, with only a few bacteria remaining as isolated cells or as cell aggregates. Pore size was reduced by about 50%, but no blockage was detected. Taken together, the results of this research provide some reassurance to conservators that biocalcification by bacteria could be a safe consolidation tool in a restoration strategy for building stone conservation.

Role of periodontal pathogenic bacteria in RANKL-mediated bone destruction in periodontal disease.

PubMed

Kajiya, Mikihito; Giro, Gabriela; Taubman, Martin A; Han, Xiaozhe; Mayer, Marcia P A; Kawai, Toshihisa

2010-11-08

Accumulated lines of evidence suggest that hyperimmune responses to periodontal bacteria result in the destruction of periodontal connective tissue and alveolar bone. The etiological roles of periodontal bacteria in the onset and progression of periodontal disease (PD) are well documented. However, the mechanism underlying the engagement of periodontal bacteria in RANKL-mediated alveolar bone resorption remains unclear. Therefore, this review article addresses three critical subjects. First, we discuss earlier studies of immune intervention, ultimately leading to the identification of bacteria-reactive lymphocytes as the cellular source of osteoclast-induction factor lymphokine (now called RANKL) in the context of periodontal bone resorption. Next, we consider (1) the effects of periodontal bacteria on RANKL production from a variety of adaptive immune effector cells, as well as fibroblasts, in inflamed periodontal tissue and (2) the bifunctional roles (upregulation vs. downregulation) of LPS produced from periodontal bacteria in a RANKL-induced osteoclast-signal pathway. Future studies in these two areas could lead to new therapeutic approaches for the management of PD by down-modulating RANKL production and/or RANKL-mediated osteoclastogenesis in the context of host immune responses against periodontal pathogenic bacteria.

Active invasion of bacteria into living fungal cells

PubMed Central

Moebius, Nadine; Üzüm, Zerrin; Dijksterhuis, Jan; Lackner, Gerald; Hertweck, Christian

2014-01-01

The rice seedling blight fungus Rhizopus microsporus and its endosymbiont Burkholderia rhizoxinica form an unusual, highly specific alliance to produce the highly potent antimitotic phytotoxin rhizoxin. Yet, it has remained a riddle how bacteria invade the fungal cells. Genome mining for potential symbiosis factors and functional analyses revealed that a type 2 secretion system (T2SS) of the bacterial endosymbiont is required for the formation of the endosymbiosis. Comparative proteome analyses show that the T2SS releases chitinolytic enzymes (chitinase, chitosanase) and chitin-binding proteins. The genes responsible for chitinolytic proteins and T2SS components are highly expressed during infection. Through targeted gene knock-outs, sporulation assays and microscopic investigations we found that chitinase is essential for bacteria to enter hyphae. Unprecedented snapshots of the traceless bacterial intrusion were obtained using cryo-electron microscopy. Beyond unveiling the pivotal role of chitinolytic enzymes in the active invasion of a fungus by bacteria, these findings grant unprecedented insight into the fungal cell wall penetration and symbiosis formation. DOI: http://dx.doi.org/10.7554/eLife.03007.001 PMID:25182414

Primary Characterization of Small RNAs in Symbiotic Nitrogen-Fixing Bacteria.

PubMed

Robledo, Marta; García-Tomsig, Natalia I; Jiménez-Zurdo, José I

2018-01-01

High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. A large fraction of sRNAs are differentially regulated and rely on protein-assisted antisense interactions to trans-encoded target mRNAs to fine-tune posttranscriptional reprogramming of gene expression in response to external cues. However, annotation and function of sRNAs are still largely overlooked in nonmodel bacteria with complex lifestyles. Here, we describe experimental protocols successfully applied for the accurate annotation, expression profiling and target mRNA identification of trans-acting sRNAs in the nitrogen-fixing α-rhizobium Sinorhizobium meliloti. The protocols presented here can be similarly applied for the characterization of trans-sRNAs in genetically tractable α-proteobacteria of agronomical or clinical relevance interacting with eukaryotic hosts.

The influence of bacteria on multitrophic interactions among plants, psyllids, and pathogen.

PubMed

Tamborindeguy, Cecilia; Huot, Ordom Brian; Ibanez, Freddy; Levy, Julien

2017-12-01

The recent emergence of several plant diseases caused by psyllid-borne bacterial pathogens worldwide (Candidatus Liberibacter spp.) has created renewed interest on the interaction between psyllids and bacteria. In spite of these efforts to understand psyllid association with bacteria, many aspects of their interactions remain poorly understood. As more organisms are studied, subtleties on the molecular interactions as well as on the effects of the bacteria on the psyllid host are being uncovered. Additionally, psyllid-borne bacterial phytopathogens can also affect the host plant, which in turn can impact psyllid physiology and behavior. Here, we review the current literature on different aspects of the influence of bacteria on multitrophic interactions among plants, psyllids, and pathogens. We then highlight gaps that need to be addressed to advance this field, which can have significant implications for controlling these newly emergent and other plant diseases. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Population genomics of early events in the ecological differentiation of bacteria

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

Shapiro, Jesse B.; Friedman, Jonatan; Cordero, Otto X.

Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observationsmore » of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.« less

Enzymatic Digestion for Improved Bacteria Separation from Leafy Green Vegetables.

PubMed

Wang, Danhui; Wang, Ziyuan; He, Fei; Kinchla, Amanda J; Nugen, Sam R

2016-08-01

An effective and rapid method for the separation of bacteria from food matrix remains a bottleneck for rapid bacteria detection for food safety. Bacteria can strongly attach to a food surface or internalize within the matrix, making their isolation extremely difficult. Traditional methods of separating bacteria from food routinely involve stomaching, blending, and shaking. However, these methods may not be efficient at removing all the bacteria from complex matrices. Here, we investigate the benefits of using enzyme digestion followed by immunomagnetic separation to isolate Salmonella from spinach and lettuce. Enzymatic digestion using pectinase and cellulase was able to break down the structure of the leafy green vegetables, resulting in the detachment and release of Salmonella from the leaves. Immunomagnetic separation of Salmonella from the liquefied sample allowed an additional separation step to achieve a more pure sample without leaf debris that may benefit additional downstream applications. We have investigated the optimal combination of pectinase and cellulase for the digestion of spinach and lettuce to improve sample detection yields. The concentrations of enzymes used to digest the leaves were confirmed to have no significant effect on the viability of the inoculated Salmonella. Results reported that the recovery of the Salmonella from the produce after enzyme digestion of the leaves was significantly higher (P < 0.05) than traditional sample preparation methods to separate bacteria (stomaching and manually shaking). The results demonstrate the potential for use of enzyme digestion prior to separation can improve the efficiency of bacteria separation and increase the likelihood of detecting pathogens in the final detection assay.

Antimicrobial susceptibility of starter culture bacteria used in Norwegian dairy products.

PubMed

Katla, A K; Kruse, H; Johnsen, G; Herikstad, H

2001-07-20

Commercial starter culture bacteria are widely used in the production of dairy products and could represent a potential source for spread of genes encoding resistance to antimicrobial agents. To learn more about the antimicrobial susceptibility of starter culture bacteria used in Norwegian dairy products, a total of 189 isolates of lactic acid bacteria were examined for susceptibility to ampicillin, penicillin G, cephalothin, vancomycin, bacitracin, gentamicin, streptomycin, erythromycin, tetracycline, chloramphenicol, quinupristin/dalfopristin, ciprofloxacin, trimethoprim and sulphadiazine using Etest for MIC determination. Most of the isolates (140) originated from 39 dairy products (yoghurt, sour cream, fermented milk and cheese), while 49 were isolated directly from nine commercial cultures. The bacteria belonged to the genera Lactobacillus, Lactococcus, Leuconostoc and Streptococcus. Only one of the 189 isolates was classified as resistant to an antimicrobial agent included in the study. This isolate, a lactobacillus, was classified as high level resistant to streptomycin. The remaining isolates were not classified as resistant to the antimicrobial agents included other than to those they are known to have a natural reduced susceptibility to. Thus, starter culture bacteria in Norwegian dairy products do not seem to represent a source for spread of genes encoding resistance to antimicrobial agents.

Vacuum cleaner emissions as a source of indoor exposure to airborne particles and bacteria.

PubMed

Knibbs, Luke D; He, Congrong; Duchaine, Caroline; Morawska, Lidia

2012-01-03

Vacuuming can be a source of indoor exposure to biological and nonbiological aerosols, although there are few data that describe the magnitude of emissions from the vacuum cleaner itself. We therefore sought to quantify emission rates of particles and bacteria from a large group of vacuum cleaners and investigate their potential determinants, including temperature, dust bags, exhaust filters, price, and age. Emissions of particles between 0.009 and 20 μm and bacteria were measured from 21 vacuums. Ultrafine (<100 nm) particle emission rates ranged from 4.0 × 10(6) to 1.1 × 10(11) particles min(-1). Emission of 0.54-20 μm particles ranged from 4.0 × 10(4) to 1.2 × 10(9) particles min(-1). PM(2.5) emissions were between 2.4 × 10(-1) and 5.4 × 10(3) μg min(-1). Bacteria emissions ranged from 0 to 7.4 × 10(5) bacteria min(-1) and were poorly correlated with dust bag bacteria content and particle emissions. Large variability in emission of all parameters was observed across the 21 vacuums, which was largely not attributable to the range of determinant factors we assessed. Vacuum cleaner emissions contribute to indoor exposure to nonbiological and biological aerosols when vacuuming, and this may vary markedly depending on the vacuum used.

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

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

Ozden, Sehmus; Macwan, Isaac G.; Owuor, Peter S.

It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamicsmore » simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. Furthermore, the 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications.« less

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

DOE PAGES

Ozden, Sehmus; Macwan, Isaac G.; Owuor, Peter S.; ...

2017-08-29

It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamicsmore » simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. Furthermore, the 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications.« less

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

PubMed Central

Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-01-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS‐based diagnosis methods for bacteria identification and typing have been created, not only on well‐accepted MALDI‐TOF‐MS‐based fingerprint matches, but also on solving the insufficiencies of MALDI‐TOF‐MS‐based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS‐based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. PMID:26751976

Probiotic Bacteria Induce a ‘Glow of Health’

PubMed Central

Smillie, Christopher; Varian, Bernard J.; Ibrahim, Yassin M.; Lakritz, Jessica R.; Alm, Eric J.; Erdman, Susan E.

2013-01-01

Radiant skin and hair are universally recognized as indications of good health. However, this ‘glow of health’ display remains poorly understood. We found that feeding of probiotic bacteria to aged mice induced integumentary changes mimicking peak health and reproductive fitness characteristic of much younger animals. Eating probiotic yogurt triggered epithelial follicular anagen-phase shift with sebocytogenesis resulting in thick lustrous fur due to a bacteria-triggered interleukin-10-dependent mechanism. Aged male animals eating probiotics exhibited increased subcuticular folliculogenesis, when compared with matched controls, yielding luxuriant fur only in probiotic-fed subjects. Female animals displayed probiotic-induced hyperacidity coinciding with shinier hair, a feature that also aligns with fertility in human females. Together these data provide insights into mammalian evolution and novel strategies for integumentary health. PMID:23342023

The role of heterotrophic bacteria in iron-limited ocean ecosystems

NASA Astrophysics Data System (ADS)

Tortell, Philippe D.; Maldonado, Maria T.; Price, Nell M.

1996-09-01

IRON availability limits phytoplankton growth in large areas of the world's oceans1-3 and may influence the strength of the biological carbon pump4,5. Very little is known of the iron requirements of oceanic heterotrophic bacteria, which constitute up to 50% of the total particulate organic carbon in open ocean waters6,7 and are important in carbon cycling as remineralizers of dissolved organic matter and hence producers of CO2 (ref. 8). Here we report that oceanic bacteria contain more iron per biomass than phytoplankton. In the subarctic Pacific, they constitute a large fraction of biogenic iron and account for 20-45% of biological iron uptake. Bacterial iron quotas in the field are similar to those of iron-deficient laboratory cultures, which exhibit reduced elec-tron transport, slow growth, and low carbon growth efficiency. Heterotrophic bacteria therefore play a major role in the biogeo-chemical cycling of iron. In situ iron limitation of heterotrophic metabolism may have profound effects on carbon flux in the ocean.

Limnoithona sinensis as refuge for bacteria: protection from UV radiation and chlorine disinfection in drinking water treatment.

PubMed

Lin, Tao; Cai, Bo; Chen, Wei

2014-11-01

In this study, we tested the potential of Limnoithona sinensis to provide its attached bacteria refuge against disinfection. The experimental results indicated that in water devoid of zooplankton, both UV radiation and chlorine disinfection significantly decreased the viability of free-living bacteria. In the presence of L. sinensis, however, the attached bacteria could survive and rapidly recover from disinfection. This demonstrated that L. sinensis provided protection from external damage to various aquatic bacteria that were attached to its body. The surviving bacteria remained on L. sinensis after disinfection exposure, which enabled a rapid increase in the bacterial population followed by their subsequent release into the surrounding water. Compared with UV radiation, chlorine disinfection was more effective in terms of inactivating attached bacteria. Both UV radiation and chlorine disinfection had little effect in terms of preventing the spread of undesirable bacteria, due to the incomplete inactivation of the bacteria associated with L. sinensis.

Synthesis of High-Molecular-Weight Polyhydroxyalkanoates by Marine Photosynthetic Purple Bacteria

PubMed Central

Higuchi-Takeuchi, Mieko; Morisaki, Kumiko; Toyooka, Kiminori; Numata, Keiji

2016-01-01

Polyhydroxyalkanoate (PHA) is a biopolyester/bioplastic that is produced by a variety of microorganisms to store carbon and increase reducing redox potential. Photosynthetic bacteria convert carbon dioxide into organic compounds using light energy and are known to accumulate PHA. We analyzed PHAs synthesized by 3 purple sulfur bacteria and 9 purple non-sulfur bacteria strains. These 12 purple bacteria were cultured in nitrogen-limited medium containing acetate and/or sodium bicarbonate as carbon sources. PHA production in the purple sulfur bacteria was induced by nitrogen-limited conditions. Purple non-sulfur bacteria accumulated PHA even under normal growth conditions, and PHA production in 3 strains was enhanced by nitrogen-limited conditions. Gel permeation chromatography analysis revealed that 5 photosynthetic purple bacteria synthesized high-molecular-weight PHAs, which are useful for industrial applications. Quantitative reverse transcription polymerase chain reaction analysis revealed that mRNA levels of phaC and PhaZ genes were low under nitrogen-limited conditions, resulting in production of high-molecular-weight PHAs. We conclude that all 12 tested strains are able to synthesize PHA to some degree, and we identify 5 photosynthetic purple bacteria that accumulate high-molecular-weight PHA molecules. Furthermore, the photosynthetic purple bacteria synthesized PHA when they were cultured in seawater supplemented with acetate. The photosynthetic purple bacteria strains characterized in this study should be useful as host microorganisms for large-scale PHA production utilizing abundant marine resources and carbon dioxide. PMID:27513570

Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains

PubMed Central

Jordan, Heather R.; Tomberlin, Jeffery K.

2017-01-01

A number of abiotic and biotic factors are known to regulate arthropod attraction, colonization, and utilization of decomposing vertebrate remains. Such information is critical when assessing arthropod evidence associated with said remains in terms of forensic relevance. Interactions are not limited to just between the resource and arthropods. There is another biotic factor that has been historically overlooked; however, with the advent of high-throughput sequencing, and other molecular techniques, the curtain has been pulled back to reveal a microscopic world that is playing a major role with regards to carrion decomposition patterns in association with arthropods. The objective of this publication is to review many of these factors and draw attention to their impact on microbial, specifically bacteria, activity associated with these remains as it is our contention that microbes serve as a primary mechanism regulating associated arthropod behavior. PMID:28538664

Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen.

PubMed

Russell, James B; Muck, Richard E; Weimer, Paul J

2009-02-01

Ruminant animals digest cellulose via a symbiotic relationship with ruminal microorganisms. Because feedstuffs only remain in the rumen for a short time, the rate of cellulose digestion must be very rapid. This speed is facilitated by rumination, a process that returns food to the mouth to be rechewed. By decreasing particle size, the cellulose surface area can be increased by up to 10(6)-fold. The amount of cellulose digested is then a function of two competing rates, namely the digestion rate (K(d)) and the rate of passage of solids from the rumen (K(p)). Estimation of bacterial growth on cellulose is complicated by several factors: (1) energy must be expended for maintenance and growth of the cells, (2) only adherent cells are capable of degrading cellulose and (3) adherent cells can provide nonadherent cells with cellodextrins. Additionally, when ruminants are fed large amounts of cereal grain along with fiber, ruminal pH can decrease to a point where cellulolytic bacteria no longer grow. A dynamic model based on STELLA software is presented. This model evaluates all of the major aspects of ruminal cellulose degradation: (1) ingestion, digestion and passage of feed particles, (2) maintenance and growth of cellulolytic bacteria and (3) pH effects.

Carbonate Crystals Precipitated by Freshwater Bacteria and Their Use as a Limestone Consolidant▿

PubMed Central

Zamarreño, Dania V.; Inkpen, Robert; May, Eric

2009-01-01

Bacterial carbonate precipitation is known to be a natural phenomenon associated with a wide range of bacterial species. Recently, the ability of bacteria to produce carbonates has been studied for its value in the conservation of limestone monuments and concrete. This paper describes investigations of carbonate crystals precipitated by freshwater bacteria by means of histological (Loeffler's methylene blue and alcian blue-periodic acid-Schiff stain) and fluorescence (CTC [5-cyano-2,3-ditolyl tetrazolium chloride]) stains, determination of cell viability inside carbonate crystals, and pore size reduction in limestone by image analysis. Carbonate crystals were found to be composed of bacteria embedded in a matrix of neutral and acid polysaccharides. Cell viability inside the carbonate crystals decreased with time. On stone, bacteria were found to form carbonate crystals, with only a few bacteria remaining as isolated cells or as cell aggregates. Pore size was reduced by about 50%, but no blockage was detected. Taken together, the results of this research provide some reassurance to conservators that biocalcification by bacteria could be a safe consolidation tool in a restoration strategy for building stone conservation. PMID:19617383

Absence of genome reduction in diverse, facultative endohyphal bacteria

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

Baltrus, David A.; Dougherty, Kevin; Arendt, Kayla R.

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, andmore » generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.« less

Absence of genome reduction in diverse, facultative endohyphal bacteria

DOE PAGES

Baltrus, David A.; Dougherty, Kevin; Arendt, Kayla R.; ...

2017-02-28

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, andmore » generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.« less

Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania.

PubMed

Lupan, Iulia; Carpa, Rahela; Oltean, Andreea; Kelemen, Beatrice Simona; Popescu, Octavian

2017-09-27

The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98-99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.

Magnetic Trapping of Bacteria at Low Magnetic Fields

NASA Astrophysics Data System (ADS)

Wang, Z. M.; Wu, R. G.; Wang, Z. P.; Ramanujan, R. V.

2016-06-01

A suspension of non-magnetic entities in a ferrofluid is referred to as an inverse ferrofluid. Current research to trap non-magnetic entities in an inverse ferrofluid focuses on using large permanent magnets to generate high magnetic field gradients, which seriously limits Lab-on-a-Chip applications. On the other hand, in this work, trapping of non-magnetic entities, e.g., bacteria in a uniform external magnetic field was studied with a novel chip design. An inverse ferrofluid flows in a channel and a non-magnetic island is placed in the middle of this channel. The magnetic field was distorted by this island due to the magnetic susceptibility difference between this island and the surrounding ferrofluid, resulting in magnetic forces applied on the non-magnetic entities. Both the ferromagnetic particles and the non-magnetic entities, e.g., bacteria were attracted towards the island, and subsequently accumulate in different regions. The alignment of the ferrimagnetic particles and optical transparency of the ferrofluid was greatly enhanced by the bacteria at low applied magnetic fields. This work is applicable to lab-on-a-chip based detection and trapping of non-magnetic entities bacteria and cells.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

NASA Astrophysics Data System (ADS)

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M.; Burns, Andrew S.; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R.; Padilla, Cory C.; Stone, Benjamin K.; Bristow, Laura A.; Larsen, Morten; Glass, Jennifer B.; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T.; Stewart, Frank J.

2016-08-01

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world’s largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth’s most abundant organismal group.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

PubMed

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M; Burns, Andrew S; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R; Padilla, Cory C; Stone, Benjamin K; Bristow, Laura A; Larsen, Morten; Glass, Jennifer B; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T; Stewart, Frank J

2016-08-11

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.

The determination and arrangement of a combination of enzyme lactate dehydrogenase of bacteria Acinetobacter sp. as a device the identity important bacteria agent composts

NASA Astrophysics Data System (ADS)

Sukmawati, D.; Puspitaningrum, R.; Muzajjanah

2017-07-01

The number of garbage generated by the industry or society is a usual problem encountered by almost all urban centers, especially large cities such as Jakarta. Waste prevention strategy required quickly and accurately. One strategy for tackling the Junk was getting lactic acid-producing bacteria. It has been shown that lactic acid can increase the acceleration of organic matter such as an overhaul of lignin and cellulose as well as out causing toxic compounds arising from decay. This research will be conducted on the determination and characterization of the enzyme-producing compost bacteria LDH lactate dehydrogenase LDH - which in isolation from the garbage Landfill Rawasari. Methodology: Research carried out consists: isolation of lactic acid-producing bacteria; identification of microscopic, macroscopic and staining Gram; cellulose assay, and optimization of PCR conditions LDH enzymes producing bacteria. Isolation is performed by dilution method and the direct method. As many as 5-point sampling. Each stage is conducted from 10 grams of soil from the top surface of the compost. Isolation results obtained 100 isolate the bacteria. Base on the characteristic of macroscopic and microscopic observations retrieved 14 isolates of bacteria have shaped rods and brought forth a negative kind of Gram positive staining. Bacterial isolates with codes (BK1; BK3; BK4; BK5; BK6; BK7; BK8; BK9; BK10; BK11: BK12; BK 13). The potential bacteria with ability produce lactate dehydrogenase was BK1 and BK3. Base for analysis phylogenetic there was identification bacteria bak1 and bak3 where Acinetobacter sp.

Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

PubMed

Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

1982-11-01

Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

Recent advances quantifying the large wood dynamics in river basins: New methods and remaining challenges

NASA Astrophysics Data System (ADS)

Ruiz-Villanueva, Virginia; Piégay, Hervé; Gurnell, Angela A.; Marston, Richard A.; Stoffel, Markus

2016-09-01

Large wood is an important physical component of woodland rivers and significantly influences river morphology. It is also a key component of stream ecosystems. However, large wood is also a source of risk for human activities as it may damage infrastructure, block river channels, and induce flooding. Therefore, the analysis and quantification of large wood and its mobility are crucial for understanding and managing wood in rivers. As the amount of large-wood-related studies by researchers, river managers, and stakeholders increases, documentation of commonly used and newly available techniques and their effectiveness has also become increasingly relevant as well. Important data and knowledge have been obtained from the application of very different approaches and have generated a significant body of valuable information representative of different environments. This review brings a comprehensive qualitative and quantitative summary of recent advances regarding the different processes involved in large wood dynamics in fluvial systems including wood budgeting and wood mechanics. First, some key definitions and concepts are introduced. Second, advances in quantifying large wood dynamics are reviewed; in particular, how measurements and modeling can be combined to integrate our understanding of how large wood moves through and is retained within river systems. Throughout, we present a quantitative and integrated meta-analysis compiled from different studies and geographical regions. Finally, we conclude by highlighting areas of particular research importance and their likely future trajectories, and we consider a particularly underresearched area so as to stress the future challenges for large wood research.

Autoinducer Sensing Microarrays by Reporter Bacteria Encapsulated in Hybrid Supramolecular-Polysaccharide Hydrogels.

PubMed

Li, Ping; Dou, Xiaoqiu; Müller, Mareike; Feng, Chuanliang; Chang, Matthew Wook; Frettlöh, Martin; Schönherr, Holger

2017-11-01

A generally applicable strategy to obtain mechanically robust hydrogels for the incorporation and containment of functional reporter bacteria for the microarray and microparticle-based detection and signaling of N-acyl homoserine lactone autoinducers (3OC 12 HSL) at relevant concentrations is reported. For reinforcing hydrogels of 1,4-bi(phenylalanine-diglycol)-benzene (PDB), a hybrid hydrogel is formed by the combination of PDB self-assembly with Ca 2+ mediated alginate crosslinking. The different assembly mechanisms are shown not to interfere with each other and despite the more than four-fold increased moduli of the hydrogels, diffusion of autoinducers into the gels remains efficient and Escherichia coli pLuxR-green fluorescent protein (GFP) reporter bacteria are proliferating. Templating affords reporter bacteria-loaded hydrogels with controllable shape and size. Upon exposure to 3OC 12 HSL, the embedded bacteria exhibit an up to 12 ± 3 times increase in fluorescence intensity due to autoinducer-triggered GFP expression. This approach can serve as a potentially generally applicable strategy to sensitively detect bacteria via their secreted autoinducers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exopolysaccharides produced by marine bacteria and their applications as glycosaminoglycan-like molecules.

NASA Astrophysics Data System (ADS)

Delbarre-Ladrat, Christine; Sinquin, Corinne; Lebellenger, Lou; Zykwinska, Agata; Colliec-Jouault, Sylvia

2014-10-01

Although polysaccharides are ubiquitous and the most abundant renewable bio-components, their studies, covered by the glycochemistry and glycobiology fields, remain a challenge due to their high molecular diversity and complexity. Polysaccharides are industrially used in food products; human therapeutics fall into a more recent research field and pharmaceutical industry is looking for more and more molecules with enhanced activities. Glycosaminoglycans (GAGs) found in animal tissues play a critical role in cellular physiological and pathological processes as they bind many cellular components. Therefore, they present a great potential for the design and preparation of therapeutic drugs. On the other hand, microorganisms producing exopolysaccharides (EPS) are renewable resources meeting well the actual industrial demand. In particular, the diversity of marine microorganisms is still largely unexplored offering great opportunities to discover high value products such as new molecules and biocatalysts. EPS-producing bacteria from the marine environment will be reviewed with a focus on marine-derived EPS from bacteria isolated from deep-sea hydrothermal vents. Information on chemical and structural features, putative pathways of biosynthesis, novel strategies for chemical and enzymatic modifications and potentialities in the biomedical field will be provided. An integrated approach should be used to increase the basic knowledge on these compounds and their applications; new clean environmentally friendly processes for the production of carbohydrate bio-active compounds should also be proposed for a sustainable industry.

Exopolysaccharides produced by marine bacteria and their applications as glycosaminoglycan-like molecules.

PubMed

Delbarre-Ladrat, Christine; Sinquin, Corinne; Lebellenger, Lou; Zykwinska, Agata; Colliec-Jouault, Sylvia

2014-01-01

Although polysaccharides are ubiquitous and the most abundant renewable bio-components, their studies, covered by the glycochemistry and glycobiology fields, remain a challenge due to their high molecular diversity and complexity. Polysaccharides are industrially used in food products; human therapeutics fall into a more recent research field and pharmaceutical industry is looking for more and more molecules with enhanced activities. Glycosaminoglycans (GAGs) found in animal tissues play a critical role in cellular physiological and pathological processes as they bind many cellular components. Therefore, they present a great potential for the design and preparation of therapeutic drugs. On the other hand, microorganisms producing exopolysaccharides (EPS) are renewable resources meeting well the actual industrial demand. In particular, the diversity of marine microorganisms is still largely unexplored offering great opportunities to discover high value products such as new molecules and biocatalysts. EPS-producing bacteria from the marine environment will be reviewed with a focus on marine-derived EPS from bacteria isolated from deep-sea hydrothermal vents. Information on chemical and structural features, putative pathways of biosynthesis, novel strategies for chemical and enzymatic modifications and potentialities in the biomedical field will be provided. An integrated approach should be used to increase the basic knowledge on these compounds and their applications; new clean environmentally friendly processes for the production of carbohydrate bioactive compounds should also be proposed for a sustainable industry.

Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture.

PubMed

Turner, Robert D; Hurd, Alexander F; Cadby, Ashley; Hobbs, Jamie K; Foster, Simon J

2013-01-01

Cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. It consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. The cellular architecture and insertion pattern of peptidoglycan have remained elusive. Here we determine the peptidoglycan architecture and dynamics during growth in rod-shaped Gram-negative bacteria. Peptidoglycan is made up of circumferentially oriented bands of material interspersed with a more porous network. Super-resolution fluorescence microscopy reveals an unexpected discontinuous, patchy synthesis pattern. We present a consolidated model of growth via architecture-regulated insertion, where we propose only the more porous regions of the peptidoglycan network that are permissive for synthesis.

Wound infections with multi-drug resistant bacteria.

PubMed

Pîrvănescu, H; Bălăşoiu, M; Ciurea, M E; Bălăşoiu, A T; Mănescu, R

2014-01-01

Wound infections remain a public health problem, despite the progress made on improving surgical techniques and antibiotic prophylaxis application. Misuse of antibiotics to prevent bacterial infections leads to increased bacterial resistance and their dissemination. The study refers to 470 samples taken from wound infections of which only multi-drug resistant strains were selected for study, using two special culture mediums (Metistaph-2 for methicillin-resistant staphylococci and ESBLs-Agar for extended-spectrum betalactamases secreting bacteria). Sensitivity of these strains was tested using the diffusion method. Of all studied samples, a rate of 27.6 bacterial strains showed multi-drug resistance. Among them stood primarily Staphylococcus aureus; both MRSA strains and ESBL Gram negative bacteria studied showed high resistance to aminoglycosides, quinolones, third generation cephalosporins and low to fourth generation cephalosporins. No vancomycin resitant nor vancomycin-intermediate Staphylococcus aureus strains were isolated. Knowing the antibiotic resistance is very useful in antibiotic "cycling"application, avoiding this way the emergence of increased resistant strains. Celsius.

Necrotizing enterocolitis and preterm infant gut bacteria

PubMed Central

Warner, Barbara B.; Tarr, Phillip I.

2016-01-01

Summary Necrotizing enterocolitis remains an intractable consequence of preterm birth. Gut microbial communities, especially bacterial communities, have long been suspected to play a role in the development of necrotizing enterocolitis. Direct-from-stool nucleic acid sequencing technology now offers insights into the make-up of these communities. Data are now converging on the roles of Gram-negative bacteria as causative agents, despite the dynamic nature of bacterial populations, the varying technologies and sampling strategies, and the overall small sample sizes in these case–control studies. Bacteria that confer protection from necrotizing enterocolitis have not been identified across studies. The beneficial effect of probiotics is not apparent in infants with birth weights <1000 g (these infants are at highest risk of, and have the highest case fatality rate from, necrotizing enterocolitis). Further work should be directed to the modulating gut microbes, or the products they produce, to prevent this devastating complication of preterm birth. PMID:27343151

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits

PubMed Central

Fu, Xiangchao; Zeng, Bo; Wang, Ping; Wang, Lihuan; Wen, Bin; Li, Ying; Liu, Hanzhong; Bai, Shiqie; Jia, Gang

2018-01-01

Gastrointestinal bacteria are essential for host health, and only viable microorganisms contribute to gastrointestinal functions. When evaluating the gut microbiota by next generation sequencing method, dead bacteria, which compose a proportion of gut bacteria, may distort analysis of the live gut microbiota. We collected stomach, jejunum, ileum, cecum, and colon contents from Rex rabbits. A modified propidium monoazide (PMA) treatment protocol was used to exclude DNA from dead bacteria. Analysis of untreated samples yielded total bacteria, and analysis of PMA-treated samples yielded live bacteria. Quantitative polymerase chain reaction and 16S rRNA gene sequencing were performed to evaluate the live-to-total bacteria ratio and compare the difference between live and total microbiota in the entire digestive tract. A low proportion of live bacteria in the foregut (stomach 1.12%, jejunum 1.2%, ileum 2.84%) and a high proportion of live bacteria in the hindgut (cecum 24.66%, colon 19.08%) were observed. A significant difference existed between total and live microbiota. Clostridiales, Ruminococcaceae, and S24-7 dominated the hindgut of both groups, while Acinetobacter and Cupriavidus dominated only in live foregut microbiota. Clostridiales and Ruminococcaceae abundance decreased, while S24-7 increased in live hindgut microbiota. The alpha- and beta-diversities differed significantly between groups. Analysis of networks showed the mutual relationship between live bacteria differed vastly when compared with total bacteria. Our study revealed a large number of dead bacteria existed in the digestive tract of Rex rabbits and distorted the community profile of the live microbiota. Total bacteria is an improper representation of the live gut microbiota, particularly in the foregut. PMID:29692775

Acetic Acid Bacteria and the Production and Quality of Wine Vinegar

PubMed Central

Torija, María Jesús; García-Parrilla, María del Carmen; Troncoso, Ana María

2014-01-01

The production of vinegar depends on an oxidation process that is mainly performed by acetic acid bacteria. Despite the different methods of vinegar production (more or less designated as either “fast” or “traditional”), the use of pure starter cultures remains far from being a reality. Uncontrolled mixed cultures are normally used, but this review proposes the use of controlled mixed cultures. The acetic acid bacteria species determine the quality of vinegar, although the final quality is a combined result of technological process, wood contact, and aging. This discussion centers on wine vinegar and evaluates the effects of these different processes on its chemical and sensory properties. PMID:24574887

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria.

PubMed

Cheng, Keding; Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-04-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS-based diagnosis methods for bacteria identification and typing have been created, not only on well-accepted MALDI-TOF-MS-based fingerprint matches, but also on solving the insufficiencies of MALDI-TOF-MS-based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS-based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. © 2016 The Authors. PROTEOMICS - Clinical Applications Published by WILEY-VCH Verlag GmbH & Co. KGaA.

Existence and control of Legionella bacteria in building water systems: A review.

PubMed

Springston, John P; Yocavitch, Liana

2017-02-01

Legionellae are waterborne bacteria which are capable of causing potentially fatal Legionnaires' disease (LD), as well as Pontiac Fever. Public concern about Legionella exploded following the 1976 outbreak at the American Legion conference in Philadelphia, where 221 attendees contracted pneumonia and 34 died. Since that time, a variety of different control methods and strategies have been developed and implemented in an effort to eradicate Legionella from building water systems. Despite these efforts, the incidence of LD has been steadily increasing in the U.S. for more than a decade. Public health and occupational hygiene professionals have maintained an active debate regarding best practices for management and control of Legionella. Professional opinion remains divided with respect to the relative merits of performing routine sampling for Legionella, vs. the passive, reactive approach that has been largely embraced by public health officials and facility owners. Given the potential risks and ramifications associated with waiting to assess systems for Legionella until after disease has been identified and confirmed, a proactive approach of periodic testing for Legionella, along with proper water treatment, is the best approach to avoiding large-scale disease outbreaks.

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

The Use of Bacteria for Remediation of Mercury Contaminated Groundwater

EPA Science Inventory

Many processes of mercury transformation in the environment are bacteria mediated. Mercury properties cause some difficulties of remediation of mercury contaminated environment. Despite the significance of the problem of mercury pollution, methods of large scale bioremediation ...

Coexistence of Fe(II)- and Mn(II)-oxidizing bacteria govern the formation of deep sea umber deposits

NASA Astrophysics Data System (ADS)

Peng, Xiaotong; Ta, Kaiwen; Chen, Shun; Zhang, Lijuan; Xu, Hengchao

2015-11-01

The genesis of umber deposits has remained controversial for several decades. Recently, microbial Fe(II) oxidation associated with low-temperature diffuse venting has been identified as a key process for the formation of umber deposits, but the exact biogeochemical mechanisms involved to the precipitation of Mn oxides in umber deposits still remain unknown. Here, we used nano secondary ion mass spectrometer, synchrotron-based X-ray absorption spectroscopy, electron microscopy, and molecular techniques to demonstrate the coexistence of two types of metal-oxidizing bacteria within deep-sea hydrothermal umber deposits at the South Mid-Atlantic Ridge, where we found unique spheroids composed of biogenic Fe oxyhydroxides and Mn oxides in the deposits. Our data show that Fe oxyhydroxides and Mn oxides are metabolic by-products of lithotrophic Fe(II)-oxidizing bacteria and heterotrophic Mn(II)-oxidizing bacteria, respectively. The hydrothermal vents fuel lithotrophic microorganisms, which constitute a trophic base that might support the activities of heterogenic Mn(II)-oxidizing bacteria. The biological origin of umber deposits shed light on the importance of geomicrobiological interaction in triggering the formation of metalliferous deposits, with important implications for the generation of submarine Mn deposits and crusts.

Detection of heavy metal resistance bioluminescence bacteria using microplate bioassay method.

PubMed

Ranjitha, P; Karthy, E S

2012-01-01

Effects of different heavy metals on Vibrio harveyi, V. fischeri, Photobacterium phosphoreum and P. leiognathi were examined. Checkerboard assay was used for the detection of the natural metal tolerance levels of a large number of marine luminous eubacteria. 57 strains of luminous bacteria were investigated for their natural patterns of heavy metal tolerance. The behaviors of these strains were not homogeneous with respect to all metals tested, even within the strains belonging to the same genus. At least 1 to 4 different MICs were detected for every metal except barium and cobalt. Isolated bacteria were tested for the presence of plasmids using the modified alkaline lysis method, was effective for identification of plasmids of different sizes. This study revealed the frequency of the occurrence of plasmids in heavy metal resistance bacteria and inferred that plasmids are highly ubiquitous and predominant in most heavy metal resistant bacteria.

Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

PubMed

Legendre, P; Baleux, B; Troussellier, M

1984-09-01

The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two types of temporal evolution: in the first four stations, it seems mainly controlled by the nutrient support capacity of the sewage input, whereas in the remaining part of the lagoon, it seems likely that the pollution-indicator bacteria are gradually replaced by other bacterial types that are better adapted to this environment. On the other hand, the pollution-indicator bacteria showed an annual cycle which increased in amplitude at distances further from the wastewater source. The main events in this cycle were produced simultaneously at all stations, indicating control of these bacterial populations by climatic factors, which act through physical and chemical factors, and also through other biological components of this ecosystem (phytoplankton and zooplankton). Finally, we use results from this study to suggest a modified design for a future study program.

Influence of surfaces on sulphidogenic bacteria.

PubMed

Bass, C J; Webb, J S; Sanders, P F; Lappin-Scott, H M

1996-01-01

Sulphidogenic bacteria in oil reservoirs are of great economic importance in terms of souring, fouling and corrosion. Mixed cultures containing these bacteria were isolated from chalk formations in North Sea oil reservoirs. These were thermophilic cultures, growing optimally at 60°C. Oil formations are porous matrices, providing a very large surface area and ideal conditions for bacterial attachment, survival and growth. This study included assessments of sulphide production rates of thermophilic (t-)sulphidogen consortia with and without additional surfaces. The availability of a surface contributed significantly to the rate and extent of sulphide generation. Surfaces were offered in varying amounts to growing planktonic cultures: significantly more sulphide was produced from cultures in contact with a surface than from identical cultures in the absence of a surface. In another series of experiments, t-sulphidogens were added to chalk rock chips in the presence of nutrients and incubated for several months. This resulted in rapid sulphide generation, the final concentration being related to the initial nutrient concentration. Subsequent nutrient addition resulted in renewed sulphide generation. It is suggested that bacteria in reservoirs can withstand long periods of nutrient deprivation while attached within the porous rock matrix and opportunistically utilise nutrients when they become available.

A lysozyme and magnetic bead based method of separating intact bacteria.

PubMed

Diler, Ebru; Obst, Ursula; Schmitz, Katja; Schwartz, Thomas

2011-07-01

As a response to environmental stress, bacterial cells can enter a physiological state called viable but noncultivable (VBNC). In this state, bacteria fail to grow on routine bacteriological media. Consequently, standard methods of contamination detection based on bacteria cultivation fail. Although they are not growing, the cells are still alive and are able to reactivate their metabolism. The VBNC state and low bacterial densities are big challenges for cultivation-based pathogen detection in drinking water and the food industry, for example. In this context, a new molecular-biological separation method for bacteria using point-mutated lysozymes immobilised on magnetic beads for separating bacteria is described. The immobilised mutated lysozymes on magnetic beads serve as bait for the specific capture of bacteria from complex matrices or water due to their remaining affinity for bacterial cell wall components. Beads with bacteria can be separated using magnetic racks. To avoid bacterial cell lysis by the lysozymes, the protein was mutated at amino acid position 35, leading to the exchange of the catalytic glutamate for alanine (LysE35A) and glutamine (LysE35Q). As proved by turbidity assay with reference bacteria, the muramidase activity was knocked out. The mutated constructs were expressed by the yeast Pichia pastoris and secreted into expression medium. Protein enrichment and purification were carried out by SO(3)-functionalised nanoscale cationic exchanger particles. For a proof of principle, the proteins were biotinylated and immobilised on streptavidin-functionalised, fluorescence dye-labelled magnetic beads. These constructs were used for the successful capture of Syto9-marked Microccocus luteus cells from cell suspension, as visualised by fluorescence microscopy, which confirmed the success of the strategy.

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization.

PubMed

Udikovic-Kolic, Nikolina; Wichmann, Fabienne; Broderick, Nichole A; Handelsman, Jo

2014-10-21

The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam-resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam-resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

PubMed Central

Udikovic-Kolic, Nikolina; Wichmann, Fabienne; Broderick, Nichole A.; Handelsman, Jo

2014-01-01

The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam–resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam–resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem. PMID:25288759

Peptidoglycan Recycling in Gram-Positive Bacteria Is Crucial for Survival in Stationary Phase

PubMed Central

Borisova, Marina; Gaupp, Rosmarie; Duckworth, Amanda; Schneider, Alexander; Dalügge, Désirée; Mühleck, Maraike; Deubel, Denise; Unsleber, Sandra; Yu, Wenqi; Muth, Günther; Bischoff, Markus; Götz, Friedrich

2016-01-01

ABSTRACT Peptidoglycan recycling is a metabolic process by which Gram-negative bacteria reutilize up to half of their cell wall within one generation during vegetative growth. Whether peptidoglycan recycling also occurs in Gram-positive bacteria has so far remained unclear. We show here that three Gram-positive model organisms, Staphylococcus aureus, Bacillus subtilis, and Streptomyces coelicolor, all recycle the sugar N-acetylmuramic acid (MurNAc) of their peptidoglycan during growth in rich medium. They possess MurNAc-6-phosphate (MurNAc-6P) etherase (MurQ in E. coli) enzymes, which are responsible for the intracellular conversion of MurNAc-6P to N-acetylglucosamine-6-phosphate and d-lactate. By applying mass spectrometry, we observed accumulation of MurNAc-6P in MurNAc-6P etherase deletion mutants but not in either the isogenic parental strains or complemented strains, suggesting that MurQ orthologs are required for the recycling of cell wall-derived MurNAc in these bacteria. Quantification of MurNAc-6P in ΔmurQ cells of S. aureus and B. subtilis revealed small amounts during exponential growth phase (0.19 nmol and 0.03 nmol, respectively, per ml of cells at an optical density at 600 nm [OD600] of 1) but large amounts during transition (0.56 nmol and 0.52 nmol) and stationary (0.53 nmol and 1.36 nmol) phases. The addition of MurNAc to ΔmurQ cultures greatly increased the levels of intracellular MurNAc-6P in all growth phases. The ΔmurQ mutants of S. aureus and B. subtilis showed no growth deficiency in rich medium compared to the growth of the respective parental strains, but intriguingly, they had a severe survival disadvantage in late stationary phase. Thus, although peptidoglycan recycling is apparently not essential for the growth of Gram-positive bacteria, it provides a benefit for long-term survival. PMID:27729505

Deathly Drool: Evolutionary and Ecological Basis of Septic Bacteria in Komodo Dragon Mouths

PubMed Central

Bull, J. J.; Jessop, Tim S.; Whiteley, Marvin

2010-01-01

Komodo dragons, the world's largest lizard, dispatch their large ungulate prey by biting and tearing flesh. If a prey escapes, oral bacteria inoculated into the wound reputedly induce a sepsis that augments later prey capture by the same or other lizards. However, the ecological and evolutionary basis of sepsis in Komodo prey acquisition is controversial. Two models have been proposed. The “bacteria as venom” model postulates that the oral flora directly benefits the lizard in prey capture irrespective of any benefit to the bacteria. The “passive acquisition” model is that the oral flora of lizards reflects the bacteria found in carrion and sick prey, with no relevance to the ability to induce sepsis in subsequent prey. A third model is proposed and analyzed here, the “lizard-lizard epidemic” model. In this model, bacteria are spread indirectly from one lizard mouth to another. Prey escaping an initial attack act as vectors in infecting new lizards. This model requires specific life history characteristics and ways to refute the model based on these characteristics are proposed and tested. Dragon life histories (some details of which are reported here) prove remarkably consistent with the model, especially that multiple, unrelated lizards feed communally on large carcasses and that escaping, wounded prey are ultimately fed on by other lizards. The identities and evolutionary histories of bacteria in the oral flora may yield the most useful additional insights for further testing the epidemic model and can now be obtained with new technologies. PMID:20574514

DETECTION OF AEROSOLIZED BACTERIA IN EXPIRED AIR SAMPLES FROM ASIAN ELEPHANTS (ELEPHAS MAXIMUS).

PubMed

Burke, Sophie M; Vogelnest, Larry; Thompson, Paul; Tovey, Euan R; Williamson, Peter

2017-06-01

Elephant-mediated transmission of tuberculosis is assumed to be similar to human models, which state close and prolonged contact with an infected individual is required for transmission. Although considered a risk factor for infection, several case studies have reported that close contact with an elephant is not always necessary for transmission, and the role of aerosolized bacteria remains unclear. To investigate aerosol-mediated transmission of pathogenic bacteria from elephants, a method for the detection of aerosols using an adapted sampling system was developed. A commensal bacterium was isolated from the upper respiratory tract of elephants ( Elephas maximus ) and was used as a proxy organism to detect aerosolized droplets in the sampling system. It was found that elephants are capable of producing aerosolized bacterial particles of a size small enough to remain airborne for prolonged periods and penetrate the lower regions of the human respiratory tract.

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

PubMed Central

Hassard, Francis; Gwyther, Ceri L.; Farkas, Kata; Andrews, Anthony; Jones, Vera; Cox, Brian; Brett, Howard; Jones, Davey L.; McDonald, James E.; Malham, Shelagh K.

2016-01-01

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and

Spatial Variability of Cyanobacteria and Heterotrophic Bacteria in Lake Taihu (China).

PubMed

Qian, Haifeng; Lu, Tao; Song, Hao; Lavoie, Michel; Xu, Jiahui; Fan, Xiaoji; Pan, Xiangliang

2017-09-01

Cyanobacterial blooms frequently occur in Lake Taihu (China), but the intertwined relationships between biotic and abiotic factors modulating the frequency and duration of the blooms remain enigmatic. To better understand the relationships between the key abiotic and biotic factors and cyanobacterial blooms, we measured the abundance and diversity of prokaryotic organisms by high-throughput sequencing, the abundance of key genes involved in microcystin production and nitrogen fixation or loss as well as several physicochemical parameters at several stations in Lake Taihu during a cyanobacterial bloom of Microcystis sp.. Measurements of the copy number of denitrification-related genes and 16S rRNA analyses show that denitrification potential and denitrifying bacteria abundance increased in concert with non-diazotrophic cyanobacteria (Microcystis sp.), suggesting limited competition between cyanobacteria and heterotrophic denitrifiers for nutrients, although potential bacteria-mediated N loss may hamper Microcystis growth. The present study provides insight into the importance of different abiotic and biotic factors in controlling cyanobacteria and heterotrophic bacteria spatial variability in Lake Taihu.

NC10 Bacteria in a Marine Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Padilla, C. C.; Bristow, L. A.; Benson, C. R.; Sarode, N. D.; Girguis, P. R.; Glass, J. B.; DiChristina, T. J.; Thamdrup, B.; Stewart, F. J.

2014-12-01

Marine oxygen minimum zones (OMZs) are key regions of nitrogen cycling and nitrogen loss as N2. The potential for methane cycling to influence OMZ nitrogen budgets remains largely unknown. The anaerobic oxidation of methane (AOM) coupled to nitrite or nitrate reduction has been shown to be a potential source of methane consumption, N loss, and oxygen production in freshwater sediments, but has not been described for marine pelagic environments. Nitrite-dependent AOM is performed by bacteria of the candidate division NC10 through an intra-aerobic pathway involving the dismutation of nitric oxide to O2 and N2. We explored the potential that NC10-like bacteria are present and active in the anoxic, nitrite-rich OMZ of the Eastern Tropical North Pacific. Community transcriptome sequencing confirmed the expression of genes with top matches to the NC10 bacterium 'Candidatus Methylomirabilis oxyfera.' NC10-like transcripts increased in relative abundance with depth into the anoxic OMZ core and included genes of aerobic methanotrophy and denitrification, as well as high numbers of transcripts matching norZ nitric oxide reductase, hypothesized to play a role in the O2-yielding dismutation reaction. Phylogenetic analysis of OMZ particulate methane monooxygenase (pmoA) and 16S rRNA gene sequences recovered by PCR revealed multiple clades of NC10 phylotypes in the OMZ. Preliminary data from OMZ enrichments revealed methane-dependent nitrite consumption, but further characterization is required to identify the pathways and organisms mediating this process. These findings expand the known environmental range of NC10 and suggest the possibility of previously uncharacterized linkages between OMZ nitrogen and methane cycles.

High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean.

PubMed

Lami, Raphaël; Cottrell, Matthew T; Ras, Joséphine; Ulloa, Osvaldo; Obernosterer, Ingrid; Claustre, Hervé; Kirchman, David L; Lebaron, Philippe

2007-07-01

Little is known about the abundance, distribution, and ecology of aerobic anoxygenic phototrophic (AAP) bacteria, particularly in oligotrophic environments, which represent 60% of the ocean. We investigated the abundance of AAP bacteria across the South Pacific Ocean, including the center of the gyre, the most oligotrophic water body of the world ocean. AAP bacteria, Prochlorococcus, and total prokaryotic abundances, as well as bacteriochlorophyll a (BChl a) and divinyl-chlorophyll a concentrations, were measured at several depths in the photic zone along a gradient of oligotrophic conditions. The abundances of AAP bacteria and Prochlorococcus were high, together accounting for up to 58% of the total prokaryotic community. The abundance of AAP bacteria alone was up to 1.94 x 10(5) cells ml(-1) and as high as 24% of the overall community. These measurements were consistent with the high BChl a concentrations (up to 3.32 x 10(-3) microg liter(-1)) found at all stations. However, the BChl a content per AAP bacterial cell was low, suggesting that AAP bacteria are mostly heterotrophic organisms. Interestingly, the biovolume and therefore biomass of AAP bacteria was on average twofold higher than that of other prokaryotic cells. This study demonstrates that AAP bacteria can be abundant in various oligotrophic conditions, including the most oligotrophic regime of the world ocean, and can account for a large part of the bacterioplanktonic carbon stock.

Aerobic Bacteria in the Diaphragmatic Portion of Stethoscope of Medical Professionals of Tertiary Care Hospital.

PubMed

Bham, G; Bhandari, J; Neupane, M R; Dawadi, R; Pradhan, P

2015-01-01

Hospital environment is a reservoir of wide varieties of microorganisms which are frequently reported colonizing in medical equipment. Stethoscopes are essential tools and of universal use in the medical profession, which might be a source of spreading nosocomial infections. This research project was conducted with an aim to assess the presence of aerobic bacteria in the stethoscope of the medical doctors working at Patan Hospital and students of Patan Academy of Health Sciences. It is a cross sectional study based on structured questionnaire and sample assessment from the stethoscope of doctors and students of Patan Hospital and Patan Academy of Health Sciences. The stethescopes used by the doctors of five major departments of Patan Hospital and students of clinical years were included in this study. Total of 99 stethoscope owned by different level of professionals (positions) and different departments were examined for bacterial contamination. Out of them, 36 were found to be considerably contaminated. Single strain of bacteria was grown from a single stethoscope. Among them 34 were Gram positive and remaining were Gram negative. Out of 34 gram postive bacteria, 29 were identified as Staphylococcus aureus, six were identified as Coagulase Negative Staphylococcus and remaining were Gram positive bacilli. There is presence of aerobic bacteria in diaphragmatic portion of stethoscope of medical professional of which the gram positives were the commonest.

Accumulation of Reserve Carbohydrate by Rumen Protozoa and Bacteria in Competition for Glucose

PubMed Central

Denton, Bethany L.; Diese, Leanne E.; Firkins, Jeffrey L.

2014-01-01

The aim of this study was to determine if rumen protozoa could form large amounts of reserve carbohydrate compared to the amounts formed by bacteria when competing for glucose in batch cultures. We separated large protozoa and small bacteria from rumen fluid by filtration and centrifugation, recombined equal protein masses of each group into one mixture, and subsequently harvested (reseparated) these groups at intervals after glucose dosing. This method allowed us to monitor reserve carbohydrate accumulation of protozoa and bacteria individually. When mixtures were dosed with a moderate concentration of glucose (4.62 or 5 mM) (n = 2 each), protozoa accumulated large amounts of reserve carbohydrate; 58.7% (standard error of the mean [SEM], 2.2%) glucose carbon was recovered from protozoal reserve carbohydrate at time of peak reserve carbohydrate concentrations. Only 1.7% (SEM, 2.2%) was recovered in bacterial reserve carbohydrate, which was less than that for protozoa (P < 0.001). When provided a high concentration of glucose (20 mM) (n = 4 each), 24.1% (SEM, 2.2%) of glucose carbon was recovered from protozoal reserve carbohydrate, which was still higher (P = 0.001) than the 5.0% (SEM, 2.2%) glucose carbon recovered from bacterial reserve carbohydrate. Our novel competition experiments directly demonstrate that mixed protozoa can sequester sugar away from bacteria by accumulating reserve carbohydrate, giving protozoa a competitive advantage and stabilizing fermentation in the rumen. Similar experiments could be used to investigate the importance of starch sequestration. PMID:25548053

Bacteria of leg atheromatous arteries responsible for inflammation.

PubMed

Olszewski, Waldemar Lech; Rutkowska, Joanna; Moscicka-Wesolowska, Maria; Swoboda-Kopec, Ewa; Stelmach, Ewa; Zaleska, Marzanna; Zagozda, Malgorzata

2016-09-01

Ischaemia of the lower limbs is frequently followed by inflammation and, in advanced cases, necrosis of peripheral tissues. Whether this is caused by arterial hypoperfusion only or by the presence of bacteria in the arterial walI as well remains unclear. The aim of the study was to prove the presence and source of bacteria in arterial specimens and evaluate their chemotactic properties resulting in the formation of periarterial cellular infiltrates. Bacterial culture and testing for 16sRNA were performed in fragments of popliteal artery harvested from amputated limbs. Carotid artery plaques served as controls. Fragments of arteries were transplanted into scid mice to evaluate their chemotactic activity for macrophages. a) higher prevalence of isolates and 16sRNA in atherosclerotic popliteal than carotid arteries, b) high density of plaque and periarterial infiltrates and mRNA level for pro-inflammatory cytokines in popliteal arteries, c) prevalent microbes were Staphylococcus aureus, S. epidermidis and Enterococci, d) foot skin and arterial bacterial phenotypes and DNA revealed evident similarities, and e) more intensive mouse macrophage accumulation in popliteal than carotid implants into scid mice. The presence of bacteria in the lower limb arterial wall was documented. They may predispose to inflammation secondary to ischaemic changes.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

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

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

SAR11 bacteria linked to ocean anoxia and nitrogen loss

DOE PAGES

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; ...

2016-08-03

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

Surface-enhanced Raman scattering spectroscopy characterization and identification of foodborne bacteria

NASA Astrophysics Data System (ADS)

Liu, Yongliang; Chen, Yud-Ren; Nou, Xiangwu; Chao, Kaunglin

2007-09-01

Rapid and routine identification of foodborne bacteria are considerably important, because of bio- / agro- terrorism threats, public health concerns, and economic loss. Conventional, PCR, and immunoassay methods for the detection of bacteria are generally time-consuming, chemical reagent necessary and multi-step procedures. Fast microbial detection requires minimal sample preparation, permits the routine analysis of large numbers of samples with negligible reagent costs, and is easy to operate. Therefore, we have developed silver colloidal nanoparticle based surface-enhanced Raman scattering (SERS) spectroscopy as a potential tool for the rapid and routine detection of E. coli and L. monocytogenes. This study presents the further results of our examination on S. typhimonium, one of the most commonly outbreak bacteria, for the characteristic bands and subsequent identification.

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.

Heme and menaquinone induced electron transport in lactic acid bacteria

PubMed Central

Brooijmans, Rob; Smit, Bart; Santos, Filipe; van Riel, Jan; de Vos, Willem M; Hugenholtz, Jeroen

2009-01-01

Background For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait. Results Heme- (and menaquinone) stimulated aerobic growth was observed for several species and genera of lactic acid bacteria. These include Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacilllus brevis, Lactobacillus paralimentarius, Streptococcus entericus and Lactococcus garviae. The increased biomass production without further acidification, which are respiration associated traits, are suitable for high-throughput screening as demonstrated by the screening of 8000 Lactococcus lactis insertion mutants. Respiration-negative insertion-mutants were found with noxA, bd-type cytochrome and menaquinol biosynthesis gene-disruptions. Phenotypic screening and in silico genome analysis suggest that respiration can be considered characteristic for certain species. Conclusion We propose that the cyd-genes were present in the common ancestor of lactic acid bacteria, and that multiple gene-loss events best explains the observed distribution of these genes among the species. PMID:19480672

Heme and menaquinone induced electron transport in lactic acid bacteria.

PubMed

Brooijmans, Rob; Smit, Bart; Santos, Filipe; van Riel, Jan; de Vos, Willem M; Hugenholtz, Jeroen

2009-05-29

For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait. Heme- (and menaquinone) stimulated aerobic growth was observed for several species and genera of lactic acid bacteria. These include Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacilllus brevis, Lactobacillus paralimentarius, Streptococcus entericus and Lactococcus garviae. The increased biomass production without further acidification, which are respiration associated traits, are suitable for high-throughput screening as demonstrated by the screening of 8000 Lactococcus lactis insertion mutants. Respiration-negative insertion-mutants were found with noxA, bd-type cytochrome and menaquinol biosynthesis gene-disruptions. Phenotypic screening and in silico genome analysis suggest that respiration can be considered characteristic for certain species. We propose that the cyd-genes were present in the common ancestor of lactic acid bacteria, and that multiple gene-loss events best explains the observed distribution of these genes among the species.

Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria.

PubMed

Li, Jianxu; Wang, Chengyuan; Yang, Gaohua; Sun, Zhe; Guo, Hui; Shao, Kai; Gu, Yang; Jiang, Weihong; Zhang, Peng

2017-08-01

d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose. The molecular mechanism underlying signal perception and integration of these processes remains elusive, however. Here we purified the N-terminal periplasmic domain of LytS (LytSN) in a complex with XylFII and determined the conformational structures of the complex in its d-xylose-free and d-xylose-bound forms. LytSN contains a four-helix bundle, and XylFII contains two Rossmann fold-like globular domains with a xylose-binding cleft between them. In the absence of d-xylose, LytSN and XylFII formed a heterodimer. Specific binding of d-xylose to the cleft of XylFII induced a large conformational change that closed the cleft and brought the globular domains closer together. This conformational change led to the formation of an active XylFII-LytSN heterotetramer. Mutations at the d-xylose binding site and the heterotetramer interface diminished heterotetramer formation and impaired the d-xylose-sensing function of XylFII-LytS. Based on these data, we propose a working model of XylFII-LytS that provides a molecular basis for d-xylose utilization and metabolic modification in bacteria.

Pyrosequencing reveals benthic bacteria changes responsing to heavy deposition of Microcystis scum in lab — searching bacteria for bloom control

NASA Astrophysics Data System (ADS)

Tang, Yali; Cheng, Dongmei; Guan, Baohua; Zhang, Xiufeng; Liu, Zhengwen; Liu, Zejun

2017-05-01

Bacteria capable of degrading cyanobacteria Microcystis are crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. Scum derived from Microcystis blooms tends to accumulate in bays of large lakes and then sink to the sediments where it is finally consumed by benthic bacteria. Understanding the response of benthic bacterial communities to massive Microcystis deposition events may help identify the bacteria best suited to Microcystis hydrolyzation and even bloom control. For that purpose, an experimental system was set up in which intact sediment cores were incubated in the laboratory with normal and heavy deposits of Microcystis detritus. Pyrosequencing was performed in order to describe a phylogenetic inventory of bacterial communities in samples taken at 0-1, 1-2 and 2-3 cm depths in incubated sediments and in original untreated sediment. A hierarchical cluster tree was constructed expose differences between sediments. Similarity percentage calculations were also performed to identify the bacterial species contributing to variation. The results of this study suggest that: (1) deposition of Microcystis scums exerts a strong effect on the bacterial community composition in the surface (0-1 cm) and sub-surface (1-2 cm) sediment layers; (2) bacterial community responses to Microcystis detritus deposition vary across vertical gradients. A list of bacteria with potential roles in Microcystis degradation was compiled. These findings may inform the development of future measures for Microcystis bloom control in lakes.

Metabolic plasticity for isoprenoid biosynthesis in bacteria.

PubMed

Pérez-Gil, Jordi; Rodríguez-Concepción, Manuel

2013-05-15

Isoprenoids are a large family of compounds synthesized by all free-living organisms. In most bacteria, the common precursors of all isoprenoids are produced by the MEP (methylerythritol 4-phosphate) pathway. The MEP pathway is absent from archaea, fungi and animals (including humans), which synthesize their isoprenoid precursors using the completely unrelated MVA (mevalonate) pathway. Because the MEP pathway is essential in most bacterial pathogens (as well as in the malaria parasites), it has been proposed as a promising new target for the development of novel anti-infective agents. However, bacteria show a remarkable plasticity for isoprenoid biosynthesis that should be taken into account when targeting this metabolic pathway for the development of new antibiotics. For example, a few bacteria use the MVA pathway instead of the MEP pathway, whereas others possess the two full pathways, and some parasitic strains lack both the MVA and the MEP pathways (probably because they obtain their isoprenoids from host cells). Moreover, alternative enzymes and metabolic intermediates to those of the canonical MVA or MEP pathways exist in some organisms. Recent work has also shown that resistance to a block of the first steps of the MEP pathway can easily be developed because several enzymes unrelated to isoprenoid biosynthesis can produce pathway intermediates upon spontaneous mutations. In the present review, we discuss the major advances in our knowledge of the biochemical toolbox exploited by bacteria to synthesize the universal precursors for their essential isoprenoids.

Back To Bacteria.

ERIC Educational Resources Information Center

Flannery, Maura C.

1997-01-01

Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

Acoustic impedance matched buffers enable separation of bacteria from blood cells at high cell concentrations.

PubMed

Ohlsson, Pelle; Petersson, Klara; Augustsson, Per; Laurell, Thomas

2018-06-14

Sepsis is a common and often deadly systemic response to an infection, usually caused by bacteria. The gold standard for finding the causing pathogen in a blood sample is blood culture, which may take hours to days. Shortening the time to diagnosis would significantly reduce mortality. To replace the time-consuming blood culture we are developing a method to directly separate bacteria from red and white blood cells to enable faster bacteria identification. The blood cells are moved from the sample flow into a parallel stream using acoustophoresis. Due to their smaller size, the bacteria are not affected by the acoustic field and therefore remain in the blood plasma flow and can be directed to a separate outlet. When optimizing for sample throughput, 1 ml of undiluted whole blood equivalent can be processed within 12.5 min, while maintaining the bacteria recovery at 90% and the blood cell removal above 99%. That makes this the fastest label-free microfluidic continuous flow method per channel to separate bacteria from blood with high bacteria recovery (>80%). The high throughput was achieved by matching the acoustic impedance of the parallel stream to that of the blood sample, to avoid that acoustic forces relocate the fluid streams.

Rapid Membrane Filtration-Epifluorescent Microscopy Technique for Direct Enumeration of Bacteria in Raw Milk

PubMed Central

Pettipher, Graham L.; Mansell, Roderick; McKinnon, Charles H.; Cousins, Christina M.

1980-01-01

Membrane filtration and epifluorescent microscopy were used for the direct enumeration of bacteria in raw milk. Somatic cells were lysed by treatment with trypsin and Triton X-100 so that 2 ml of milk containing up to 5 × 106 somatic cells/ml could be filtered. The majority of the bacteria (ca. 80%) remained intact and were concentrated on the membrane. After being stained with acridine organe, the bacteria fluoresced under ultraviolet light and could easily be counted. The clump count of orange fluorescing cells on the membrane correlated well (r = 0.91) with the corresponding plate count for farm, tanker, and silo milks. Differences between counts obtained by different operators and between the membrane clump count and plate count were not significant. The technique is rapid, taking less than 25 min, inexpensive, costing less than 50 cents per sample, and is suitable for milks containing 5 × 103 to 5 × 108 bacteria per ml. Images PMID:16345515

Pseudomonas mesophilica and an unnamed taxon, clinical isolates of pink-pigmented oxidative bacteria.

PubMed

Gilardi, G L; Faur, Y C

1984-10-01

Twenty-one strains of pink-pigmented bacteria, isolated from human clinical specimens and an environmental source, were compared with Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. These isolates were gram-negative, oxidative rods which were motile by means of a single polar flagellum; gave positive catalase, indophenol oxidase, urease, and amylase reactions; and grew slowly at 30 degrees C. Fourteen isolates conformed to the designated type strains Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. The remaining seven strains represented an undescribed taxon. These pink bacteria appear to be invaders of debilitated patients with an underlying chronic disease.

Pseudomonas mesophilica and an unnamed taxon, clinical isolates of pink-pigmented oxidative bacteria.

PubMed Central

Gilardi, G L; Faur, Y C

1984-01-01

Twenty-one strains of pink-pigmented bacteria, isolated from human clinical specimens and an environmental source, were compared with Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. These isolates were gram-negative, oxidative rods which were motile by means of a single polar flagellum; gave positive catalase, indophenol oxidase, urease, and amylase reactions; and grew slowly at 30 degrees C. Fourteen isolates conformed to the designated type strains Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. The remaining seven strains represented an undescribed taxon. These pink bacteria appear to be invaders of debilitated patients with an underlying chronic disease. PMID:6490848

Co-electrospinning of bacteria and viruses

NASA Astrophysics Data System (ADS)

Salalha, Wael; Kuhn, Jonathan; Chervinsky, Shmuel; Zussman, Eyal

2006-03-01

Co-electrospinning provides a novel and highly versatile approach towards composite fibers with diameters ranging from a few hundred nm down to 30 nm with embedded elements. In the present work, co-electrospinning of poly(vinyl alcohol) (PVA) and viruses (T7, T4, λ) or bacteria (Escherichia coli, Staphylococcus albus) was carried out. These preparations should have applications for tissue engineering, gene therapy, phage therapy and biosensing. The average diameter of the co-spun nanofibers was about 300 nm. We found that the encapsulated viruses and bacteria manage to survive the electrospinning process, its pressure buildup in the core of the fiber and the electrostatic field in the co-electrospinning process. Approximately 10% of the Escherichia coli and 20% of Staphylococcus albus cells are viable after spinning. Approximately 5% of the bacterial viruses were also viable after the electrospinning. It should be noted that the encapsulated cells and viruses remain stable for two months without a further decrease in number. These results demonstrate the potential of the co-electrospinning process for the encapsulation and immobilization of bio-objects and the possibility of adapting them to technical applications (e.g., bio-chips).

Prediction of serine/threonine phosphorylation sites in bacteria proteins.

PubMed

Li, Zhengpeng; Wu, Ping; Zhao, Yuanyuan; Liu, Zexian; Zhao, Wei

2015-01-01

As a critical post-translational modification, phosphorylation plays important roles in regulating various biological processes, while recent studies suggest that phosphorylation in bacteria is also critical for functional signaling transduction. Since identification of phosphorylation substrates and sites is fundamental for understanding the phosphorylation mediated regulatory mechanism, a number of studies have been contributed to this area. Since experimental identification of phosphorylation sites is time-consuming and labor-intensive, computational predictions attract much attention for its convenience to provide helpful information. However, although there are a large number of computational studies in eukaryotes, predictions in bacteria are still rare. In this study, we present a new predictor of cPhosBac to predict phosphorylation serine/threonine in bacteria proteins. The predictor is developed with CKSAAP algorithm, which was combined with motif length selection to optimize the prediction, which achieves promising performance. The online service of cPhosBac is available at: http://netalign.ustc.edu.cn/cphosbac/ .

Carious Dentine Provides a Habitat for a Complex Array of Novel Prevotella-Like Bacteria

PubMed Central

Nadkarni, Mangala A.; Caldon, C. Elizabeth; Chhour, Kim-Ly; Fisher, Ilana P.; Martin, F. Elizabeth; Jacques, Nicholas A.; Hunter, Neil

2004-01-01

Previous analysis of the microbiology of advanced caries by culture and real-time PCR emphasized the high incidence and abundance of gram-negative anaerobic species, particularly Prevotella-like bacteria. The diversity of Prevotella-like bacteria was further explored by analyzing pooled bacterial DNA from lesions of carious dentine. This was achieved by amplification of a region of the 16S ribosomal DNA with a Prevotella genus-specific forward primer and a universal bacterial reverse primer, followed by cloning and sequencing. Cultured Prevotella species commonly associated with oral tissues constituted only 12% of the Prevotella clones isolated from advanced carious lesions. The remaining 88% consisted of a diverse range of phylotypes. These included five clusters of previously recognized but uncultured oral Prevotella spp. and a major cluster containing Prevotella-like bacteria most closely related to uncharacterized rumen bacteria. Cluster-specific primers were designed, and the numbers of bacteria within clusters were quantified by real-time PCR, confirming the abundance of these organisms. The data indicated that advanced dental caries provides a unique environment for a complex array of novel and uncultured Prevotella and Prevotella-like bacteria which, in some cases, may dominate the diverse polymicrobial community associated with the disease. PMID:15528720

Inactivation of biofilm bacteria.

PubMed Central

LeChevallier, M W; Cawthon, C D; Lee, R G

1988-01-01

The current project was developed to examine inactivation of biofilm bacteria and to characterize the interaction of biocides with pipe surfaces. Unattached bacteria were quite susceptible to the variety of disinfectants tested. Viable bacterial counts were reduced 99% by exposure to 0.08 mg of hypochlorous acid (pH 7.0) per liter (1 to 2 degrees C) for 1 min. For monochloramine, 94 mg/liter was required to kill 99% of the bacteria within 1 min. These results were consistent with those found by other investigators. Biofilm bacteria grown on the surfaces of granular activated carbon particles, metal coupons, or glass microscope slides were 150 to more than 3,000 times more resistant to hypochlorous acid (free chlorine, pH 7.0) than were unattached cells. In contrast, resistance of biofilm bacteria to monochloramine disinfection ranged from 2- to 100-fold more than that of unattached cells. The results suggested that, relative to inactivation of unattached bacteria, monochloramine was better able to penetrate and kill biofilm bacteria than free chlorine. For free chlorine, the data indicated that transport of the disinfectant into the biofilm was a major rate-limiting factor. Because of this phenomenon, increasing the level of free chlorine did not increase disinfection efficiency. Experiments where equal weights of disinfectants were used suggested that the greater penetrating power of monochloramine compensated for its limited disinfection activity. These studies showed that monochloramine was as effective as free chlorine for inactivation of biofilm bacteria. The research provides important insights into strategies for control of biofilm bacteria. Images PMID:2849380

Establishment of the first international repository for transfusion-relevant bacteria reference strains: ISBT working party transfusion-transmitted infectious diseases (WP-TTID), subgroup on bacteria.

PubMed

Störmer, M; Arroyo, A; Brachert, J; Carrero, H; Devine, D; Epstein, J S; Gabriel, C; Gelber, C; Goodrich, R; Hanschmann, K-M; Heath, D G; Jacobs, M R; Keil, S; de Korte, D; Lambrecht, B; Lee, C-K; Marcelis, J; Marschner, S; McDonald, C; McGuane, S; McKee, M; Müller, T H; Muthivhi, T; Pettersson, A; Radziwon, P; Ramirez-Arcos, S; Reesink, H W; Rojo, J; Rood, I; Schmidt, M; Schneider, C K; Seifried, E; Sicker, U; Wendel, S; Wood, E M; Yomtovian, R A; Montag, T

2012-01-01

Bacterial contamination of platelet concentrates (PCs) still remains a significant problem in transfusion with potential important clinical consequences, including death. The International Society of Blood Transfusion Working Party on Transfusion-Transmitted Infectious Diseases, Subgroup on Bacteria, organised an international study on Transfusion-Relevant Bacteria References to be used as a tool for development, validation and comparison of both bacterial screening and pathogen reduction methods. Four Bacteria References (Staphylococcus epidermidis PEI-B-06, Streptococcus pyogenes PEI-B-20, Klebsiella pneumoniae PEI-B-08 and Escherichia coli PEI-B-19) were selected regarding their ability to proliferate to high counts in PCs and distributed anonymised to 14 laboratories in 10 countries for identification, enumeration and bacterial proliferation in PCs after low spiking (0·3 and 0·03 CFU/ml), to simulate contamination occurring during blood donation. Bacteria References were correctly identified in 98% of all 52 identifications. S. pyogenes and E. coli grew in PCs in 11 out of 12 laboratories, and K. pneumoniae and S. epidermidis replicated in all participating laboratories. The results of bacterial counts were very consistent between laboratories: the 95% confidence intervals were for S. epidermidis: 1·19-1·32 × 10(7) CFU/ml, S. pyogenes: 0·58-0·69 × 10(7) CFU/ml, K. pneumoniae: 18·71-20·26 × 10(7) CFU/ml and E. coli: 1·78-2·10 × 10(7) CFU/ml. The study was undertaken as a proof of principle with the aim to demonstrate (i) the quality, stability and suitability of the bacterial strains for low-titre spiking of blood components, (ii) the property of donor-independent proliferation in PCs, and (iii) their suitability for worldwide shipping of deep frozen, blinded pathogenic bacteria. These aims were successfully fulfilled. The WHO Expert Committee Biological Standardisation has approved the adoption of these four bacteria strains as the first

Have sex or not? Lessons from bacteria.

PubMed

Lodé, T

2012-01-01

Sex is one of the greatest puzzles in evolutionary biology. A true meiotic process occurs only in eukaryotes, while in bacteria, gene transcription is fragmentary, so asexual reproduction in this case really means clonal reproduction. Sex could stem from a signal that leads to increased reproductive output of all interacting individuals and could be understood as a secondary consequence of primitive metabolic reactions. Meiotic sex evolved in proto-eukaryotes to solve a problem that bacteria did not have, namely a large amount of DNA material, occurring in an archaic step of proto-cell formation and genetic exchanges. Rather than providing selective advantages through reproduction, sex could be thought of as a series of separate events which combines step-by-step some very weak benefits of recombination, meiosis, gametogenesis and syngamy. Copyright © 2012 S. Karger AG, Basel.

TRIF Licenses Caspase-11-Dependent NLRP3 Inflammasome Activation by Gram-Negative Bacteria

PubMed Central

Rathinam, Vijay A.K.; Vanaja, Sivapriya Kailasan; Waggoner, Lisa; Sokolovska, Anna; Becker, Christine; Stuart, Lynda M.; Leong, John M.; Fitzgerald, Katherine A.

2013-01-01

SUMMARY Systemic infections with Gram-negative bacteria are characterized by high mortality rates due to the “sepsis syndrome,” a widespread and uncontrolled inflammatory response. Though it is well recognized that the immune response during Gram-negative bacterial infection is initiated after the recognition of endotoxin by Toll-like receptor 4, the molecular mechanisms underlying the detrimental inflammatory response during Gram-negative bacteremia remain poorly defined. Here, we identify a TRIF pathway that licenses NLRP3 inflammasome activation by all Gram-negative bacteria. By engaging TRIF, Gram-negative bacteria activate caspase-11. TRIF activates caspase-11 via type I IFN signaling, an event that is both necessary and sufficient for caspase-11 induction and autoactivation. Caspase-11 subsequently synergizes with the assembled NLRP3 inflammasome to regulate caspase-1 activation and leads to caspase-1-independent cell death. These events occur specifically during infection with Gram-negative, but not Gram-positive, bacteria. The identification of TRIF as a regulator of caspase-11 underscores the importance of TLRs as master regulators of inflammasomes during Gram-negative bacterial infection. PMID:22819539

[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.

How microbial ancient DNA, found in association with human remains, can be interpreted.

PubMed Central

Rollo, F; Marota, I

1999-01-01

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies. PMID:10091251

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.

Amino acid metabolism in intestinal bacteria and its potential implications for mammalian reproduction.

PubMed

Dai, Zhaolai; Wu, Zhenlong; Hang, Suqin; Zhu, Weiyun; Wu, Guoyao

2015-05-01

Reproduction is vital for producing offspring and preserving genetic resources. However, incidences of many reproductive disorders (e.g. miscarriage, intrauterine growth restriction, premature delivery and lower sperm quality) have either increased dramatically or remained at high rates over the last decades. Mounting evidence shows a strong correlation between enteral protein nutrition and reproduction. Besides serving as major nutrients in the diet, amino acids (AA) are signaling molecules in the regulation of diverse physiological processes, ranging from spermatogenesis to oocyte fertilization and to embryo implantation. Notably, the numbers of bacteria in the intestine exceed the numbers of host cells by 10 times. Microbes in the small-intestinal lumen actively metabolize large amounts of dietary AA and, therefore, affect the entry of AA into the portal circulation for whole-body utilization. Changes in the composition and abundance of AA-metabolizing bacteria in the gut during pregnancy, as well as their translocation to the uterus, may alter uterine function and epigenetic modifications of maternal physiology and metabolism, which are crucial for pregnancy recognition and fetal development. Thus, the presence of the maternal gut microbiota and AA metabolites in the intrauterine environments (e.g. endometrium and placenta) and breast milk is likely a unique signature for the programming of the whole-body microbiome and metabolism in both the fetus and infant. Dietary intervention with functional AA, probiotics and prebiotics to alter the abundance and activity of intestinal bacteria may ameliorate or prevent the development of metabolic syndrome, while improving reproductive performance in both males and females as well as their offspring. © The Author 2015. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Contribution of acetate to butyrate formation by human faecal bacteria.

PubMed

Duncan, Sylvia H; Holtrop, Grietje; Lobley, Gerald E; Calder, A Graham; Stewart, Colin S; Flint, Harry J

2004-06-01

Acetate is normally regarded as an endproduct of anaerobic fermentation, but butyrate-producing bacteria found in the human colon can be net utilisers of acetate. The butyrate formed provides a fuel for epithelial cells of the large intestine and influences colonic health. [1-(13)C]Acetate was used to investigate the contribution of exogenous acetate to butyrate formation. Faecalibacterium prausnitzii and Roseburia spp. grown in the presence of 60 mm-acetate and 10 mm-glucose derived 85-90 % butyrate-C from external acetate. This was due to rapid interchange between extracellular acetate and intracellular acetyl-CoA, plus net acetate uptake. In contrast, a Coprococcus-related strain that is a net acetate producer derived only 28 % butyrate-C from external acetate. Different carbohydrate-derived energy sources affected butyrate formation by mixed human faecal bacteria growing in continuous or batch cultures. The ranking order of butyrate production rates was amylopectin > oat xylan > shredded wheat > inulin > pectin (continuous cultures), and inulin > amylopectin > oat xylan > shredded wheat > pectin (batch cultures). The contribution of external acetate to butyrate formation in these experiments ranged from 56 (pectin) to 90 % (xylan) in continuous cultures, and from 72 to 91 % in the batch cultures. This is consistent with a major role for bacteria related to F. prausnitzii and Roseburia spp. in butyrate formation from a range of substrates that are fermented in the large intestine. Variations in the dominant metabolic type of butyrate producer between individuals or with variations in diet are not ruled out, however, and could influence butyrate supply in the large intestine.

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

Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria.

PubMed

Grylak-Mielnicka, Aleksandra; Bidnenko, Vladimir; Bardowski, Jacek; Bidnenko, Elena

2016-03-01

Factor-dependent termination of transcription in bacteria relies on the activity of a specific RNA helicase, the termination factor Rho. Rho is nearly ubiquitous in bacteria, but the extent to which its physiological functions are conserved throughout the different phyla remains unknown. Most of our current knowledge concerning the mechanism of Rho's activity and its physiological roles comes from the model micro-organism Escherichia coli, where Rho is essential and involved in the control of several important biological processes. However, the rather comprehensive knowledge about the general mechanisms of action and activities of Rho based on the E. coli paradigm cannot be directly extrapolated to other bacteria. Recent studies performed in different species favour the view that Rho-dependent termination plays a significant role even in bacteria where Rho is not essential. Here, we summarize the current state of the ever-increasing knowledge about the various aspects of the physiological functions of Rho, such as limitation of deleterious foreign DNA expression, control of gene expression, suppression of pervasive transcription, prevention of R-loops and maintenance of chromosome integrity, focusing on similarities and differences of the activities of Rho in various bacterial species.

Association study of Demodex bacteria and facial dermatoses based on DGGE technique.

PubMed

Zhao, YaE; Yang, Fan; Wang, RuiLing; Niu, DongLing; Mu, Xin; Yang, Rui; Hu, Li

2017-03-01

The role of bacteria is unclear in the facial skin lesions caused by Demodex. To shed some light on this issue, we conducted a case-control study comparing cases with facial dermatoses with controls with healthy skin using denaturing gradient gel electrophoresis (DGGE) technique. The bacterial diversity, composition, and principal component were analyzed for Demodex bacteria and the matched facial skin bacteria. The result of mite examination showed that all 33 cases were infected with Demodex folliculorum (D. f), whereas 16 out of the 30 controls were infected with D. f, and the remaining 14 controls were infected with Demodex brevis (D. b). The diversity analysis showed that only evenness index presented statistical difference between mite bacteria and matched skin bacteria in the cases. The composition analysis showed that the DGGE bands of cases and controls were assigned to 12 taxa of 4 phyla, including Proteobacteria (39.37-52.78%), Firmicutes (2.7-26.77%), Actinobacteria (0-5.71%), and Bacteroidetes (0-2.08%). In cases, the proportion of Staphylococcus in Firmicutes was significantly higher than that in D. f controls and D. b controls, while the proportion of Sphingomonas in Proteobacteria was significantly lower than that in D. f controls. The between-group analysis (BGA) showed that all the banding patterns clustered into three groups, namely, D. f cases, D. f controls, and D. b controls. Our study suggests that the bacteria in Demodex should come from the matched facial skin bacteria. Proteobacteria and Firmicutes are the two main taxa. The increase of Staphylococcus and decrease of Sphingomonas might be associated with the development of facial dermatoses.

Protein aggregation in bacteria: the thin boundary between functionality and toxicity.

PubMed

Bednarska, Natalia G; Schymkowitz, Joost; Rousseau, Frederic; Van Eldere, Johan

2013-09-01

Misfolding and aggregation of proteins have a negative impact on all living organisms. In recent years, aggregation has been studied in detail due to its involvement in neurodegenerative diseases, including Alzheimer's, Parkinson's and Huntington's diseases, and type II diabetes--all associated with accumulation of amyloid fibrils. This research highlighted the central importance of protein homeostasis, or proteostasis for short, defined as the cellular state in which the proteome is both stable and functional. It implicates an equilibrium between synthesis, folding, trafficking, aggregation, disaggregation and degradation. In accordance with the eukaryotic systems, it has been documented that protein aggregation also reduces fitness of bacterial cells, but although our understanding of the cellular protein quality control systems is perhaps most detailed in bacteria, the use of bacterial proteostasis as a drug target remains little explored. Here we describe protein aggregation as a normal physiological process and its role in bacterial virulence and we shed light on how bacteria defend themselves against the toxic threat of aggregates. We review the impact of aggregates on bacterial viability and look at the ways that bacteria use to maintain a balance between aggregation and functionality. The proteostasis in bacteria can be interrupted via overexpression of proteins, certain antibiotics such as aminoglycosides, as well as antimicrobial peptides--all leading to loss of cell viability. Therefore intracellular protein aggregation and disruption of proteostatic balance in bacteria open up another strategy that should be explored towards the discovery of new antimicrobials.

Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

PubMed Central

Legendre, P; Baleux, B; Troussellier, M

1984-01-01

The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two types of temporal evolution: in the first four stations, it seems mainly controlled by the nutrient support capacity of the sewage input, whereas in the remaining part of the lagoon, it seems likely that the pollution-indicator bacteria are gradually replaced by other bacterial types that are better adapted to this environment. On the other hand, the pollution-indicator bacteria showed an annual cycle which increased in amplitude at distances further from the wastewater source. The main events in this cycle were produced simultaneously at all stations, indicating control of these bacterial populations by climatic factors, which act through physical and chemical factors, and also through other biological components of this ecosystem (phytoplankton and zooplankton). Finally, we use results from this study to suggest a modified design for a future study program. Images PMID:6497372

The reaction of monochloramine and hydroxylamine: implications for ammonia–oxidizing bacteria in chloraminated drinking water

EPA Science Inventory

Drinking water chloramine use may promote ammonia–oxidizing bacteria (AOB) growth because of naturally occurring ammonia, residual ammonia remaining from chloramine formation, and ammonia released from chloramine decay and demand. A rapid chloramine residual loss is often associa...

Accumulation of reserve carbohydrate by rumen protozoa and bacteria in competition for glucose.

PubMed

Denton, Bethany L; Diese, Leanne E; Firkins, Jeffrey L; Hackmann, Timothy J

2015-03-01

The aim of this study was to determine if rumen protozoa could form large amounts of reserve carbohydrate compared to the amounts formed by bacteria when competing for glucose in batch cultures. We separated large protozoa and small bacteria from rumen fluid by filtration and centrifugation, recombined equal protein masses of each group into one mixture, and subsequently harvested (reseparated) these groups at intervals after glucose dosing. This method allowed us to monitor reserve carbohydrate accumulation of protozoa and bacteria individually. When mixtures were dosed with a moderate concentration of glucose (4.62 or 5 mM) (n = 2 each), protozoa accumulated large amounts of reserve carbohydrate; 58.7% (standard error of the mean [SEM], 2.2%) glucose carbon was recovered from protozoal reserve carbohydrate at time of peak reserve carbohydrate concentrations. Only 1.7% (SEM, 2.2%) was recovered in bacterial reserve carbohydrate, which was less than that for protozoa (P < 0.001). When provided a high concentration of glucose (20 mM) (n = 4 each), 24.1% (SEM, 2.2%) of glucose carbon was recovered from protozoal reserve carbohydrate, which was still higher (P = 0.001) than the 5.0% (SEM, 2.2%) glucose carbon recovered from bacterial reserve carbohydrate. Our novel competition experiments directly demonstrate that mixed protozoa can sequester sugar away from bacteria by accumulating reserve carbohydrate, giving protozoa a competitive advantage and stabilizing fermentation in the rumen. Similar experiments could be used to investigate the importance of starch sequestration. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Rapid Separation of Bacteria from Blood—Review and Outlook

PubMed Central

Alizadeh, Mahsa; Husseini, Ghaleb A.; McClellan, Daniel S.; Buchanan, Clara M.; Bledsoe, Colin G.; Robison, Richard A.; Blanco, Rae; Roeder, Beverly L.; Melville, Madison; Hunter, Alex K.

2017-01-01

The high morbidity and mortality rate of bloodstream infections involving antibiotic-resistant bacteria necessitate a rapid identification of the infectious organism and its resistance profile. Traditional methods based on culturing the blood typically require at least 24 h, and genetic amplification by PCR in the presence of blood components has been problematic. The rapid separation of bacteria from blood would facilitate their genetic identification by PCR or other methods so that the proper antibiotic regimen can quickly be selected for the septic patient. Microfluidic systems that separate bacteria from whole blood have been developed, but these are designed to process only microliter quantities of whole blood or only highly diluted blood. However, symptoms of clinical blood infections can be manifest with bacterial burdens perhaps as low as 10 CFU/mL, and thus milliliter quantities of blood must be processed to collect enough bacteria for reliable genetic analysis. This review considers the advantages and shortcomings of various methods to separate bacteria from blood, with emphasis on techniques that can be done in less than 10 min on milliliter-quantities of whole blood. These techniques include filtration, screening, centrifugation, sedimentation, hydrodynamic focusing, chemical capture on surfaces or beads, field-flow fractionation, and dielectrophoresis. Techniques with the most promise include screening, sedimentation, and magnetic bead capture, as they allow large quantities of blood to be processed quickly. Some microfluidic techniques can be scaled up. PMID:27160415

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

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

Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas

The number of genomes from uncultivated microbes will soon surpass the number of isolate genomes in public databases (Hugenholtz, Skarshewski, & Parks, 2016). Technological advancements in high-throughput sequencing and assembly, including single-cell genomics and the computational extraction of genomes from metagenomes (GFMs), are largely responsible. Here we propose community standards for reporting the Minimum Information about a Single-Cell Genome (MIxS-SCG) and Minimum Information about Genomes extracted From Metagenomes (MIxS-GFM) specific for Bacteria and Archaea. The standards have been developed in the context of the International Genomics Standards Consortium (GSC) community (Field et al., 2014) and can be viewed as amore » supplement to other GSC checklists including the Minimum Information about a Genome Sequence (MIGS), Minimum information about a Metagenomic Sequence(s) (MIMS) (Field et al., 2008) and Minimum Information about a Marker Gene Sequence (MIMARKS) (P. Yilmaz et al., 2011). Community-wide acceptance of MIxS-SCG and MIxS-GFM for Bacteria and Archaea will enable broad comparative analyses of genomes from the majority of taxa that remain uncultivated, improving our understanding of microbial function, ecology, and evolution.« less

Bacteriophage sensitivity patterns among bacteria isolated from marine waters

NASA Astrophysics Data System (ADS)

Moebus, K.; Nattkemper, H.

1981-09-01

Phage-host cross-reaction tests were performed with 774 bacterial strains and 298 bacteriophages. The bacteria (bacteriophages) were isolated at different times from water samples collected in the Atlantic Ocean between the European continental shelf and the Sargasso Sea: 733 (258) strains; in the North Sea near Helgoland: 31 (31) strains; and in the Bay of Biscay: 10 (9) strains. Of the Atlantic Ocean bacteria 326 were found to be susceptible to one or more Atlantic Ocean bacteriophage(s). The bacteriophage sensitivity patterns of these bacteria vary considerably, placing 225 of them in two large clusters of bacteriophage-host systems. Taking all into account, 250 of the 326 Atlantic Ocean bacteria are different from each other. This high degree of variation among the bacteria distinguishes microbial populations derived from widely separated eastern and western regions of the Atlantic Ocean. It also sets apart from each other the populations derived from samples collected at successive stations some 200 miles apart, although to a lesser degree. With bacterial populations found from samples collected on the way back and forth between Europe and the Sargasso Sea a gradual change was observed from "western" phage sensitivity patterns to "eastern" ones. Sixty-nine Atlantic Ocean bacteria are sensitive to bacteriophages isolated from the North Sea and the Bay of Biscay; of these only 26 strains are also susceptible to Atlantic Ocean phages. The interpretation of the results is based on the hydrographical conditions prevailing in the northern Atlantic Ocean including the North Sea, and on the assumption that the microbial populations investigated have undergone genetic changes while being transported within water masses from west to east.

Imaging of bacteria: is there any hope for the future based on past experience?

PubMed

Ebenhan, Thomas; Lazzeri, Elena; Gheysens, Olivier

2017-11-21

Infectious diseases remain a major health problem and cause of death worldwide. It is expected that the socio-economic impact will further intensify due to escalating resistance to antibiotics, an ageing population and an increase in the number of patients under immunosuppressive therapy and implanted medical devices. Even though radiolabeled probes and leukocytes are routinely used in clinical practice, it might still be difficult to distinguish sterile inflammation from inflammation caused by bacteria. Moreover, the majority of these probes are based on the attraction of leukocytes which may be hampered in neutropenic patients. Novel approaches that can be implemented in clinical practice and allow for swift diagnosis of infection by targeting the microorganism directly, are posing an attractive strategy. Here we review the current strategies to directly image bacteria using radionuclides and we provide an overview of the preclinical efforts to develop and validate new approaches. Indeed, significant progress has been made in the past years, but very few radiopharmaceuticals (that were promising in preclinical studies) have made it into clinical practice. We will discuss the challenges that remain to select good candidates for imaging agents targeting bacteria. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters.

PubMed

Dussud, C; Meistertzheim, A L; Conan, P; Pujo-Pay, M; George, M; Fabre, P; Coudane, J; Higgs, P; Elineau, A; Pedrotti, M L; Gorsky, G; Ghiglione, J F

2018-05-01

Plastic pollution is widespread in ocean ecosystems worldwide, but it is unknown if plastic offers a unique habitat for bacteria compared to communities in the water column and attached to naturally-occurring organic particles. The large set of samples taken during the Tara-Mediterranean expedition revealed for the first time a clear niche partitioning between free-living (FL), organic particle-attached (PA) and the recently introduced plastic marine debris (PMD). Bacterial counts in PMD presented higher cell enrichment factors than generally observed for PA fraction, when compared to FL bacteria in the surrounding waters. Taxonomic diversity was also higher in the PMD communities, where higher evenness indicated a favorable environment for a very large number of species. Cyanobacteria were particularly overrepresented in PMD, together with essential functions for biofilm formation and maturation. The community distinction between the three habitats was consistent across the large-scale sampling in the Western Mediterranean basin. 'Plastic specific bacteria' recovered only on the PMD represented half of the OTUs, thus forming a distinct habitat that should be further considered for understanding microbial biodiversity in changing marine ecosystems. Copyright © 2017. Published by Elsevier Ltd.

A Recombinant Horseshoe Crab Plasma Lectin Recognizes Specific Pathogen-Associated Molecular Patterns of Bacteria through Rhamnose

PubMed Central

Ng, Sim-Kun; Huang, Yu-Tsyr; Lee, Yuan-Chuan; Low, Ee-Ling; Chiu, Cheng-Hsun; Chen, Shiu-Ling; Mao, Liang-Chi; Chang, Margaret Dah-Tsyr

2014-01-01

Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens. PMID:25541995

Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria.

PubMed

Hwang, In Young; Koh, Elvin; Kim, Hye Rim; Yew, Wen Shan; Chang, Matthew Wook

2016-07-01

The discovery of antimicrobial drugs and their subsequent use has offered an effective treatment option for bacterial infections, reducing morbidity and mortality over the past 60 years. However, the indiscriminate use of antimicrobials in the clinical, community and agricultural settings has resulted in selection for multidrug-resistant bacteria, which has led to the prediction of possible re-entrance to the pre-antibiotic era. The situation is further exacerbated by significantly reduced antimicrobial drug discovery efforts by large pharmaceutical companies, resulting in a steady decline in the number of new antimicrobial agents brought to the market in the past several decades. Consequently, there is a pressing need for new antimicrobial therapies that can be readily designed and implemented. Recently, it has become clear that the administration of broad-spectrum antibiotics can lead to collateral damage to the human commensal microbiota, which plays several key roles in host health. Advances in genetic engineering have opened the possibility of reprogramming commensal bacteria that are in symbiotic existence throughout the human body to implement antimicrobial drugs with high versatility and efficacy against pathogenic bacteria. In this review, we discuss recent advances and potentialities of engineered bacteria in providing a novel antimicrobial strategy against antibiotic resistance. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Darwin and bacteria].

PubMed

Ledermann D, Walter

2009-02-01

As in 2009 the scientific world celebrates two hundreds years from the birthday of Charles Darwin and one hundred and fifty from the publication of The Origin of Species, an analysis of his complete work is performed, looking for any mention of bacteria. But it seems that the great naturahst never took knowledge about its existence, something rather improbable in a time when the discovery of bacteria shook the medical world, or he deliberately ignored them, not finding a place for such microscopic beings into his theory of evolution. But the bacteria badly affected his familiar life, killing scarlet fever one of his children and worsening to death the evolution of tuberculosis of his favourite Annie. Darwin himself could suffer the sickness of Chagas, whose etiological agent has a similar level to bacteria in the scale of evolution.

Acetate Utilization and Butyryl Coenzyme A (CoA):Acetate-CoA Transferase in Butyrate-Producing Bacteria from the Human Large Intestine

PubMed Central

Duncan, Sylvia H.; Barcenilla, Adela; Stewart, Colin S.; Pryde, Susan E.; Flint, Harry J.

2002-01-01

Seven strains of Roseburia sp., Faecalibacterium prausnitzii, and Coprococcus sp. from the human gut that produce high levels of butyric acid in vitro were studied with respect to key butyrate pathway enzymes and fermentation patterns. Strains of Roseburia sp. and F. prausnitzii possessed butyryl coenzyme A (CoA):acetate-CoA transferase and acetate kinase activities, but butyrate kinase activity was not detectable either in growing or in stationary-phase cultures. Although unable to use acetate as a sole source of energy, these strains showed net utilization of acetate during growth on glucose. In contrast, Coprococcus sp. strain L2-50 is a net producer of acetate and possessed detectable butyrate kinase, acetate kinase, and butyryl-CoA:acetate-CoA transferase activities. These results demonstrate that different functionally distinct groups of butyrate-producing bacteria are present in the human large intestine. PMID:12324374

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.

Chlor-alkali plant contamination of Aussa River sediments induced a large Hg-resistant bacterial community

NASA Astrophysics Data System (ADS)

Baldi, Franco; Marchetto, Davide; Gallo, Michele; Fani, Renato; Maida, Isabel; Covelli, Stefano; Fajon, Vesna; Zizek, Suzana; Hines, Mark; Horvat, Milena

2012-11-01

A closed chlor-alkali plant (CAP) discharged Hg for decades into the Aussa River, which flows into Marano Lagoon, resulting in the large-scale pollution of the lagoon. In order to get information on the role of bacteria as mercury detoxifying agents, analyses of anions in the superficial part (0-1 cm) of sediments were conducted at four stations in the Aussa River. In addition, measurements of biopolymeric carbon (BPC) as a sum of the carbon equivalent of proteins (PRT), lipids (LIP), and carbohydrates (CHO) were performed to correlate with bacterial biomass such as the number of aerobic heterotrophic cultivable bacteria and their percentage of Hg-resistant bacteria. All these parameters were used to assess the bioavailable Hg fraction in sediments and the potential detoxification activity of bacteria. In addition, fifteen isolates were characterized by a combination of molecular techniques, which permitted their assignment into six different genera. Four out of fifteen were Gram negative with two strains of Stenotrophomonas maltophilia, one Enterobacter sp., and one strain of Brevibacterium frigoritolerans. The remaining strains (11) were Gram positive belonging to the genera Bacillus and Staphylococcus. We found merA genes in only a few isolates. Mercury volatilization from added HgCl2 and the presence of plasmids with the merA gene were also used to confirm Hg reductase activity. We found the highest number of aerobic heterotrophic Hg-resistant bacteria (one order magnitude higher) and the highest number of Hg-resistant species (11 species out of 15) at the confluence of the River Aussa and Banduzzi's channel, which transport Hg from the CAP, suggesting that Hg is strongly detoxified [reduced to Hg(0)] at this location.

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

Bacteria associated with Amblyomma cajennense tick eggs

PubMed Central

Machado-Ferreira, Erik; Vizzoni, Vinicius Figueiredo; Piesman, Joseph; Gazeta, Gilberto Salles; Soares, Carlos Augusto Gomes

2015-01-01

Abstract Ticks represent a large group of pathogen vectors that blood feed on a diversity of hosts. In the Americas, the Ixodidae ticks Amblyomma cajennense are responsible for severe impact on livestock and public health. In the present work, we present the isolation and molecular identification of a group of culturable bacteria associated with A. cajennense eggs from females sampled in distinct geographical sites in southeastern Brazil. Additional comparative analysis of the culturable bacteria from Anocentor nitens, Rhipicephalus sanguineus and Ixodes scapularis tick eggs were also performed. 16S rRNA gene sequence analyses identified 17 different bacterial types identified as Serratia marcescens, Stenotrophomonas maltophilia, Pseudomonas fluorescens, Enterobacter spp., Micrococcus luteus, Ochrobactrum anthropi, Bacillus cereus and Staphylococcus spp., distributed in 12 phylogroups. Staphylococcus spp., especially S. sciuri, was the most prevalent bacteria associated with A. cajennense eggs, occurring in 65% of the samples and also frequently observed infecting A. nitens eggs. S. maltophilia, S. marcescens and B. cereus occurred infecting eggs derived from specific sampling sites, but in all cases rising almost as pure cultures from infected A. cajennense eggs. The potential role of these bacterial associations is discussed and they possibly represent new targets for biological control strategies of ticks and tick borne diseases. PMID:26537602

Sialidases from gut bacteria: a mini-review.

PubMed

Juge, Nathalie; Tailford, Louise; Owen, C David

2016-02-01

Sialidases are a large group of enzymes, the majority of which catalyses the cleavage of terminal sialic acids from complex carbohydrates on glycoproteins or glycolipids. In the gastrointestinal (GI) tract, sialic acid residues are mostly found in terminal location of mucins via α2-3/6 glycosidic linkages. Many enteric commensal and pathogenic bacteria can utilize sialic acids as a nutrient source, but not all express the sialidases that are required to release free sialic acid. Sialidases encoded by gut bacteria vary in terms of their substrate specificity and their enzymatic reaction. Most are hydrolytic sialidases, which release free sialic acid from sialylated substrates. However, there are also examples with transglycosylation activities. Recently, a third class of sialidases, intramolecular trans-sialidase (IT-sialidase), has been discovered in gut microbiota, releasing (2,7-anhydro-Neu5Ac) 2,7-anydro-N-acetylneuraminic acid instead of sialic acid. Reaction specificity varies, with hydrolytic sialidases demonstrating broad activity against α2,3-, α2,6- and α2,8-linked substrates, whereas IT-sialidases tend to be specific for α2,3-linked substrates. In this mini-review, we summarize the current knowledge on the structural and biochemical properties of sialidases involved in the interaction between gut bacteria and epithelial surfaces. © 2016 Authors.

Bleach vs. Bacteria

MedlinePlus

... Inside Life Science > Bleach vs. Bacteria Inside Life Science View All Articles | Inside Life Science Home Page Bleach vs. Bacteria By Sharon Reynolds ... For Proteins, Form Shapes Function This Inside Life Science article also appears on LiveScience . Learn about related ...

Ocean acidification impacts bacteria-phytoplankton coupling at low-nutrient conditions

NASA Astrophysics Data System (ADS)

Hornick, Thomas; Bach, Lennart T.; Crawfurd, Katharine J.; Spilling, Kristian; Achterberg, Eric P.; Woodhouse, Jason N.; Schulz, Kai G.; Brussaard, Corina P. D.; Riebesell, Ulf; Grossart, Hans-Peter

2017-01-01

The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm ( ˜ 55 m3) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO2) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO2-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO2 treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO2 as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO2 impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

PubMed Central

Kozlowski, Jessica A; Stieglmeier, Michaela; Schleper, Christa; Klotz, Martin G; Stein, Lisa Y

2016-01-01

Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76T exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196T. In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions. PMID:26882267

Phototargeting oral black-pigmented bacteria.

PubMed

Soukos, Nikolaos S; Som, Sovanda; Abernethy, Abraham D; Ruggiero, Karriann; Dunham, Joshua; Lee, Chul; Doukas, Apostolos G; Goodson, J Max

2005-04-01

We have found that broadband light (380 to 520 nm) rapidly and selectively kills oral black-pigmented bacteria (BPB) in pure cultures and in dental plaque samples obtained from human subjects with chronic periodontitis. We hypothesize that this killing effect is a result of light excitation of their endogenous porphyrins. Cultures of Prevotella intermedia and P. nigrescens were killed by 4.2 J/cm2, whereas P. melaninogenica required 21 J/cm2. Exposure to light with a fluence of 42 J/cm2 produced 99% killing of P. gingivalis. High-performance liquid chromatography demonstrated the presence of various amounts of different porphyrin molecules in BPB. The amounts of endogenous porphyrin in BPB were 267 (P. intermedia), 47 (P. nigrescens), 41 (P. melaninogenica), and 2.2 (P. gingivalis) ng/mg. Analysis of bacteria in dental plaque samples by DNA-DNA hybridization for 40 taxa before and after phototherapy showed that the growth of the four BPB was decreased by 2 and 3 times after irradiation at energy fluences of 4.2 and 21 J/cm2, respectively, whereas the growth of the remaining 36 microorganisms was decreased by 1.5 times at both energy fluences. The present study suggests that intraoral light exposure may be used to control BPB growth and possibly benefit patients with periodontal disease.

Phototargeting Oral Black-Pigmented Bacteria

PubMed Central

Soukos, Nikolaos S.; Som, Sovanda; Abernethy, Abraham D.; Ruggiero, Karriann; Dunham, Joshua; Lee, Chul; Doukas, Apostolos G.; Goodson, J. Max

2005-01-01

We have found that broadband light (380 to 520 nm) rapidly and selectively kills oral black-pigmented bacteria (BPB) in pure cultures and in dental plaque samples obtained from human subjects with chronic periodontitis. We hypothesize that this killing effect is a result of light excitation of their endogenous porphyrins. Cultures of Prevotella intermedia and P. nigrescens were killed by 4.2 J/cm2, whereas P. melaninogenica required 21 J/cm2. Exposure to light with a fluence of 42 J/cm2 produced 99% killing of P. gingivalis. High-performance liquid chromatography demonstrated the presence of various amounts of different porphyrin molecules in BPB. The amounts of endogenous porphyrin in BPB were 267 (P. intermedia), 47 (P. nigrescens), 41 (P. melaninogenica), and 2.2 (P. gingivalis) ng/mg. Analysis of bacteria in dental plaque samples by DNA-DNA hybridization for 40 taxa before and after phototherapy showed that the growth of the four BPB was decreased by 2 and 3 times after irradiation at energy fluences of 4.2 and 21 J/cm2, respectively, whereas the growth of the remaining 36 microorganisms was decreased by 1.5 times at both energy fluences. The present study suggests that intraoral light exposure may be used to control BPB growth and possibly benefit patients with periodontal disease. PMID:15793117

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR

PubMed Central

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-01

AIM: To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. METHODS: Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. RESULTS: cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. CONCLUSION: The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well. PMID:22294830

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR.

PubMed

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-21

To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well.

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.

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

Marine Protists Are Not Just Big Bacteria.

PubMed

Keeling, Patrick J; Campo, Javier Del

2017-06-05

The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

Changes in Bacteria Induce Inflammatory Skin Diseases | Center for Cancer Research

Cancer.gov

Atopic dermatitis (AD) is a chronic inflammatory skin disease that manifests as dry skin with a relentless itch and eczema. AD is considered an allergic disease in which the skin inflammation manifests in response to chronic exposure to contact allergens. However, identification of a responsible allergen is uncommon. Meanwhile, analyses have demonstrated that the surface of the human body is colonized by large numbers of diverse bacteria. This observation has led researchers to examine the roles these bacteria play in healthy and diseased skin. In a variety of genetic and chronic inflammatory skin diseases, including in patients with AD or with cancer who receive epidermal growth factor receptor (EGFR) inhibitors, Staphylococcus aureus and Corynebacterium species are the predominant bacteria isolated from the skin. However, the cause-and-effect relationship between this microbial imbalance and skin inflammation has not been determined.

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

Evolved to fail: Bacteria induce flagellar buckling to reorient

NASA Astrophysics Data System (ADS)

Son, Kwangmin; Guasto, Jeffrey S.; Stocker, Roman

2012-11-01

Many marine bacteria swim with a single helical flagellum connected to a rotary motor via a 100 nm long universal joint called the ``hook.'' While these bacteria have seemingly just one degree of freedom, allowing them to swim only back and forth, they in fact exhibit large angular reorientations mediated by off-axis ``flicks'' of their flagellum. High-speed video microscopy revealed the mechanism underpinning this turning behavior: the buckling of the hook during the exceedingly brief (10 ms) forward run that follows a reversal. Direct measurements of the hook's mechanical properties corroborated this result, as the hook's structural stability is governed by the Sperm number, which compares the compressive load from propulsion to the elastic restoring force of the hook. Upon decreasing the Sperm number below a critical value by reducing the swimming speed, the frequency of flicks diminishes sharply, consistent with the criticality of buckling. This elegant, under-actuated turning mechanism appears widespread among marine bacteria and may provide a novel design concept in micro-robotics.

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach

PubMed Central

2012-01-01

Background Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data. PMID:22759462

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach.

PubMed

Ratkovic, Zorana; Golik, Wiktoria; Warnier, Pierre

2012-06-26

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

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

Diversity of Both the Cultivable Protease-Producing Bacteria and Bacterial Extracellular Proteases in the Coastal Sediments of King George Island, Antarctica

PubMed Central

Zhou, Ming-Yang; Wang, Guang-Long; Li, Dan; Zhao, Dian-Li; Qin, Qi-Long; Chen, Xiu-Lan; Chen, Bo; Zhou, Bai-Cheng; Zhang, Xi-Ying; Zhang, Yu-Zhong

2013-01-01

Protease-producing bacteria play a vital role in degrading sedimentary organic nitrogen. However, the diversity of these bacteria and their extracellular proteases in most regions remain unknown. In this paper, the diversity of the cultivable protease-producing bacteria and of bacterial extracellular proteases in the sediments of Maxwell Bay, King George Island, Antarctica was investigated. The cultivable protease-producing bacteria reached 105 cells/g in all 8 sediment samples. The cultivated protease-producing bacteria were mainly affiliated with the phyla Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, and the predominant genera were Bacillus (22.9%), Flavobacterium (21.0%) and Lacinutrix (16.2%). Among these strains, Pseudoalteromonas and Flavobacteria showed relatively high protease production. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria were serine proteases or metalloproteases. These results begin to address the diversity of protease-producing bacteria and bacterial extracellular proteases in the sediments of the Antarctic Sea. PMID:24223990

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

NASA Astrophysics Data System (ADS)

Pachiadaki, Maria G.; Sintes, Eva; Bergauer, Kristin; Brown, Julia M.; Record, Nicholas R.; Swan, Brandon K.; Mathyer, Mary Elizabeth; Hallam, Steven J.; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J.; Stepanauskas, Ramunas

2017-11-01

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean’s interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.

Meat, dairy and plant proteins alter bacterial composition of rat gut bacteria.

PubMed

Zhu, Yingying; Lin, Xisha; Zhao, Fan; Shi, Xuebin; Li, He; Li, Yingqiu; Zhu, Weiyun; Xu, Xinglian; Li, Chunbao; Lu, Chunbao; Zhou, Guanghong

2015-10-14

Long-term consumption of red meat has been considered a potential risk to gut health, but this is based on clinic investigations, excessive intake of fat, heme and some injurious compounds formed during cooking or additions to processed meat products. Whether intake of red meat protein affects gut bacteria and the health of the host remains unclear. In this work, we compared the composition of gut bacteria in the caecum, by sequencing the V4-V5 region of 16S ribosomal RNA gene, obtained from rats fed with proteins from red meat (beef and pork), white meat (chicken and fish) and other sources (casein and soy). The results showed significant differences in profiles of gut bacteria between the six diet groups. Rats fed with meat proteins had a similar overall structure of caecal bacterial communities separated from those fed non-meat proteins. The beneficial genus Lactobacillus was higher in the white meat than in the red meat or non-meat protein groups. Also, rats fed with meat proteins and casein had significantly lower levels of lipopolysaccharide-binding proteins, suggesting that the intake of meat proteins may maintain a more balanced composition of gut bacteria, thereby reducing the antigen load and inflammatory response in the host.

Changing epidemiology of infections due to extended spectrum beta-lactamase producing bacteria

PubMed Central

2014-01-01

Background Community-associated infections caused by extended-spectrum beta-lactamase (ESBL) producing bacteria are a growing concern. Methods Retrospective cohort study of clinical infections due to ESBL-producing bacteria requiring admission from 2006-2011 at a tertiary care academic medical center in Providence, RI. Results A total of 321 infections due to ESBL-producing bacteria occurred during the study period. Fifty-eight cases (18%) were community-acquired, 170 (53%) were healthcare–associated, and 93 (29%) were hospital-acquired. The incidence of ESBL infections per 10,000 discharges increased during the study period for both healthcare-associated infections, 1.9 per year (95% CI 1-2.8), and for community-acquired infections, 0.85 per year (95% CI 0.3-1.4) but the rate remained unchanged for hospital-acquired infections. For ESBL-producing E. coli isolates, resistance to both ciprofloxacin and trimethoprim-sulfamethoxazole was 95% and 65%, respectively but 94% of isolates were susceptible to nitrofurantoin. Conclusions Community-acquired and healthcare-associated infections due to ESBL-producing bacteria are increasing in our community, particularly urinary tract infections due to ESBL-producing E. coli. Most isolates are resistant to oral antibiotics commonly used to treat urinary tract infections. Thus, our findings have important implications for outpatient management of such infections. PMID:24666610

Meat, dairy and plant proteins alter bacterial composition of rat gut bacteria

PubMed Central

Zhu, Yingying; Lin, Xisha; Zhao, Fan; Shi, Xuebin; Li, He; Li, Yingqiu; Zhu, Weiyun; Xu, Xinglian; Lu, Chunbao; Zhou, Guanghong

2015-01-01

Long-term consumption of red meat has been considered a potential risk to gut health, but this is based on clinic investigations, excessive intake of fat, heme and some injurious compounds formed during cooking or additions to processed meat products. Whether intake of red meat protein affects gut bacteria and the health of the host remains unclear. In this work, we compared the composition of gut bacteria in the caecum, by sequencing the V4-V5 region of 16S ribosomal RNA gene, obtained from rats fed with proteins from red meat (beef and pork), white meat (chicken and fish) and other sources (casein and soy). The results showed significant differences in profiles of gut bacteria between the six diet groups. Rats fed with meat proteins had a similar overall structure of caecal bacterial communities separated from those fed non-meat proteins. The beneficial genus Lactobacillus was higher in the white meat than in the red meat or non-meat protein groups. Also, rats fed with meat proteins and casein had significantly lower levels of lipopolysaccharide-binding proteins, suggesting that the intake of meat proteins may maintain a more balanced composition of gut bacteria, thereby reducing the antigen load and inflammatory response in the host. PMID:26463271

Single-Cell Force Spectroscopy of Probiotic Bacteria

PubMed Central

Beaussart, Audrey; El-Kirat-Chatel, Sofiane; Herman, Philippe; Alsteens, David; Mahillon, Jacques; Hols, Pascal; Dufrêne, Yves F.

2013-01-01

Single-cell force spectroscopy is a powerful atomic force microscopy modality in which a single living cell is attached to the atomic force microscopy cantilever to quantify the forces that drive cell-cell and cell-substrate interactions. Although various single-cell force spectroscopy protocols are well established for animal cells, application of the method to individual bacterial cells remains challenging, mainly owing to the lack of appropriate methods for the controlled attachment of single live cells on cantilevers. We present a nondestructive protocol for single-bacterial cell force spectroscopy, which combines the use of colloidal probe cantilevers and of a bioinspired polydopamine wet adhesive. Living cells from the probiotic species Lactobacillus plantarum are picked up with a polydopamine-coated colloidal probe, enabling us to quantify the adhesion forces between single bacteria and biotic (lectin monolayer) or abiotic (hydrophobic monolayer) surfaces. These minimally invasive single-cell experiments provide novel, to our knowledge, insight into the specific and nonspecific forces driving the adhesion of L. plantarum, and represent a generic platform for studying the molecular mechanisms of cell adhesion in probiotic and pathogenic bacteria. PMID:23663831

Manganese Oxidizing Bacteria in Guaymas Basin Hydrothermal Fluids, Sediments, and Plumes

NASA Astrophysics Data System (ADS)

Dick, G. J.; Tebo, B. M.

2002-12-01

The active seafloor hydrothermal system at Guaymas Basin in the Gulf of California is unique in that spreading centers are covered with thick sediments, and hydrothermal fluids are injected into a semi-enclosed basin. This hydrothermal activity is the source of a large input of dissolved manganese [Mn(II)] into Guaymas Basin, and the presence of a large standing stock of particulate manganese in this basin has been taken as evidence for a short residence time of dissolved Mn(II) with respect to oxidation, suggestive of bacterial catalysis. During a recent Atlantis/Alvin expedition (R/V Atlantis Cruise #7, Leg 11, Jim Cowen Chief Scientist), large amounts of particulate manganese oxides were again observed in Guaymas Basin hydrothermal plumes. The goal of the work presented here was to identify bacteria involved in the oxidation of Mn(II) in Guaymas Basin, and to determine what molecular mechanisms drive this process. Culture-based methods were employed to isolate Mn(II)-oxidizing bacteria from Guaymas Basin hydrothermal fluids, sediments, and plumes, and numerous Mn(II)-oxidizing bacteria were identified based on the formation of orange, brown, or black manganese oxides on bacterial colonies on agar plates. The Mn(II)-oxidizing bacteria were able to grow at temperatures from 12 to 50°C, and a selection of the isolates were chosen for phylogenetic (16S rRNA genes) and microscopic characterization. Endospore-forming Bacillus species accounted for many of the Mn(II)-oxidizing isolates obtained from both hydrothermal sediments and plumes, while members of the alpha- and gamma-proteobacteria were also found. Mn(II)-oxidizing enzymes from previously characterized Bacillus spores are known to be active at temperatures greater than 50°C. The presence of Mn(II)-oxidizing spores - some of which are capable of growing at elevated temperatures - in hydrothermal fluids and sediments at Guaymas Basin suggests that Mn(II) oxidation may be occurring immediately or very soon

A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

PubMed Central

Hulcr, Jiri; Latimer, Andrew M.; Henley, Jessica B.; Rountree, Nina R.; Fierer, Noah; Lucky, Andrea; Lowman, Margaret D.; Dunn, Robert R.

2012-01-01

The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (∼1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons. PMID:23144827

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources.

PubMed

Mika, K B; Imamura, G; Chang, C; Conway, V; Fernandez, G; Griffith, J F; Kampalath, R A; Lee, C M; Lin, C-C; Moreno, R; Thompson, S; Whitman, R L; Jay, J A

2009-07-01

Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills. Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0.23 and -1.02 per day, and for enterococci between -0.5 and -1.0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall. Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels. Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent.

Bacteria as Emerging Indicators of Soil Condition

PubMed Central

Hermans, Syrie M.; Buckley, Hannah L.; Case, Bradley S.; Curran-Cournane, Fiona; Taylor, Matthew

2016-01-01

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial

Bacteria as Emerging Indicators of Soil Condition.

PubMed

Hermans, Syrie M; Buckley, Hannah L; Case, Bradley S; Curran-Cournane, Fiona; Taylor, Matthew; Lear, Gavin

2017-01-01

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and

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.

Study on immobilization of marine oil-degrading bacteria by carrier of algae materials.

PubMed

Zhang, Yiran; Gao, Wei; Lin, Faxiang; Han, Bin; He, Changfei; Li, Qian; Gao, Xiangxing; Cui, Zhisong; Sun, Chengjun; Zheng, Li

2018-05-18

This study investigated the immobilizations with of bacteria two kinds of algal materials, Enteromorpha residue and kelp residue. The lipophilicity of them were compared by diesel absorption rates. The immobilization efficiency of Bacillus sp. E3 was measured to evaluate whether these carriers would satisfy the requirement for biodegradation of oil spills. The bacteria were immobilized through adsorption with the sterilized and non-sterilized carriers to compare the differences between the two treatments. Oil degradation rates were determined using gravimetric and GC-MS methods. Results showed the absorption rates of Enteromorpha residue and kelp residue for diesel were 411 and 273% respectively and remained approximately 105 and 120% after 2 h of erosion in simulated seawater system. After immobilized of Bacillus sp. E3, the oil degradation rates of them were higher than 65% after 21 days biodegradations. GC-MS analysis showed that two immobilizations degraded higher than 70% of the total alkane and the total PAHs, whereas the free bacteria degraded 63% of the total alkane and 66% the total PAHs. And the bacteria immobilized with the carriers degraded more HMW-alkanes and HMW-PAHs than the free bacteria. The bacteria immobilized by non-sterilized kelp residue showed a considerably higher degradation rate than that using sterilized kelp residue. A considerably higher cells absorption rate of immobilization was obtained when using kelp residue, and the preparation of immobilization was low cost and highly efficient. The experiments show the two algae materials, especially the kelp residue, present potential application in bioremediation of marine oil spills.

Gut bacteria mediate aggregation in the German cockroach

PubMed Central

Wada-Katsumata, Ayako; Zurek, Ludek; Nalyanya, Godfrey; Roelofs, Wendell L.; Zhang, Aijun; Schal, Coby

2015-01-01

Aggregation of the German cockroach, Blattella germanica, is regulated by fecal aggregation agents (pheromones), including volatile carboxylic acids (VCAs). We demonstrate that the gut microbial community contributes to production of these semiochemicals. Chemical analysis of the fecal extract of B. germanica revealed 40 VCAs. Feces from axenic cockroaches (no microorganisms in the alimentary tract) lacked 12 major fecal VCAs, and 24 of the remaining compounds were represented at extremely low amounts. Olfactory and aggregation bioassays demonstrated that nymphs strongly preferred the extract of control feces over the fecal extract of axenic cockroaches. Additionally, nymphs preferred a synthetic blend of 6 fecal VCAs over a solvent control or a previously identified VCA blend. To test whether gut bacteria contribute to the production of fecal aggregation agents, fecal aerobic bacteria were cultured, isolated, and identified. Inoculation of axenic cockroaches with individual bacterial taxa significantly rescued the aggregation response to the fecal extract, and inoculation with a mix of six bacterial isolates was more effective than with single isolates. The results indicate that the commensal gut microbiota contributes to production of VCAs that act as fecal aggregation agents and that cockroaches discriminate among the complex odors that emanate from a diverse microbial community. Our results highlight the pivotal role of gut bacteria in mediating insect–insect communication. Moreover, because the gut microbial community reflects the local environment, local plasticity in fecal aggregation pheromones enables colony-specific odors and fidelity to persistent aggregation sites. PMID:26644557

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks.

PubMed

Amanidaz, Nazak; Zafarzadeh, Ali; Mahvi, Amir Hossein

2015-12-01

This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms.

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks

PubMed Central

AMANIDAZ, Nazak; ZAFARZADEH, Ali; MAHVI, Amir Hossein

2015-01-01

Background: This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. Methods: This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. Results: In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Conclusion: Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms. PMID:26811820

Enhanced Retention of Chemotactic Bacteria in a Pore Network with Residual NAPL Contamination

NASA Astrophysics Data System (ADS)

Ford, R.; Wang, X.

2013-12-01

Nonaqueous phase liquid (NAPL) contaminants are difficult to eliminate from natural aquifers due, in part, to the heterogeneous structure of the soil matrix. Residual NAPL ganglia remain trapped in regions where the hydraulic conductivity is relatively low. Bioremediation processes depend on adequate mixing of microbial populations and the groundwater contaminants that they degrade. The ability of bacteria to sense a chemical gradient and swim preferentially toward locations of higher concentration, known as chemotaxis, can enhance the mixing of bacteria with contaminant sources that may not be readily accessible by advection and dispersion alone. The impact of chemotaxis on bacterial abundance within a low conductivity NAPL-contaminated region of a well-characterized porous matrix was investigated. A microfluidic device was designed to mimic heterogeneous features of a contaminated groundwater system. NAPL ganglia (toluene) were trapped within a fine pore network, and bacteria were injected into the system through a highly conductive adjacent channel. Chemotactic bacteria (P. putida F1) migrated preferentially towards and accumulated in the vicinity of NAPL contaminant sources. The accumulation of chemotactic bacteria was 15% greater in comparison to a nonchemotactic mutant (P. putida F1 CheA). Bacteria in the microfluidic device were subjected to different flow velocities from 0.25 to 5 m/d encompassing the range of typical groundwater flow rates. Chemotactic bacteria exhibited greater accumulation near the intersection between the macrochannel and the porous network at a flow velocity of 0.5 m/d than both the nonchemotactic mutant control and the chemotactic bacteria at a higher flow velocity of 5 m/d. Breakthrough curves observed at the outlet provided indirect evidence that chemotactic bacteria were retained within the contaminated low permeable region for a longer time than the nonchemotactic bacteria at a flow velocity of 0.25 m/d. This retention was

Pilot study of using UAV to reveal spatial patterns of indicator bacteria concentrations in ponds and reservoirs used for irrigation

USDA-ARS?s Scientific Manuscript database

Determination of indicator bacteria concentrations in irrigation water recently became mandatory for farmers. These concentrations are known to have large spatial variability in ponds and reservoirs. This variability is partially attributed to affinity of indicator bacteria to algae accumulations. W...

Raman microspectrometer combined with scattering microscopy and lensless imaging for bacteria identification

NASA Astrophysics Data System (ADS)

Strola, S. A.; Schultz, E.; Allier, C. P.; DesRoches, B.; Lemmonier, J.; Dinten, J.-M.

2013-03-01

In this paper, we report on a compact prototype capable both of lensfree imaging, Raman spectrometry and scattering microscopy from bacteria samples. This instrument allows high-throughput real-time characterization without the need of markers, making it potentially suitable to field label-free biomedical and environmental applications. Samples are illuminated from above with a focused-collimated 532nm laser beam and can be x-y-z scanned. The bacteria detection is based on emerging lensfree imaging technology able to localize cells of interest over a large field-of-view of 24mm2. Raman signal and scattered light are then collected by separate measurement arms simultaneously. In the first arm the emission light is fed by a fiber into a prototype spectrometer, developed by Tornado Spectral System based on Tornado's High Throughput Virtual Slit (HTVS) novel technology. The enhanced light throughput in the spectral region of interest (500-1800 cm-1) reduces Raman acquisition time down to few seconds, thus facilitating experimental protocols and avoiding the bacteria deterioration induced by laser thermal heating. Scattered light impinging in the second arm is collected onto a charge-coupled-device. The reconstructed image allows studying the single bacteria diffraction pattern and their specific structural features. The characterization and identification of different bacteria have been performed to validate and optimize the acquisition system and the component setup. The results obtained demonstrate the benefits of these three techniques combination by providing the precise bacteria localization, their chemical composition and a morphology description. The procedure for a rapid identification of particular pathogen bacteria in a sample is illustrated.

By their genes ye shall know them: genomic signatures of predatory bacteria

PubMed Central

Pasternak, Zohar; Pietrokovski, Shmuel; Rotem, Or; Gophna, Uri; Lurie-Weinberger, Mor N; Jurkevitch, Edouard

2013-01-01

Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria. PMID:23190728

Bacteria-surface interactions.

PubMed

Tuson, Hannah H; Weibel, Douglas B

2013-05-14

The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field.

Genomics of Probiotic Bacteria

NASA Astrophysics Data System (ADS)

O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

Probiotic bacteria affect the composition of salivary pellicle and streptococcal adhesion in vitro.

PubMed

Haukioja, A; Loimaranta, V; Tenovuo, J

2008-08-01

The use of probiotic bacteria is increasing worldwide and at least some of them can transiently colonize the oral cavity. Several studies have shown that probiotic bacteria, which are often thought of in relation only to intestinal health, can also affect the oral ecology, but the mechanisms for this are largely unknown. The aim of this study was to investigate in vitro if the probiotic bacteria used in commercial products affect the protein composition of the salivary pellicle and the adherence of other oral bacteria. Salivary pellicle on hydroxyapatite and the adhesion of two oral streptococci, Streptococcus mutans and Streptococcus gordonii, were used as a model. Probiotic bacteria that bound to saliva-coated hydroxyapatite reduced the adhesion of S. mutans but the inhibitory effect on the adherence of S. gordonii was weaker. Salivary pellicle protein composition was modified by all the strains tested. The modifications in the pellicle affected the adherence of S. mutans but not of S. gordonii. Two of the proteins missing from the pellicles made of saliva-treated with the probiotic bacteria were identified as salivary agglutinin gp340 and salivary peroxidase. All bacterial strains bound salivary agglutinin gp340. The ability of the probiotic bacteria to degrade peroxidase was demonstrated with purified bovine lactoperoxidase and two of the probiotic strains. This in vitro study showed that probiotic strains used in commercial products may affect the oral ecology by specifically preventing the adherence of other bacteria and by modifying the protein composition of the salivary pellicle.

Biotechnology of Anoxygenic Phototrophic Bacteria.

PubMed

Frigaard, Niels-Ulrik

Anoxygenic phototrophic bacteria are a diverse collection of organisms that are defined by their ability to grow using energy from light without evolving oxygen. The dominant groups are purple sulfur bacteria, purple nonsulfur bacteria, green sulfur bacteria, and green and red filamentous anoxygenic phototrophic bacteria. They represent several bacterial phyla but they all have bacteriochlorophylls and carotenoids and photochemical reaction centers which generate ATP and cellular reductants used for CO 2 fixation. They typically have an anaerobic lifestyle in the light, although some grow aerobically in the dark. Some of them oxidize inorganic sulfur compounds for light-dependent CO 2 fixation; this ability can be exploited for photobiological removal of hydrogen sulfide from wastewater and biogas. The anoxygenic phototrophic bacteria also perform bioremediation of recalcitrant dyes, pesticides, and heavy metals under anaerobic conditions. Finally, these organisms may be useful for overexpression of membrane proteins and photobiological production of H 2 and other valuable compounds.

Resistance of Bacteria to Biocides.

PubMed

Maillard, Jean-Yves

2018-04-01

Biocides and formulated biocides are used worldwide for an increasing number of applications despite tightening regulations in Europe and in the United States. One concern is that such intense usage of biocides could lead to increased bacterial resistance to a product and cross-resistance to unrelated antimicrobials including chemotherapeutic antibiotics. Evidence to justify such a concern comes mostly from the use of health care-relevant bacterial isolates, although the number of studies of the resistance characteristics of veterinary isolates to biocides have increased the past few years. One problem remains the definition of "resistance" and how to measure resistance to a biocide. This has yet to be addressed globally, although the measurement of resistance is becoming more pressing, with regulators both in Europe and in the United States demanding that manufacturers provide evidence that their biocidal products will not impact on bacterial resistance. Alongside in vitro evidence of potential antimicrobial cross-resistance following biocide exposure, our understanding of the mechanisms of bacterial resistance and, more recently, our understanding of the effect of biocides to induce a mechanism(s) of resistance in bacteria has improved. This article aims to provide an understanding of the development of antimicrobial resistance in bacteria following a biocide exposure. The sections provide evidence of the occurrence of bacterial resistance and its mechanisms of action and debate how to measure bacterial resistance to biocides. Examples pertinent to the veterinary field are used where appropriate.

Viable bacteria associated with red blood cells and plasma in freshly drawn blood donations.

PubMed

Damgaard, Christian; Magnussen, Karin; Enevold, Christian; Nilsson, Martin; Tolker-Nielsen, Tim; Holmstrup, Palle; Nielsen, Claus Henrik

2015-01-01

Infection remains a leading cause of post-transfusion mortality and morbidity. Bacterial contamination is, however, detected in less than 0.1% of blood units tested. The aim of the study was to identify viable bacteria in standard blood-pack units, with particular focus on bacteria from the oral cavity, and to determine the distribution of bacteria revealed in plasma and in the red blood cell (RBC)-fraction. Cross-sectional study. Blood were separated into plasma and RBC-suspensions, which were incubated anaerobically or aerobically for 7 days on trypticase soy blood agar (TSA) or blue lactose plates. For identification colony PCR was performed using primers targeting 16S rDNA. Blood donors attending Capital Region Blood Bank, Copenhagen University Hospital, Rigshospitalet, Hvidovre, Denmark, October 29th to December 10th 2013. 60 donors (≥50 years old), self-reported medically healthy. Bacterial growth was observed on plates inoculated with plasma or RBCs from 62% of the blood donations. Growth was evident in 21 (35%) of 60 RBC-fractions and in 32 (53%) of 60 plasma-fractions versus 8 of 60 negative controls (p = 0.005 and p = 2.6x10-6, respectively). Propionibacterium acnes was found in 23% of the donations, and Staphylococcus epidermidis in 38%. The majority of bacteria identified in the present study were either facultative anaerobic (59.5%) or anaerobic (27.8%) species, which are not likely to be detected during current routine screening. Viable bacteria are present in blood from donors self-reported as medically healthy, indicating that conventional test systems employed by blood banks insufficiently detect bacteria in plasma. Further investigation is needed to determine whether routine testing for anaerobic bacteria and testing of RBC-fractions for adherent bacteria should be recommended.

Characterization of airborne ice-nucleation-active bacteria and bacterial fragments

NASA Astrophysics Data System (ADS)

Šantl-Temkiv, Tina; Sahyoun, Maher; Finster, Kai; Hartmann, Susan; Augustin-Bauditz, Stefanie; Stratmann, Frank; Wex, Heike; Clauss, Tina; Nielsen, Niels Woetmann; Sørensen, Jens Havskov; Korsholm, Ulrik Smith; Wick, Lukas Y.; Karlson, Ulrich Gosewinkel

2015-05-01

Some bacteria have the unique capacity of synthesising ice-nucleation-active (INA) proteins and exposing them at their outer membrane surface. As INA bacteria enter the atmosphere, they may impact the formation of clouds and precipitation. We studied members of airborne bacterial communities for their capacity to catalyse ice formation and we report on the excretion of INA proteins by airborne Pseudomonas sp. We also observed for the first time that INA biological fragments <220 nm were present in precipitation samples (199 and 482 INA fragments per L of precipitation), which confirms the presence of submicron INA biological fragments in the atmosphere. During 14 precipitation events, strains affiliated with the genus Pseudomonas, which are known to carry ina genes, were dominant. A screening for INA properties revealed that ∼12% of the cultivable bacteria caused ice formation at ≤-7 °C. They had likely been emitted to the atmosphere from terrestrial surfaces, e.g. by convective transport. We tested the ability of isolated INA strains to produce outer membrane vesicles and found that two isolates could do so. However, only very few INA vesicles were released per INA cell. Thus, the source of the submicron INA proteinaceous particles that we detected in the atmosphere remains to be elucidated.

Membrane-active macromolecules kill antibiotic-tolerant bacteria and potentiate antibiotics towards Gram-negative bacteria

PubMed Central

Uppu, Divakara S. S. M.; Konai, Mohini M.; Sarkar, Paramita; Samaddar, Sandip; Fensterseifer, Isabel C. M.; Farias-Junior, Celio; Krishnamoorthy, Paramanandam; Shome, Bibek R.; Franco, Octávio L.

2017-01-01

Chronic bacterial biofilms place a massive burden on healthcare due to the presence of antibiotic-tolerant dormant bacteria. Some of the conventional antibiotics such as erythromycin, vancomycin, linezolid, rifampicin etc. are inherently ineffective against Gram-negative bacteria, particularly in their biofilms. Here, we report membrane-active macromolecules that kill slow dividing stationary-phase and antibiotic tolerant cells of Gram-negative bacteria. More importantly, these molecules potentiate antibiotics (erythromycin and rifampicin) to biofilms of Gram-negative bacteria. These molecules eliminate planktonic bacteria that are liberated after dispersion of biofilms (dispersed cells). The membrane-active mechanism of these molecules forms the key for potentiating the established antibiotics. Further, we demonstrate that the combination of macromolecules and antibiotics significantly reduces bacterial burden in mouse burn and surgical wound infection models caused by Acinetobacter baumannii and Carbapenemase producing Klebsiella pneumoniae (KPC) clinical isolate respectively. Colistin, a well-known antibiotic targeting the lipopolysaccharide (LPS) of Gram-negative bacteria fails to kill antibiotic tolerant cells and dispersed cells (from biofilms) and bacteria develop resistance to it. On the contrary, these macromolecules prevent or delay the development of bacterial resistance to known antibiotics. Our findings emphasize the potential of targeting the bacterial membrane in antibiotic potentiation for disruption of biofilms and suggest a promising strategy towards developing therapies for topical treatment of Gram-negative infections. PMID:28837596

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria

PubMed Central

Ibarra-Arellano, Miguel A.; Campos-González, Adrián I.; Treviño-Quintanilla, Luis G.; Tauch, Andreas; Freyre-González, Julio A.

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy (Across-bacteria systems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

PubMed

Pachiadaki, Maria G; Sintes, Eva; Bergauer, Kristin; Brown, Julia M; Record, Nicholas R; Swan, Brandon K; Mathyer, Mary Elizabeth; Hallam, Steven J; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J; Stepanauskas, Ramunas

2017-11-24

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed. Copyright © 2017, American Association for the Advancement of Science.

Mineralized Remains of Morphotypes of Filamentous Cyanobacteria in Carbonaceous Meteorites

NASA Technical Reports Server (NTRS)

Hoover, Richard B.

2005-01-01

The quest for conclusive evidence of microfossils in meteorites has been elusive. One difficulty arises from the fact than many abiotic or inorganic microstructures, mineral grains, and coating artifacts can mimic the smaller representatives of the microbial world that possess very simple morphologies (unicellular cocci or bacilli). However, there exist a wide variety of large, filamentous trichomic prokaryotic microorganisms (cyanobacteria and sulfur bacteria) with sufficiently well known and complex morphologies that they can be recognized and are known to be of unquestionable biogenic origin. The taphonomic modes of fossilization and their of their life habits and processes frequently result in distinctive chemical biosignatures associated with carbonization, silicification, calcification, phosphatization and metal-binding properties of their cell-walls, trichomes, sheaths and extracellular polymeric substances (EPS). Strong differences of mineral concentrations in closely associated and visibly differentiated cellular microstructures provide strong evidence of biogenicity. This evidence is further enhanced by the detection of recognizable and distinct microstructures (e.g., uniseriate or multiseriate filaments, trichomes, sheaths, cells of proper sizes and size distributions) and growth characteristics (e.g., basal or apical cells, true or false branching of trichomes, tapered or uniform filaments, robust or thin sheaths) and reproductive and nitrogen fixation habits (e.g., baeocytes, hormogonia, akinetes and heterocysts), Microfossils of cyanobacteria and cyanobacterial mats and stromatolites have been recognized a described from many of the most ancient rocks on Earth. The crucial problem lies in developing valid protocols and methodologies for establishing that the putative microfossils are truly indigenous and not merely recent microbial contaminants. During the past several years, we have conducted Field Emission Scanning Electron Microscopy (FESEM

Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

NASA Technical Reports Server (NTRS)

Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

2013-01-01

A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

Application of bacteriophages in post-harvest control of human pathogenic and food spoiling bacteria.

PubMed

Pérez Pulido, Rubén; Grande Burgos, Maria José; Gálvez, Antonio; Lucas López, Rosario

2016-10-01

Bacteriophages have attracted great attention for application in food biopreservation. Lytic bacteriophages specific for human pathogenic bacteria can be isolated from natural sources such as animal feces or industrial wastes where the target bacteria inhabit. Lytic bacteriophages have been tested in different food systems for inactivation of main food-borne pathogens including Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Salmonella enterica, Shigella spp., Campylobacter jejuni and Cronobacter sakazkii, and also for control of spoilage bacteria. Application of lytic bacteriophages could selectively control host populations of concern without interfering with the remaining food microbiota. Bacteriophages could also be applied for inactivation of bacteria attached to food contact surfaces or grown as biofilms. Bacteriophages may receive a generally recognized as safe status based on their lack of toxicity and other detrimental effects to human health. Phage preparations specific for L. monocytogenes, E. coli O157:H7 and S. enterica serotypes have been commercialized and approved for application in foods or as part of surface decontamination protocols. Phage endolysins have a broader host specificity compared to lytic bacteriophages. Cloned endolysins could be used as natural preservatives, singly or in combination with other antimicrobials such as bacteriocins.

Inactivation of koi-herpesvirus in water using bacteria isolated from carp intestines and carp habitats.

PubMed

Yoshida, N; Sasaki, R-K; Kasai, H; Yoshimizu, M

2013-12-01

Since its first outbreak in Japan in 2003, koi-herpesvirus (KHV) remains a challenge to the carp Cyprinus carpio L. breeding industry. In this study, inactivation of KHV in water from carp habitats (carp habitat water) was investigated with the aim of developing a model for rapidly inactivating the pathogen in aquaculture effluent. Experiments with live fish showed that, in carp habitat water, KHV lost its infectivity within 3 days. Indications were that inactivation of KHV was caused by the antagonistic activity of bacteria (anti-KHV bacteria) in the water from carp habitats. Carp habitat water and the intestinal contents of carp were therefore screened for anti-KHV bacteria. Of 581 bacterial isolates, 23 showed anti-KHV activity. An effluent treatment model for the disinfection of KHV in aquaculture effluent water using anti-KHV bacteria was developed and evaluated. The model showed a decrease in cumulative mortality and in the number of KHV genome copies in kidney tissue of fish injected with treated effluent compared with a positive control. It is thought that anti-KHV bacteria isolated from the intestinal contents of carp and from carp habitat water can be used to control KHV outbreaks. © 2013 John Wiley & Sons Ltd.

Method of Detecting Coliform Bacteria and Escherichia Coli Bacteria from Reflected Light

NASA Technical Reports Server (NTRS)

Vincent, Robert (Inventor)

2013-01-01

The present invention relates to a method of detecting coliform bacteria in water from reflected light and a method of detecting Eschericha Coli bacteria in water from reflected light, and also includes devices for the measurement, calculation and transmission of data relating to that method.

The production of anaerobic bacteria and biogas from dairy cattle waste in various growth mediums

NASA Astrophysics Data System (ADS)

Hidayati, Y. A.; Kurnani, T. B. A.; Marlina, E. T.; Rahmah, K. N.; Harlia, E.; Joni, I. M.

2018-02-01

The growth of anaerobic bacteria except the ruminal fluid quailty is strongly influenced by the media formulations. Previous researchers have set a standard media formulation for anaerobic bacteria from rumen, however the use of standard media formulations require chemicals with high cost. Moreover, other constraint of using standard media formulations is requires large quantities of media for anaerobic bacteria to grow. Therefore, it is necessary to find media with a new culture media formulation. Media used in this research were minimalist media consist of Nutrient Agar (NA), Lactose broth and rumen fluid; enriched media Rumen Fluid-Glucose-Agar (RGCA); and enriched media 98-5. The dairy cattle waste is utilized as source of anaerobic bacteria. The obtained data was analyzed by descriptive approach. The results showed that minimalist media produced anaerobic bacteria 2148 × 104 cfu/ml and biogas production: 1.06% CH4, 9.893% CO2; enriched media Rumen Fluid-Glucose-Agar (RGCA) produced anaerobic bacteria 1848 × 104 cfu/ml and biogas production 4.644% CH4, 9.5356% CO2; enriched media 98-5 produced anaerobic bacteria growth 15400 × 104 cfu/ml and biogas production 0.83% of CH4, 42.2% of CO2. It is conclude that the minimalist media was showed the best performance for the dairy cattle waste as source of anaerobic bacteria.

Production and transformation of dissolved neutral sugars and amino acids by bacteria in seawater

NASA Astrophysics Data System (ADS)

Jørgensen, L.; Lechtenfeld, O. J.; Benner, R.; Middelboe, M.; Stedmon, C. A.

2014-10-01

Dissolved organic matter (DOM) in the ocean consists of a heterogeneous mixture of molecules, most of which are of unknown origin. Neutral sugars and amino acids are among the few recognizable biomolecules in DOM, and the molecular composition of these biomolecules is shaped primarily by biological production and degradation processes. This study provides insight into the bioavailability of biomolecules as well as the chemical composition of DOM produced by bacteria. The molecular compositions of combined neutral sugars and amino acids were investigated in DOM produced by bacteria and in DOM remaining after 32 days of bacterial degradation. Results from bioassay incubations with natural seawater (sampled from water masses originating from the surface waters of the Arctic Ocean and the North Atlantic Ocean) and artificial seawater indicate that the molecular compositions following bacterial degradation are not strongly influenced by the initial substrate or bacterial community. The molecular composition of neutral sugars released by bacteria was characterized by a high glucose content (47 mol %) and heterogeneous contributions from other neutral sugars (3-14 mol %). DOM remaining after bacterial degradation was characterized by a high galactose content (33 mol %), followed by glucose (22 mol %) and the remaining neutral sugars (7-11 mol %). The ratio of D-amino acids to L-amino acids increased during the experiments as a response to bacterial degradation, and after 32 days, the D/L ratios of aspartic acid, glutamic acid, serine and alanine reached around 0.79, 0.32, 0.30 and 0.51 in all treatments, respectively. The striking similarity in neutral sugar and amino acid compositions between natural (representing marine semi-labile and refractory DOM) and artificial (representing bacterially produced DOM) seawater samples, suggests that microbes transform bioavailable neutral sugars and amino acids into a common, more persistent form.

Method for establishing the presence of salmonella bacteria in eggs

DOEpatents

Johnston, Roger G.; Sinha, Dipen N.

1995-01-01

Measurement of the acoustical resonances in eggs is shown to provide a rapid, noninvasive technique for establishing the presence of Salmonella bacteria. The technique is also sensitive to yolk puncture, shell cracks, and may be sensitive to other yolk properties and to egg freshness. Remote characterization, potentially useful for characterizing large numbers of eggs, has been demonstrated.

Plant colonization by pink-pigmented facultative methylotrophic bacteria (PPFMs).

PubMed

Omer, Zahra S; Tombolini, Riccardo; Gerhardson, Berndt

2004-03-01

Bacteria belonging to the genus Methylobacterium are characterized by being able to rely on methanol as a sole carbon and energy source and by presenting a more or less intense pink reddish pigmentation. These bacteria, also referred to as pink-pigmented methylotrophic bacteria (PPFMs), are common inhabitants of the phyllosphere and are found in many other environmental samples. Since they grow slowly they are often overlooked and their impact on phyllosphere microbial communities and on the plants harboring them is not well studied nor has their ecology been elucidated. In a survey of PPFM colonization in three different agricultural sites, PPFM populations were identified on both red clover and winter wheat, but red clover was more consistently colonized. Isolations from collected leaves showed PPFM populations to decrease from spring towards summer, but they increased again towards the end of the cropping season. Isolates from red clover readily colonized winter wheat leaves and vice versa in greenhouse experiments, but population sizes were dependent on the application procedure. Tested isolates had also good potential to colonize the rhizosphere, especially after seed inoculations. Confocal scanning laser microscopy showed gfp-tagged isolates to colonize the surface of clover leaves by forming large aggregates.

Molecular Viability Testing of UV-Inactivated Bacteria.

PubMed

Weigel, Kris M; Nguyen, Felicia K; Kearney, Moira R; Meschke, John S; Cangelosi, Gerard A

2017-05-15

PCR is effective in detecting bacterial DNA in samples, but it is unable to differentiate viable bacteria from inactivated cells or free DNA fragments. New PCR-based analytical strategies have been developed to address this limitation. Molecular viability testing (MVT) correlates bacterial viability with the ability to rapidly synthesize species-specific rRNA precursors (pre-rRNA) in response to brief nutritional stimulation. Previous studies demonstrated that MVT can assess bacterial inactivation by chlorine, serum, and low-temperature pasteurization. Here, we demonstrate that MVT can detect inactivation of Escherichia coli , Aeromonas hydrophila , and Enterococcus faecalis cells by UV irradiation. Some UV-inactivated E. coli cells transiently retained the ability to synthesize pre-rRNA postirradiation (generating false-positive MVT results), but this activity ceased within 1 h following UV exposure. Viable but transiently undetectable (by culture) E. coli cells were consistently detected by MVT. An alternative viability testing method, viability PCR (vPCR), correlates viability with cell envelope integrity. This method did not distinguish viable bacteria from UV-inactivated bacteria under some conditions, indicating that the inactivated cells retained intact cell envelopes. MVT holds promise as a means to rapidly assess microbial inactivation by UV treatment. IMPORTANCE UV irradiation is increasingly being used to disinfect water, food, and other materials for human use. Confirming the effectiveness of UV disinfection remains a challenging task. In particular, microbiological methods that rely on rapid detection of microbial DNA can yield misleading results, due to the detection of remnant DNA associated with dead microbial cells. This report describes a novel method that rapidly distinguishes living microbial cells from dead microbial cells after UV disinfection. Copyright © 2017 American Society for Microbiology.

Bioleaching of Ilmenite and Basalt in the Presence of Iron-oxidizing and Iron-scavenging Bacteria

NASA Astrophysics Data System (ADS)

Navarrete, J. U.; Cappelle, I.; Borrok, D.; Isru-Bio Team

2010-12-01

Understanding the biogeochemical processes that control mineral weathering rates is not only important for Earth systems, but may be a useful for developing technologies for the in-situ utilization of resources from other planets, moons, and asteroids. Traditional techniques that may be used to extract metals like iron, titanium, and aluminum from planetary rocks have large energy and/or hardware requirements that may not always be feasible. In this study, we performed biotic and abiotic leaching experiments with basalt and ilmenite (FeTiO3) to determine whether bacteria increased elemental leaching rates. Our secondary objectives were (1) to determine whether Acidithiobacillus ferrooxidans, an Fe-oxidizing bacterial strain, could grow on the low concentrations of ferrous Fe generated by the available substrates, and (2) to determine whether Pseudomonas mendocina, a heterotrophic Fe-scavenging bacteria, could grow on the low concentrations of nutrient elements generated by the available substrates. Experimental results demonstrate that the Fe(II) leached from ilmenite was rapidly depleted and replaced by Fe(III) in the presence of the Fe-oxidizing bacteria. The Fe in the abiotic control system remained as Fe(II) over the entire duration of the experiment. This suggests that the bacteria were able to grow using the Fe(II) from ilmenite (and the metal-free growth media) as a substrate. The iron-oxidizing bacteria were also able to grow in the presence of basaltic rock types; however the elemental release rates of Si, Ca, and Al in the presence of A. ferrooxidans were actually the same or lower than those from the abiotic control experiments. This may be attributable to the metabolically active bacteria creating a thick altered layer at the mineral surface that decreased the rate of diffusion or it may be caused in part by adsorption or precipitation of Fe(III) onto the existing mineral surfaces. Blending of the basaltic rock with ilmenite to further stimulate the

Use of Extract of Citrus sinensis as an antimicrobial agent for foodborne zoonotic pathogens and spoilage bacteria

USDA-ARS?s Scientific Manuscript database

Foodborne pathogens remain global health problems despite concerted efforts to control the transmission of these microorganisms through food. The resurgence of drug resistant bacteria has renewed interest in developing and testing new sources of antimicrobial agents to control foodborne illness. Thi...

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.

The antibiotic pipeline for multi-drug resistant gram negative bacteria: what can we expect?

PubMed

Falagas, Matthew E; Mavroudis, Andreas D; Vardakas, Konstantinos Z

2016-08-01

A real concern in the medical community is the increasing resistance of bacteria, especially that of Gram-negative types. New antibiotics are currently under clinical development, promising to tackle severe infections caused, especially, by multi-drug resistant (MDR) bacteria and broaden the armamentarium of clinicians. We searched PUBMED and GOOGLE databases. Combinations of already approved β-lactams or monobactams with new β-lactamase inhibitors [imipenem-cilastatin/MK-7655 (relebactam), meropenem/RPX7009 (vaborbactam), ceftaroline/avibactam, aztreonam/avibactam], new β-lactams (S-649266, BAL30072), aminoglycosides (plazomicin), quinolones (finafloxacin) and tetracyclines (eravacycline) were included in the review. Expert commentary: For the majority of the upcoming antibiotics the currently available data is limited to their microbiology and pharmacokinetics. Their effectiveness and safety against infections due to MDR bacteria remain to be proved. Significant issues are also the impact of these antibiotics on the human intestinal microbiota and their possible co-administration with already-known antimicrobial agents in difficult-to-treat-infections; further studies should be conducted for these objectives.

Increased survival of honeybees in the laboratory after simultaneous exposure to low doses of pesticides and bacteria.

PubMed

Dickel, Franziska; Münch, Daniel; Amdam, Gro Vang; Mappes, Johanna; Freitak, Dalial

2018-01-01

Recent studies of honeybees and bumblebees have examined combinatory effects of different stressors, as insect pollinators are naturally exposed to multiple stressors. At the same time the potential influences of simultaneously occurring agricultural agents on insect pollinator health remain largely unknown. Due to different farming methods, and the drift of applied agents and manure, pollinators are most probably exposed to insecticides but also bacteria from organic fertilizers at the same time. We orally exposed honeybee workers to sub-lethal doses of the insecticide thiacloprid and two strains of the bacterium Enterococcus faecalis, which can occur in manure from farming animals. Our results show that under laboratory conditions the bees simultaneously exposed to the a bacterium and the pesticide thiacloprid thiacloprid had significant higher survival rates 11 days post exposure than the controls, which surprisingly showed the lowest survival. Bees that were exposed to diet containing thiacloprid showed decreased food intake. General antibacterial activity is increased by the insecticide and the bacteria, resulting in a higher immune response observed in treated individuals compared to control individuals. We thus propose that caloric restriction through behavioural and physiological adaptations may have mediated an improved survival and stress resistance in our tests. However, the decreased food consumption could in long-term also result in possible negative effects at colony level. Our study does not show an additive negative impact of sub-lethal insecticide and bacteria doses, when tested under laboratory conditions. In contrast, we report seemingly beneficial effects of simultaneous exposure of bees to agricultural agents, which might demonstrate a surprising biological capacity for coping with stressors, possibly through hormetic regulation.

[The electron microscopic findings of helicoid bacteria lining the mucosa of the cecum in guinea pigs].

PubMed

Raygoza-Anaya, M; Bondarenko, V M; Mora-Galindo, H; González-Robles, A

1991-08-01

This study has revealed that helical bacteria inhabiting the mucous membrane of the cecum of guinea pigs are localized in the parietal zone of the epithelium and can be detected as biological film consisting of many microcolonies. Helical bacteria are attached to the epithelium by insertion of one of the ends of an eukaryotic cell into the space between microvilli without damaging epithelial cells and their microvilli. Helical bacteria have been found to use the "anchor" type of attachment to the epithelium, which ensures the stability of their high population level in the biotope. These microorganisms appear on the mucous membrane of the epithelium, starting from day 15 of the life of guinea pigs. At the period of the transition of suckling guinea pigs to independent nourishment the population of helical bacteria is partially suppressed due to the appearance of bacillary and filamentous forms of bacteria, but later, after the adaptation of the animals to their diet, helical bacteria become normal resident microflora which forms biofilm covering large areas of the mucous membrane and the entrances of crypts of Lieberkühn.

Quantifying viruses and bacteria in wastewater - results, quality control, and interpretation methods

USDA-ARS?s Scientific Manuscript database

Membrane bioreactors (MBR), used for wastewater treatment in Ohio and elsewhere in the United States, have pore sizes large enough to theoretically reduce concentrations of protozoa and bacteria, but not viruses. Sampling for viruses in wastewater is seldom done and not required. Instead, the bac...

OVERVIEW OF CYANIDE PLANT REMAINS, TAILINGS PILES, PARKING LOT, AND ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

OVERVIEW OF CYANIDE PLANT REMAINS, TAILINGS PILES, PARKING LOT, AND MINE MANAGER'S HOME, LOOKING SOUTH SOUTHEAST. RIGHT, TAILINGS PILES ARE AT CENTER WITH CYANIDE PLANT FOUNDATIONS TO THE LEFT OF THE PILES. PARKING LOT IS AT UPPER LEFT. THE AREA BETWEEN THE COLLAPSED TANK AT CENTER LEFT AND THE REMAINS OF THE MANAGER'S HOUSE AT LOWER RIGHT IS A TAILINGS HOLDING AREA. TAILINGS FROM THE MILL WERE HELD HERE. THE LARGE SETTLING TANKS WERE CHARGED FROM THIS HOLDING AREA BY A TRAM ON RAILS AND BY A SLUICEWAY SEEN AS THE DARK SPOT ON THE CENTER LEFT EDGE OF THE FRAME. AFTER THE TAILINGS WERE LEACHED, THEY WERE DEPOSITED ON THE LARGE WASTE PILE AT CENTER RIGHT. THE TANK AT CENTER RIGHT EDGE IS WHERE THE WATER PIPELINE ENTERED THE WORKS. A STRAIGHT LINE OF POSTS IN THE GROUND GO ACROSS THE CENTER FROM LEFT TO RIGHT, WHICH ORIGINALLY SUSPENDED THE WATER PIPELINE GOING FROM THE WATER HOLDING TANK AT RIGHT UP TO THE SECONDARY WATER TANKS ABOVE THE MILL. - Keane Wonder Mine, Park Route 4 (Daylight Pass Cutoff), Death Valley Junction, Inyo County, CA

Antibiotic Resistance in Plant-Pathogenic Bacteria.

PubMed

Sundin, George W; Wang, Nian

2018-06-01

Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases. Expected final online publication date for the Annual Review of Phytopathology Volume 56 is August 25, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Magnetotactic bacteria on Earth and on Mars.

PubMed

McKay, Christopher P; Friedmann, E Imre; Frankel, Richard B; Bazylinski, Dennis A

2003-01-01

Continued interest in the possibility of evidence for life in the ALH84001 Martian meteorite has focused on the magnetite crystals. This review is structured around three related questions: is the magnetite in ALH84001 of biological or non-biological origin, or a mixture of both? does magnetite on Earth provide insight to the plausibility of biogenic magnetite on Mars? could magnetotaxis have developed on Mars? There are credible arguments for both the biological and non-biological origin of the magnetite in ALH84001, and we suggest that more studies of ALH84001, extensive laboratory simulations of non-biological magnetite formation, as well as further studies of magnetotactic bacteria on Earth will be required to further address this question. Magnetite grains produced by bacteria could provide one of the few inorganic traces of past bacterial life on Mars that could be recovered from surface soils and sediments. If there was biogenic magnetite on Mars in sufficient abundance to leave fossil remains in the volcanic rocks of ALH84001, then it is likely that better-preserved magnetite will be found in sedimentary deposits on Mars. Deposits in ancient lakebeds could contain well-preserved chains of magnetite clearly indicating a biogenic origin.

Magnetotactic bacteria on Earth and on Mars

NASA Technical Reports Server (NTRS)

McKay, Christopher P.; Friedmann, E. Imre; Frankel, Richard B.; Bazylinski, Dennis A.

2003-01-01

Continued interest in the possibility of evidence for life in the ALH84001 Martian meteorite has focused on the magnetite crystals. This review is structured around three related questions: is the magnetite in ALH84001 of biological or non-biological origin, or a mixture of both? does magnetite on Earth provide insight to the plausibility of biogenic magnetite on Mars? could magnetotaxis have developed on Mars? There are credible arguments for both the biological and non-biological origin of the magnetite in ALH84001, and we suggest that more studies of ALH84001, extensive laboratory simulations of non-biological magnetite formation, as well as further studies of magnetotactic bacteria on Earth will be required to further address this question. Magnetite grains produced by bacteria could provide one of the few inorganic traces of past bacterial life on Mars that could be recovered from surface soils and sediments. If there was biogenic magnetite on Mars in sufficient abundance to leave fossil remains in the volcanic rocks of ALH84001, then it is likely that better-preserved magnetite will be found in sedimentary deposits on Mars. Deposits in ancient lakebeds could contain well-preserved chains of magnetite clearly indicating a biogenic origin.

Re-engineering bacteria for ethanol production

DOEpatents

Yomano, Lorraine P; York, Sean W; Zhou, Shengde; Shanmugam, Keelnatham; Ingram, Lonnie O

2014-05-06

The invention provides recombinant bacteria, which comprise a full complement of heterologous ethanol production genes. Expression of the full complement of heterologous ethanol production genes causes the recombinant bacteria to produce ethanol as the primary fermentation product when grown in mineral salts medium, without the addition of complex nutrients. Methods for producing the recombinant bacteria and methods for producing ethanol using the recombinant bacteria are also disclosed.

Denitrification by extremely halophilic bacteria

NASA Technical Reports Server (NTRS)

Hochstein, L. I.; Tomlinson, G. A.

1985-01-01

Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.

Quantification of two forms of green sulfur bacteria in their natural habitat using bacteriochlorophyll fluorescence spectra

NASA Astrophysics Data System (ADS)

Kharcheva, Anastasia V.; Zhiltsova, Anna A.; Lunina, Olga N.; Savvichev, Alexander S.; Patsaeva, Svetlana V.

2016-04-01

Detection of phototropic organisms in their natural habitat using optical instruments operating under water is urgently needed for many tasks of ecological monitoring. While fluorescence methods are widely applied nowadays to detect and characterize phytoplankton communities, the techniques for detection and recognition of anoxygenic phototrophs are considered challenging. Differentiation of the forms of anoxygenic green sulfur bacteria in natural water using spectral techniques remains problematic. Green sulfur bacteria could be found in two forms, green-colored (containing BChl d in pigment compound) and brown-colored (containing BChl e), have the special ecological niche in such reservoirs. Separate determination of these microorganisms by spectral methods is complicated because of similarity of spectral characteristics of their pigments. We describe the novel technique of quantification of two forms of green sulfur bacteria directly in water using bacteriochlorophyll fluorescence without pigment extraction. This technique is noninvasive and could be applied in remote mode in the water bodies with restricted water circulation to determine simultaneously concentrations of two forms of green sulfur bacteria in their natural habitat.

Genome dynamics and evolution in yeasts: A long-term yeast-bacteria competition experiment

PubMed Central

Katz, Michael; Knecht, Wolfgang; Compagno, Concetta; Piškur, Jure

2018-01-01

There is an enormous genetic diversity evident in modern yeasts, but our understanding of the ecological basis of such diversifications in nature remains at best fragmented so far. Here we report a long-term experiment mimicking a primordial competitive environment, in which yeast and bacteria co-exist and compete against each other. Eighteen yeasts covering a wide phylogenetic background spanning approximately 250 million years of evolutionary history were used to establish independent evolution lines for at most 130 passages. Our collection of hundreds of modified strains generated through such a rare two-species cross-kingdom competition experiment re-created the appearance of large-scale genomic rearrangements and altered phenotypes important in the diversification history of yeasts. At the same time, the methodology employed in this evolutionary study would also be a non-gene-technological method of reprogramming yeast genomes and then selecting yeast strains with desired traits. Cross-kingdom competition may therefore be a method of significant value to generate industrially useful yeast strains with new metabolic traits. PMID:29624585

Mechanism for longitudinal growth of rod-shaped bacteria

NASA Astrophysics Data System (ADS)

Taneja, Swadhin; Levitan, Ben; Rutenberg, Andrew

2013-03-01

The peptidoglycan (PG) cell wall along with MreB proteins are major determinants of shape in rod-shaped bacteria. However the mechanism guiding the growth of this elastic network of cross-linked PG (sacculus) that maintains the integrity and shape of the rod-shaped cell remains elusive. We propose that the known anisotropic elasticity and anisotropic loading, due to the shape and turgor pressure, of the sacculus is sufficient to direct small gaps in the sacculus to elongate around the cell, and that subsequent repair leads to longitudinal growth without radial growth. We computationally show in our anisotropically stressed anisotropic elasticity model small gaps can extend stably in the circumferential direction for the known elasticity of the sacculus. We suggest that MreB patches that normally propagate circumferentially, are associated with these gaps and are steered with this common mechanism. This basic picture is unchanged in Gram positive and Gram negative bacteria. We also show that small changes of elastic properties can in fact lead to bi-stable propagation of gaps, both longitudinal and circumferential, that can explain the bi-stability in patch movement observed in ΔmblΔmreb mutants.

Novel anti-infective compounds from marine bacteria.

PubMed

Rahman, Hafizur; Austin, Brian; Mitchell, Wilfrid J; Morris, Peter C; Jamieson, Derek J; Adams, David R; Spragg, Andrew Mearns; Schweizer, Michael

2010-03-05

As a result of the continuous evolution of microbial pathogens towards antibiotic-resistance, there have been demands for the development of new and effective antimicrobial compounds. Since the 1960s, the scientific literature has accumulated many publications about novel pharmaceutical compounds produced by a diverse range of marine bacteria. Indeed, marine micro-organisms continue to be a productive and successful focus for natural products research, with many newly isolated compounds possessing potentially valuable pharmacological activities. In this regard, the marine environment will undoubtedly prove to be an increasingly important source of novel antimicrobial metabolites, and selective or targeted approaches are already enabling the recovery of a significant number of antibiotic-producing micro-organisms. The aim of this review is to consider advances made in the discovery of new secondary metabolites derived from marine bacteria, and in particular those effective against the so called "superbugs", including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE), which are largely responsible for the increase in numbers of hospital acquired, i.e., nosocomial, infections.

Light controlled 3D micromotors powered by bacteria

NASA Astrophysics Data System (ADS)

Vizsnyiczai, Gaszton; Frangipane, Giacomo; Maggi, Claudio; Saglimbeni, Filippo; Bianchi, Silvio; di Leonardo, Roberto

2017-06-01

Self-propelled bacteria can be integrated into synthetic micromachines and act as biological propellers. So far, proposed designs suffer from low reproducibility, large noise levels or lack of tunability. Here we demonstrate that fast, reliable and tunable bio-hybrid micromotors can be obtained by the self-assembly of synthetic structures with genetically engineered biological propellers. The synthetic components consist of 3D interconnected structures having a rotating unit that can capture individual bacteria into an array of microchambers so that cells contribute maximally to the applied torque. Bacterial cells are smooth swimmers expressing a light-driven proton pump that allows to optically control their swimming speed. Using a spatial light modulator, we can address individual motors with tunable light intensities allowing the dynamic control of their rotational speeds. Applying a real-time feedback control loop, we can also command a set of micromotors to rotate in unison with a prescribed angular speed.

Light controlled 3D micromotors powered by bacteria

PubMed Central

Vizsnyiczai, Gaszton; Frangipane, Giacomo; Maggi, Claudio; Saglimbeni, Filippo; Bianchi, Silvio; Di Leonardo, Roberto

2017-01-01

Self-propelled bacteria can be integrated into synthetic micromachines and act as biological propellers. So far, proposed designs suffer from low reproducibility, large noise levels or lack of tunability. Here we demonstrate that fast, reliable and tunable bio-hybrid micromotors can be obtained by the self-assembly of synthetic structures with genetically engineered biological propellers. The synthetic components consist of 3D interconnected structures having a rotating unit that can capture individual bacteria into an array of microchambers so that cells contribute maximally to the applied torque. Bacterial cells are smooth swimmers expressing a light-driven proton pump that allows to optically control their swimming speed. Using a spatial light modulator, we can address individual motors with tunable light intensities allowing the dynamic control of their rotational speeds. Applying a real-time feedback control loop, we can also command a set of micromotors to rotate in unison with a prescribed angular speed. PMID:28656975

Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria

PubMed Central

Ilmjärv, Tanel; Naanuri, Eve; Kivisaar, Maia

2017-01-01

Bacteria can rapidly evolve mechanisms allowing them to use toxic environmental pollutants as a carbon source. In the current study we examined whether the survival and evolution of indigenous bacteria with the capacity to degrade organic pollutants could be connected with increased mutation frequency. The presence of constitutive and transient mutators was monitored among 53 pollutants-degrading indigenous bacterial strains. Only two strains expressed a moderate mutator phenotype and six were hypomutators, which implies that constitutively increased mutability has not been prevalent in the evolution of pollutants degrading bacteria. At the same time, a large proportion of the studied indigenous strains exhibited UV-irradiation-induced mutagenesis, indicating that these strains possess error-prone DNA polymerases which could elevate mutation frequency transiently under the conditions of DNA damage. A closer inspection of two Pseudomonas fluorescens strains PC20 and PC24 revealed that they harbour genes for ImuC (DnaE2) and more than one copy of genes for Pol V. Our results also revealed that availability of other nutrients in addition to aromatic pollutants in the growth environment of bacteria affects mutagenic effects of aromatic compounds. These results also implied that mutagenicity might be affected by a factor of how long bacteria have evolved to use a particular pollutant as a carbon source. PMID:28777807

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

Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

PubMed

Pouillot, Régis; Chen, Yuhuan; Hoelzer, Karin

2015-02-01

When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise. Published by Elsevier Ltd.

The s29x gene of symbiotic bacteria in Amoeba proteus with a novel promoter.

PubMed

Pak, J W; Jeon, K W

1996-05-24

Gram-symbiotic bacteria (called X-bacteria), present in the xD strain of Amoeba proteus as required cell components, synthesize and export a large amount of a 29-kDa protein, S29x. S29x is exported into the host's cytoplasm across the bacterial membranes and the symbiosome membrane. The complete nucleotide (nt) sequence of the s29x gene of X-bacteria has been determined, and the promoter sequence and tsp have also been identified. The gene has a nonconventional promoter with putative nt sequences different from the known consensus sequences. When Escherichia coli cells are transformed with s29x, the gene is expressed and the product is secreted into the culture medium. Functions of S29x are not fully known, but it is suspected that S29x plays an important role in the symbiotic relationship between amoebae and X-bacteria.

Fossil human remains from Bolomor Cave (Valencia, Spain).

PubMed

Arsuaga, Juan Luis; Fernández Peris, Josep; Gracia-Téllez, Ana; Quam, Rolf; Carretero, José Miguel; Barciela González, Virginia; Blasco, Ruth; Cuartero, Felipe; Sañudo, Pablo

2012-05-01

Systematic excavations carried out since 1989 at Bolomor Cave have led to the recovery of four Pleistocene human fossil remains, consisting of a fibular fragment, two isolated teeth, and a nearly complete adult parietal bone. All of these specimens date to the late Middle and early Late Pleistocene (MIS 7-5e). The fibular fragment shows thick cortical bone, an archaic feature found in non-modern (i.e. non-Homo sapiens) members of the genus Homo. Among the dental remains, the lack of a midtrigonid crest in the M(1) represents a departure from the morphology reported for the majority of Neandertal specimens, while the large dimensions and pronounced shoveling of the marginal ridges in the C(1) are similar to other European Middle and late Pleistocene fossils. The parietal bone is very thick, with dimensions that generally fall above Neandertal fossils and resemble more closely the Middle Pleistocene Atapuerca (SH) adult specimens. Based on the presence of archaic features, all the fossils from Bolomor are attributed to the Neandertal evolutionary lineage. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacteria entombed in the center of cholesterol gallstones induce fewer infectious manifestations than bacteria in the matrix of pigment stones.

PubMed

Stewart, Lygia; Griffiss, J McLeod; Jarvis, Gary A; Way, Lawrence W

2007-10-01

The clinical significance of bacteria in the pigment centers of cholesterol stones is unknown. We compared the infectious manifestations and characteristics of bacteria from pigment stones and predominantly cholesterol stones. Three hundred forty patients were studied. Bile was cultured. Gallstones were cultured and examined with scanning electron microscopy. Level of bacterial immunoglobulin G (bile, serum), complement killing, and tumor necrosis factor-alpha production were determined. Twenty-three percent of cholesterol stones and 68% of pigment stones contained bacteria (P < 0.0001). Stone culture correlated with scanning electron microscopy results. Pigment stone bacteria were more often present in bile and blood. Cholesterol stone bacteria caused more severe infections (19%) than sterile stones (0%), but less than pigment stone bacteria (57%) (P < 0.0001). Serum and bile from patients with cholesterol stone bacteria had less bacterial-specific immunoglobulin G. Cholesterol stone bacteria produced more slime. Pigment stone bacteria were more often killed by a patient's serum. Tumor necrosis factor-alpha production of the groups was similar. Bacteria are readily cultured from cholesterol stones with pigment centers, allowing for analysis of their virulence factors. Bacteria sequestered in cholesterol stones cause infectious manifestations, but less than bacteria in pigment stones. Possibly because of their isolation, cholesterol stone bacteria were less often present in bile and blood, induced less immunoglobulin G, were less often killed by a patient's serum, and demonstrated fewer infectious manifestations than pigment stone bacteria. This is the first study to analyze the clinical relevance of bacteria within cholesterol gallstones.

Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States ▿ †

PubMed Central

Bowers, Robert M.; Sullivan, Amy P.; Costello, Elizabeth K.; Collett, Jeff L.; Knight, Rob; Fierer, Noah

2011-01-01

Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere. PMID:21803902

Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes

PubMed Central

Chaston, John M.; Murfin, Kristen E.; Heath-Heckman, Elizabeth A.; Goodrich-Blair, Heidi

2013-01-01

Summary The specificity of a horizontally transmitted microbial symbiosis is often defined by molecular communication between host and microbe during initial engagement, which can occur in discrete stages. In the symbiosis between Steinernema nematodes and Xenorhabdus bacteria, previous investigations focused on bacterial colonization of the intestinal lumen (receptacle) of the nematode infective juvenile (IJ), as this was the only known persistent, intimate, and species-specific contact between the two. Here we show that bacteria colonize the anterior intestinal cells of other nematode developmental stages in a species-specific manner. Also, we describe three processes that only occur in juveniles that are destined to become IJs. First, a few bacterial cells colonize the nematode pharyngeal-intestinal valve (PIV) anterior to the intestinal epithelium. Second, the nematode intestine constricts while bacteria initially remain in the PIV. Third, anterior intestinal constriction relaxes and colonizing bacteria occupy the receptacle. At each stage, colonization requires X. nematophila symbiosis region 1 (SR1) genes and is species-specific: X. szentirmaii, which naturally lacks SR1, does not colonize unless SR1 is ectopically expressed. These findings reveal new aspects of Xenorhabdus bacteria interactions with and transmission by their Steinernema nematode hosts, and demonstrate that bacterial SR1 genes aid in colonizing nematode epithelial surfaces. PMID:23480552

Radiation, radionuclides and bacteria: An in-perspective review.

PubMed

Shukla, Arpit; Parmar, Paritosh; Saraf, Meenu

2017-12-01

There has been a significant surge in consumption of radionuclides for various academic and commercial purposes. Correspondingly, there has been a considerable amount of generation of radioactive waste. Bacteria and archaea, being earliest inhabitants on earth serve as model microorganisms on earth. These microbes have consistently proven their mettle by surviving extreme environments, even extreme ionizing radiations. Their ability to accept and undergo stable genetic mutations have led to development of recombinant mutants that are been exploited for remediation of various pollutants such as; heavy metals, hydrocarbons and even radioactive waste (radwaste). Thus, microbes have repeatedly presented themselves to be prime candidates suitable for remediation of radwaste. It is interesting to study the behind-the-scenes interactions these microbes possess when observed in presence of radionuclides. The emphasis is on the indigenous bacteria isolated from radionuclide containing environments as well as the five fundamental interaction mechanisms that have been studied extensively, namely; bioaccumulation, biotransformation, biosorption, biosolubilisation and bioprecipitation. Application of microbes exhibiting such mechanisms in remediation of radioactive waste depends largely on the individual capability of the species. Challenges pertaining to its potential bioremediation activity is also been briefly discussed. This review provides an insight into the various mechanisms bacteria uses to tolerate, survive and carry out processes that could potentially lead the eco-friendly approach for removal of radionuclides. Copyright © 2017 Elsevier Ltd. All rights reserved.

Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

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

Hu, Haiyan; Lin, Hui; Zheng, Wang

2013-08-04

Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury1-4. One strain of sulphate-reducing bacteria (Desulfovibrio desulfuricans ND132) can also methylate elemental mercury5. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidise and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally-relevant concentrations ofmore » elemental mercury. We report differences in the ability of these organisms to oxidise and methylate elemental mercury. In line with recent findings5, we show that Desulfovibrio desulfuricans ND132 can both oxidise and methylate elemental mercury. However, the rate of methylation of elemental mercury is only about one third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidise, but not methylate, elemental mercury. Geobacter sulfurreducens PCA is able to oxidise and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.« less

Human body may produce bacteria.

PubMed

Salerian, Alen J

2017-06-01

"Human body may produce bacteria" proposes that human body may produce bacteria and represent an independent source of infections contrary to the current paradigm of infectious disorders proposed by Louis Pasteur in 1880. The following observations are consistent with this hypothesis: A. Bidirectional transformations of both living and nonliving things have been commonly observed in nature. B. Complex multicellular organisms harbor the necessary properties to produce bacteria (water, nitrogen and oxygen). C. Physical laws suggest any previously observed phenomenon or action will occur again (life began on earth; a non living thing). D. Animal muscle cells may generate energy (fermentation). E. Sterilized food products (i.e. boiled eggs), may produce bacteria and fungus under special conditions and without any exposure to foreign living cells. "Human body may produce bacteria" may challenge the current medical paradigm that views human infectious disorders as the exclusive causative byproducts of invading foreign cells. It may also introduce new avenues to treat infectious disorders. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns

PubMed Central

Spencer, J.; Schwarzacher, W.

2016-01-01

ABSTRACT In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli. Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. IMPORTANCE Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved

Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns.

PubMed

Correia Carreira, S; Spencer, J; Schwarzacher, W; Seddon, A M

2016-06-15

In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved within 15 min. This

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

PubMed

Robinson, Kelly M; Crabtree, Jonathan; Mattick, John S A; Anderson, Kathleen E; Dunning Hotopp, Julie C

2017-01-25

A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.

Some bacteria are beneficial!

USGS Publications Warehouse

McMahon, Peter B.

1995-01-01

Most people would agree that bacteria usually spell trouble where the quality of drinking water is con cerned. However, recent studies conducted by the U.S. Geological Survey (USGS) under the National Water-Quality Assessment (NAWQA) program have shown that some bacteria can improve the quality of water.

Enteric bacteria in aerobically digested sludge.

PubMed Central

Farrah, S R; Bitton, G

1984-01-01

Indicator bacteria, Salmonella spp., and total aerobic bacteria were determined in samples of undigested sludge and sludge that had been treated by one or two stages of aerobic digestion. Aerobic sludge digestion reduced the level of indicator bacteria by 1 to 2 log10 per g. The level of Salmonella spp. was also reduced during aerobic treatment of sludge. In general, aerobic treatment of sludge reduced, but did not eliminate, indicator bacteria and Salmonella spp. PMID:6721492

Antibiotic Production by Anaerobic Bacteria1

PubMed Central

Sturgen, Nancy O.; Casida, L. E.

1962-01-01

Soils from aerobic and anaerobic sources were investigated for the possible presence of bacteria which produce antibiotics under anaerobic conditions of growth. The screening techniques devised for this study yielded 157 soil bacteria which, during anaerobic growth, produced antibiotic activity against aerobic test bacteria. Studies on choice of media, presence of oxygen, and changes in antibiotic activity during growth indicated that representative strains of these bacteria produced mixtures of antibiotics. The activity was heat labile. PMID:13918037

Correlative Electron and Fluorescence Microscopy of Magnetotactic Bacteria in Liquid: Toward In Vivo Imaging

PubMed Central

Woehl, Taylor J.; Kashyap, Sanjay; Firlar, Emre; Perez-Gonzalez, Teresa; Faivre, Damien; Trubitsyn, Denis; Bazylinski, Dennis A.; Prozorov, Tanya

2014-01-01

Magnetotactic bacteria biomineralize ordered chains of uniform, membrane-bound magnetite or greigite nanocrystals that exhibit nearly perfect crystal structures and species-specific morphologies. Transmission electron microscopy (TEM) is a critical technique for providing information regarding the organization of cellular and magnetite structures in these microorganisms. However, conventional TEM can only be used to image air-dried or vitrified bacteria removed from their natural environment. Here we present a correlative scanning TEM (STEM) and fluorescence microscopy technique for imaging viable cells of Magnetospirillum magneticum strain AMB-1 in liquid using an in situ fluid cell TEM holder. Fluorescently labeled cells were immobilized on microchip window surfaces and visualized in a fluid cell with STEM, followed by correlative fluorescence imaging to verify their membrane integrity. Notably, the post-STEM fluorescence imaging indicated that the bacterial cell wall membrane did not sustain radiation damage during STEM imaging at low electron dose conditions. We investigated the effects of radiation damage and sample preparation on the bacteria viability and found that approximately 50% of the bacterial membranes remained intact after an hour in the fluid cell, decreasing to ~30% after two hours. These results represent a first step toward in vivo studies of magnetite biomineralization in magnetotactic bacteria. PMID:25358460

Correlative Electron and Fluorescence Microscopy of Magnetotactic Bacteria in Liquid: Toward In Vivo Imaging

DOE PAGES

Woehl, Taylor J.; Kashyap, Sanjay; Firlar, Emre; ...

2014-10-31

Magnetotactic bacteria biomineralize ordered chains of uniform, membrane-bound magnetite or greigite nanocrystals that exhibit nearly perfect crystal structures and species-specific morphologies. Transmission electron microscopy (TEM) is a critical technique for providing information regarding the organization of cellular and magnetite structures in these microorganisms. However, conventional TEM can only be used to image air-dried or vitrified bacteria removed from their natural environment. Here we present a correlative scanning TEM (STEM) and fluorescence microscopy technique for imaging viable cells of Magnetospirillum magneticum strain AMB-1 in liquid using an in situ fluid cell TEM holder. Fluorescently labeled cells were immobilized on microchip windowmore » surfaces and visualized in a fluid cell with STEM, followed by correlative fluorescence imaging to verify their membrane integrity. Notably, the post-STEM fluorescence imaging indicated that the bacterial cell wall membrane did not sustain radiation damage during STEM imaging at low electron dose conditions. We investigated the effects of radiation damage and sample preparation on the bacteria viability and found that approximately 50% of the bacterial membranes remained intact after an hour in the fluid cell, decreasing to ~30% after two hours. These results represent a first step toward in vivo studies of magnetite biomineralization in magnetotactic bacteria.« less

Modified extraction procedure for gas-liquid chromatography applied to the identification of anaerobic bacteria.

PubMed Central

Thomann, W R; Hill, G B

1986-01-01

Chloroform and ether commonly are used as solvents to extract metabolic organic acids for analysis by gas-liquid chromatography in the identification of anaerobic bacteria. Because these solvents are potentially hazardous to personnel, modified extraction procedures involving the use of a safer solvent, methyl tert-butyl ether were developed which remained both simple to perform and effective for organism identification. PMID:3700623

Improvement of the trace metal composition of medium for nitrite-dependent anaerobic methane oxidation bacteria: Iron (II) and copper (II) make a difference.

PubMed

He, Zhanfei; Geng, Sha; Pan, Yawei; Cai, Chaoyang; Wang, Jiaqi; Wang, Liqiao; Liu, Shuai; Zheng, Ping; Xu, Xinhua; Hu, Baolan

2015-11-15

Nitrite-dependent anaerobic methane oxidation (n-damo) is a potential bioprocess for treating nitrogen-containing wastewater. This process uses methane, an inexpensive and nontoxic end-product of anaerobic digestion, as an external electron donor. However, the low turnover rate and slow growth rate of n-damo functional bacteria limit the practical application of this process. In the present study, the short- and long-term effects of variations in trace metal concentrations on n-damo bacteria were investigated, and the concentrations of trace metal elements of medium were improved. The results were subsequently verified by a group of long-term inoculations (90 days) and were applied in a sequencing batch reactor (SBR) (84 days). The results indicated that iron (Fe(II)) and copper (Cu(II)) (20 and 10 μmol L(-1), respectively) significantly stimulated the activity and the growth of n-damo bacteria, whereas other trace metal elements, including zinc (Zn), molybdenum (Mo), cobalt (Co), manganese (Mn), and nickel (Ni), had no significant effect on n-damo bacteria in the tested concentration ranges. Interestingly, fluorescence in situ hybridization (FISH) showed that a large number of dense, large aggregates (10-50 μm) of n-damo bacteria were formed by cell adhesion in the SBR reactor after using the improved medium, and to our knowledge this is the first discovery of large aggregates of n-damo bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rhizosphere Competitiveness of Trichloroethylene-Degrading, Poplar-Colonizing Recombinant Bacteria

PubMed Central

Shim, Hojae; Chauhan, Sadhana; Ryoo, Doohyun; Bowers, Kally; Thomas, Stuart M.; Canada, Keith A.; Burken, Joel G.; Wood, Thomas K.

2000-01-01

Indigenous bacteria from poplar tree (Populus canadensis var. eugenei ‘Imperial Carolina’) and southern California shrub rhizospheres, as well as two tree-colonizing Rhizobium strains (ATCC 10320 and ATCC 35645), were engineered to express constitutively and stably toluene o-monooxygenase (TOM) from Burkholderia cepacia G4 by integrating the tom locus into the chromosome. The poplar and Rhizobium recombinant bacteria degraded trichloroethylene at a rate of 0.8 to 2.1 nmol/min/mg of protein and were competitive against the unengineered hosts in wheat and barley rhizospheres for 1 month (colonization occurred at a level of 1.0 × 105 to 23 × 105 CFU/cm of root). In addition, six of these recombinants colonized poplar roots stably and competitively with populations as large as 79% ± 12% of all rhizosphere bacteria after 28 days (0.2 × 105 to 31 × 105 CFU/cm of root). Furthermore, five of the most competitive poplar recombinants (e.g., Pb3-1 and Pb5-1, which were identified as Pseudomonas sp. strain PsK recombinants) retained the ability to express TOM for 29 days as 100% ± 0% of the recombinants detected in the poplar rhizosphere expressed TOM constitutively. PMID:11055909

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources

USGS Publications Warehouse

Mika, K.B.; Imamura, G.; Chang, C.; Conway, V.; Fernandez, G.; Griffith, J.F.; Kampalath, R.A.; Lee, C.M.; Lin, C.-C.; Moreno, R.; Thompson, S.; Whitman, R.L.; Jay, J.A.

2009-01-01

Aim: Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills. Methods and Results: Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0??23 and -1??02 per day, and for enterococci between -0??5 and -1??0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall. Conclusions: Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels. Significance and Impact of the Study: Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent. ?? 2009 The Society for Applied Microbiology.

Radiography-based score indicative for the pathogenicity of bacteria in odontogenic infections.

PubMed

Cachovan, Georg; Blessmann, Marco; Schön, Gerhard; Rother, Uwe; Heiland, Max; Stürenburg, Enno; Platzer, Ursula; Sobottka, Ingo

2014-10-01

To develop a new radiography-based score to assess the potential of bacteria to cause odontogenic infections derived from the occurrence of bacteria at small or large radiographical lesions. The patients analyzed were a sub-population from a large randomized clinical trial comparing moxifloxacin and clindamycin in the treatment of inflammatory infiltrates and odontogenic abscesses. Routine radiographs were used to analyze the area of the periapical radiolucent lesions. Lesions were stratified by their radiographically measured area as large (>9 mm(2)) or small (≤9 mm(2)). A risk ratio was calculated for each species from the frequency of their occurrence in large vs in small lesions. Fifty-one patients, 19 with abscesses and 32 with infiltrates, were evaluated. Overall, the radiographical lesion areas ranged from 0.4-46.2 mm(2) (median = 9 mm(2)). An increased risk (risk ratio >1) to occur at large abscess lesions was observed for Prevotella (P.) oralis, P. buccae, P. oris, P. intermedia, Fusobacterium nucleatum and Streptococcus (Strep.) anginosus group. An increased risk to occur at large infiltrate lesions was found for Strep. salivarius, Strep. parasanguis, Strep. anginosus group, Capnocytophaga spp., Neisseria (N.) sicca, Neisseria spp., Staphylococcus (Staph.) aureus, P. intermedia, P. buccae, Prevotella spp. and P. melaninogenica. The radiography-based score suggests that certain Prevotella spp., F. nucleatum and Strep. anginosus groups play a crucial role in the pathogenesis of odontogenic abscesses, and that various streptococci, Neisseria spp., Capnocytophaga spp., Staph. aureus and Prevotella spp. are involved in the pathogenesis of odontogenic infiltrates.

Bacteriophages: the possible solution to treat infections caused by pathogenic bacteria.

PubMed

El-Shibiny, Ayman; El-Sahhar, Salma

2017-11-01

Since their discovery in 1915, bacteriophages have been used to treat bacterial infections in animals and humans because of their unique ability to infect their specific bacterial hosts without affecting other bacterial populations. The research carried out in this field throughout the 20th century, largely in Georgia, part of USSR and Poland, led to the establishment of phage therapy protocols. However, the discovery of penicillin and sulfonamide antibiotics in the Western World during the 1930s was a setback in the advancement of phage therapy. The misuse of antibiotics has reduced their efficacy in controlling pathogens and has led to an increase in the number of antibiotic-resistant bacteria. As an alternative to antibiotics, bacteriophages have become a topic of interest with the emergence of multidrug-resistant bacteria, which are a threat to public health. Recent studies have indicated that bacteriophages can be used indirectly to detect pathogenic bacteria or directly as biocontrol agents. Moreover, they can be used to develop new molecules for clinical applications, vaccine production, drug design, and in the nanomedicine field via phage display.

Do foliar endophytic bacteria fix nitrogen?

NASA Astrophysics Data System (ADS)

Kueppers, L. M.; Moyes, A. B.; Frank, C.; Pett-Ridge, J.; Carper, D.; Vandehey, N.; O'Neil, J.; Dekas, A.

2015-12-01

Endophytic microorganisms - bacteria and fungi that live inside healthy plant tissue - are a relatively unexplored source of functional diversity in natural ecosystems. Prior to modern sequencing technology, detecting uncultured endophytic bacteria and assessing their putative functions was challenging. However, recent work has revealed a remarkable diversity of as yet non-culturable endophytic taxa and is beginning to identify functional roles within plant microbiomes. We recently examined bacterial communities in the foliage of a long-lived, high-elevation conifer species, limber pine (Pinus flexilis), and discovered a community strongly dominated by acetic acid bacteria (Acetobacteraceae), with several taxa closely related to known nitrogen fixers. Given limber pine's status as a pioneer species that is able to grow in low fertility soils, we hypothesized that this bacterial community has a potential functional role in fixing atmospheric nitrogen, providing a source of this limiting nutrient to the host tree. We used the radioisotope 13N2 to confirm that N2 rapidly diffuses into pine needles, where it could potentially be fixed. With an acetylene reduction assay we confirmed nitrogenase enzyme activity inside excised twigs 4 times over a growing season, and estimate potential rates of N2 fixation at 0.1 nmol N2 g needle-1 hr-1. Scaled to the stand level, this N input could be on the order of ~20 mg N m-2 d-1 over a growing season. While these rates are low, the long lifespan of individual trees (~1000 years) makes them biologically meaningful. Still, measured rates of acetylene reduction and bulk 15N2 incorporation are quite variable in space and time. Much work remains to better characterize the plant-microbial interactions in this system, including the rates of nitrogen fixation and their variability over the growing season, across edaphic conditions, among host species, and through plant development; and to determine which community members are responsible

Influence of adhesion to activated carbon particles on the viability of waterborne pathogenic bacteria under flow.

PubMed

van der Mei, Henny C; Atema-Smit, Jelly; Jager, Debbie; Langworthy, Don E; Collias, Dimitris I; Mitchell, Michael D; Busscher, Henk J

2008-07-01

In rural areas around the world, people often rely on water filtration plants using activated carbon particles for safe water supply. Depending on the carbon surface, adhering microorganisms die or grow to form a biofilm. Assays to assess the efficacy of activated carbons in bacterial removal do not allow direct observation of bacterial adhesion and the determination of viability. Here we propose to use a parallel plate flow chamber with carbon particles attached to the bottom plate to study bacterial adhesion to individual carbon particles and determine the viability of adhering bacteria. Observation and enumeration is done after live/dead staining in a confocal laser scanning microscope. Escherichiae coli adhered in higher numbers than Raoultella terrigena, except to a coconut-based carbon, which showed low bacterial adhesion compared to other wood-based carbon types. After adhesion, 83-96% of the bacteria adhering to an acidic carbon were dead, while on a basic carbon 54-56% were dead. A positively charged, basic carbon yielded 76-78% bacteria dead, while on a negatively charged coconut-based carbon only 32-37% were killed upon adhesion. The possibility to determine both adhesion as well as the viability of adhering bacteria upon adhesion to carbon particles is most relevant, because if bacteria adhere but remain viable, this still puts the water treatment system at risk, as live bacteria can grow and form a biofilm that can then be shedded to cause contamination. (c) 2008 Wiley Periodicals, Inc.

New Approach To Produce Water Free of Bacteria, Viruses, and Halogens in a Recyclable System▿

PubMed Central

Ahmed, Abd El-Shafey I.; Cavalli, Gabriel; Bushell, Michael E.; Wardell, John N.; Pedley, Steve; Charles, Katarina; Hay, John N.

2011-01-01

The antimicrobial activity of a new cross-linked N-halamine polymer against bacteria and viruses was evaluated. The polymer achieved a 9-log10 reduction of bacteria (both Escherichia coli and Staphylococcus aureus) in 1.5 h and a 5-log10 reduction of bacteriophage PRD1 in 3 h. At the same time, the ability of the nonhalogenated polymer to trap halide ions was examined. The polymer was incorporated into a multifiltration system to study the ability to produce water free of bacteria, viruses, and halide ions. The antimicrobial activity, useful lifetime, halide ion level, and recycling possibilities of the system were quantified on a laboratory scale. A design for a large-scale multifiltration system based on this polymer is proposed. PMID:21115711

Aptamer-based hydrogel barcodes for the capture and detection of multiple types of pathogenic bacteria.

PubMed

Xu, Yueshuang; Wang, Huan; Luan, Chengxin; Liu, Yuxiao; Chen, Baoan; Zhao, Yuanjin

2018-02-15

Rapid and sensitive diagnosing hematological infections based on the separation and detection of pathogenic bacteria in the patient's blood is a significant challenge. To address this, we herein present a new barcodes technology that can simultaneously capture and detect multiple types of pathogenic bacteria from a complex sample. The barcodes are poly (ethylene glycol) (PEG) hydrogel inverse opal particles with characteristic reflection peak codes that remain stable during bacteria capture on their surfaces. As the spherical surface of the particles has ordered porous nanostructure, the barcodes can provide not only more surface area for probe immobilization and reaction, but also a nanopatterned platform for highly efficient bioreactions. In addition, the PEG hydrogel scaffold could decrease the non-specificity adsorption by its anti-adhesive effect, and the decorated aptamer probes in the scaffolds could increase the sensitivity, reliability, and specificity of the bacteria capture and detection. Moreover, the tagged magnetic nanoparticles in the PEG scaffold could impart the barcodes with controllable movement under magnetic fields, which can be used to significantly increase the reaction speed and simplify the processing of the bioassays. Based on the describe barcodes, it was demonstrated that the bacteria could be captured and identified even at low bacterial concentrations (100 CFU mL -1 ) within 2.5h, which is effectively shortened in comparison with the "gold standard" in clinic. These features make the barcodes ideal for capturing and detecting multiple bacteria from clinical samples for hematological infection diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

PubMed

Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

2013-10-01

The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

[Toxic shock syndrome caused by pyogenic bacteria].

PubMed

Gábor, Zsuzsa; Szekeres, Sándor; Gacs, Mária

2003-01-12

Case reports and review of the literature. Severe toxic shock syndrome caused by invasive infection with pyogenic bacteria Staphylococcus aureus or group A Streptococcus pyogenes, with high mortality rates in cases of the latter, remained one of the most problematic chapters of critical care medicine to date. To give an overview on the epidemiology, clinical manifestations, the complex therapeutical approaches of the syndrome and, on the role and mechanisms of action of bacterial superantigens in the pathophysiological processes as well. Literary data, and some illustrative selected cases demonstrate that, the incidence of TSS shows increasing tendency worldwide and, that otherwise healthy, younger people are the most frequently affected. As for prognosis: early diagnosis and treatment with sufficient radicality are of decisive importance.

Ecology of the oral microbiome: beyond bacteria

PubMed Central

Baker, Jonathon L.; Bor, Batbileg; Agnello, Melissa; Shi, Wenyuan; He, Xuesong

2017-01-01

Although great strides have been made in understanding the complex bacterial community inhabiting the human oral cavity, for a variety of (mainly technical) reasons the ecological contributions of oral fungi, viruses, phages, and the candidate phyla radiation (CPR) group of ultra-small bacteria have remained understudied. Several recent reports have illustrated the diversity and importance of these organisms in the oral cavity, while TM7x and Candida albicans have served as crucial paradigms for CPR species and oral fungi, respectively. A comprehensive understanding of the oral microbiota and its influence on host health and disease will require a holistic view that emphasizes interactions among different residents within the oral community, as well as their interaction with the host. PMID:28089325

Living biointerfaces based on non-pathogenic bacteria support stem cell differentiation

NASA Astrophysics Data System (ADS)

Hay, Jake J.; Rodrigo-Navarro, Aleixandre; Hassi, Karoliina; Moulisova, Vladimira; Dalby, Matthew J.; Salmeron-Sanchez, Manuel

2016-02-01

Lactococcus lactis, a non-pathogenic bacteria, has been genetically engineered to express the III7-10 fragment of human fibronectin as a membrane protein. The engineered L. lactis is able to develop biofilms on different surfaces (such as glass and synthetic polymers) and serves as a long-term substrate for mammalian cell culture, specifically human mesenchymal stem cells (hMSC). This system constitutes a living interface between biomaterials and stem cells. The engineered biofilms remain stable and viable for up to 28 days while the expressed fibronectin fragment induces hMSC adhesion. We have optimised conditions to allow long-term mammalian cell culture, and found that the biofilm is functionally equivalent to a fibronectin-coated surface in terms of osteoblastic differentiation using bone morphogenetic protein 2 (BMP-2) added to the medium. This living bacteria interface holds promise as a dynamic substrate for stem cell differentiation that can be further engineered to express other biochemical cues to control hMSC differentiation.

PCR detection of uncultured rumen bacteria.

PubMed

Rosero, Jaime A; Strosová, Lenka; Mrázek, Jakub; Fliegerová, Kateřina; Kopečný, Jan

2012-07-01

16S rRNA sequences of ruminal uncultured bacterial clones from public databases were phylogenetically examined. The sequences were found to form two unique clusters not affiliated with any known bacterial species: cluster of unidentified sequences of free floating rumen fluid uncultured bacteria (FUB) and cluster of unidentified sequences of bacteria associated with rumen epithelium (AUB). A set of PCR primers targeting 16S rRNA of ruminal free uncultured bacteria and rumen epithelium adhering uncultured bacteria was designed based on these sequences. FUB primers were used for relative quantification of uncultured bacteria in ovine rumen samples. The effort to increase the population size of FUB group has been successful in sulfate reducing broth and culture media supplied with cellulose.

Mineralized remains of morphotypes of filamentous cyanobacteria in carbonaceous meteorites

NASA Astrophysics Data System (ADS)

Hoover, Richard B.

2005-09-01

The quest for conclusive evidence of microfossils in meteorites has been elusive. Abiotic microstructures, mineral grains, and even coating artifacts may mimic unicellular bacteria, archaea and nanobacteria with simple spherical or rod morphologies (i.e., cocci, diplococci, bacilli, etc.). This is not the case for the larger and more complex microorganisms, colonies and microbial consortia and ecosystems. Microfossils of algae, cyanobacteria, and cyanobacterial and microbial mats have been recognized and described from many of the most ancient rocks on Earth. The filamentous cyanobacteria and sulphur-bacteria have very distinctive size ranges, complex and recognizable morphologies and visibly differentiated cellular microstructures. The taphonomic modes of fossilization and the life habits and processes of these microorganisms often result in distinctive chemical biosignatures associated with carbonization, silicification, calcification, phosphatization and metal-binding properties of their cell-walls, trichomes, sheaths and extracellular polymeric substances (EPS). Valid biogenicity is provided by the combination of a suite of known biogenic elements (that differ from the meteorite matrix) found in direct association with recognizable and distinct biological features and microstructures (e.g., uniseriate or multiseriate filaments, trichomes, sheaths and cells of proper size/size range); specialized cells (e.g., basal or apical cells, hormogonia, akinetes, and heterocysts); and evidence of growth characteristics (e.g., spiral filaments, robust or thin sheaths, laminated sheaths, true or false branching of trichomes, tapered or uniform filaments) and evidence of locomotion (e.g. emergent cells and trichomes, coiling hormogonia, and hollow or flattened and twisted sheaths). Since 1997 we have conducted Environmental and Field Emission Scanning Electron Microscopy (ESEM and FESEM) studies of freshly fractured interior surfaces of carbonaceous meteorites, terrestrial

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

PubMed

Erwin, Patrick M; Olson, Julie B; Thacker, Robert W

2011-01-01

Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient

Lipoteichoic acid (LTA) and lipopolysaccharides (LPS) from periodontal pathogenic bacteria facilitate oncogenic herpesvirus infection within primary oral cells.

PubMed

Dai, Lu; DeFee, Michael R; Cao, Yueyu; Wen, Jiling; Wen, Xiaofei; Noverr, Mairi C; Qin, Zhiqiang

2014-01-01

Kaposi's sarcoma (KS) remains the most common tumor arising in patients with HIV/AIDS, and involvement of the oral cavity represents one of the most common clinical manifestations of this tumor. HIV infection incurs an increased risk for periodontal diseases and oral carriage of a variety of bacteria. Whether interactions involving pathogenic bacteria and oncogenic viruses in the local environment facilitate replication or maintenance of these viruses in the oral cavity remains unknown. In the current study, our data indicate that pretreatment of primary human oral fibroblasts with two prototypical pathogen-associated molecular patterns (PAMPs) produced by oral pathogenic bacteria-lipoteichoic acid (LTA) and lipopolysaccharide (LPS), increase KSHV entry and subsequent viral latent gene expression during de novo infection. Further experiments demonstrate that the underlying mechanisms induced by LTA and/or LPS include upregulation of cellular receptor, increasing production of reactive oxygen species (ROS), and activating intracellular signaling pathways such as MAPK and NF-κB, and all of which are closely associated with KSHV entry or gene expression within oral cells. Based on these findings, we hope to provide the framework of developing novel targeted approaches for treatment and prevention of oral KSHV infection and KS development in high-risk HIV-positive patients.

Horizontal gene transfer between bacteria.

PubMed

Heuer, Holger; Smalla, Kornelia

2007-01-01

Horizontal gene transfer (HGT) refers to the acquisition of foreign genes by organisms. The occurrence of HGT among bacteria in the environment is assumed to have implications in the risk assessment of genetically modified bacteria which are released into the environment. First, introduced genetic sequences from a genetically modified bacterium could be transferred to indigenous micro-organisms and alter their genome and subsequently their ecological niche. Second, the genetically modified bacterium released into the environment might capture mobile genetic elements (MGE) from indigenous micro-organisms which could extend its ecological potential. Thus, for a risk assessment it is important to understand the extent of HGT and genome plasticity of bacteria in the environment. This review summarizes the present state of knowledge on HGT between bacteria as a crucial mechanism contributing to bacterial adaptability and diversity. In view of the use of GM crops and microbes in agricultural settings, in this mini-review we focus particularly on the presence and role of MGE in soil and plant-associated bacteria and the factors affecting gene transfer.

As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases

PubMed Central

Siqueira, José F.; Rôças, Isabela N.

2013-01-01

It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease. PMID:23717756

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

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

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.

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.

[The antagonistic properties of microaerophilic bacteria isolated from the human and mink digestive tracts].

PubMed

Sudenko, V I; Groma, L I; Podgorskiĭ, V S

1996-01-01

Study of antagonistic properties of microaerophilic bacteria isolated from human and mink gastroenteric tract have helped to establish differences in species composition, quantity and level of antagonistic activity of the studied microorganisms in respect to pathogenic microflora. It is shown that lactic acid bacteria identified as Lactobacillus fermentum and L. reuteri prevail among the strains isolated from the stomach and thin intestine of minks kept in the 30-km zone of Chernobyl NPP. Species composition of microaerophilic bacteria isolated from the digestive tract of the control minks is more variable. Antagonistically active bifidobacteria prevail in large intestine of experimental and control animals. Strains of lactic acid bacteria with the expressed antagonistic activity belonging to L. bavaricus, L. reuteri, L. coryniformis and L. maltaromicus have been found parallel with such known producers of antibiotic-like substances as L. fermentum. L. acidophilum. Streptococcus faecalis and bifidobacteria. L. maltaromicus most frequently occurred among antagonistically active strains revealed in feces of people which stayed in the zone of liquidation of the Chernobyl accident. Microaerophilic strains of bacteria (lactic acid, bifidobacteria and enterococci) manifest the expressed antagonistic activity connected with the capacity to not only acid formation but also to accumulation of antibiotic products of unknown nature. A strain of lactic acid bacteria L. fermentum 91 has been isolated from the contents of human gastroenteric tract. These bacteria are distinguished by most expressed and stable antagonism and characterized by the lack of pathogenicity in respect of albino mice that may be used to raise the microorganism resistance to gastric diseases.

Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan, Indonesia.

PubMed

Isobe, Kazuo; Otsuka, Shigeto; Sudiana, Imade; Nurkanto, Arif; Senoo, Keishi

2009-10-01

Soil bacterial community compositions in burnt and unburnt areas in a tropical rainforest in East Kalimantan, Indonesia, were investigated 8 and 9 years after a fire by denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene. Three study sites were set in the forest area devoid of fire damage (control), and in the lightly damaged and heavily damaged forest areas. Succession of aboveground vegetation in the two damaged areas had clearly proceeded after the fire, but the vegetation types still differed from the unburnt area at the time of this study. Community composition of total soil bacteria was similar among the three areas, and so was that of actinobacteria. However, the composition of ammonia oxidizing bacteria clearly differed depending on the presence or absence of past fire damage. These results indicate that even nearly a decade after the forest fire, impacts of the fire remained on the community composition of ammonia oxidizing bacteria, but not apparently on those of dominant bacteria and actinobacteria.

Mycorrhiza helper bacteria

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

Deveau, Aurelie; Labbe, Jessy

This chapter focuses on the Mycorrhiza Helper Bacteria (MHB), a generic name given to bacteria which stimulate the formation of mycorrhizal symbiosis. By extension, some bacterial strains that positively impact the functioning of mycorrhizal symbiosis are also called MHB. These bacteria have applicative interests, as they indirectly improve the health and growth of tree seedlings. MHB are not restricted to a specific type of ecosystem, but are rather generalist in the way that they associate with both herbaceous and woody mycorrhizal plants from boreal, temperate, arid and tropical ecosystems. However, understanding the molecular mechanisms and their specificities will help usmore » to know more about the ecology of the MHB. The process of acquisition varies between fungal species; while ectomycorrhizal fungi most probably recurrently acquire them from the environment, the association between bacterial endosymbionts and Glomeromycota probably dates back to very ancient times, and has since been vertically transmitted.« less

Devescovinid features, a remarkable surface cytoskeleton, and epibiotic bacteria revisited in Mixotricha paradoxa, a parabasalid flagellate.

PubMed

Brugerolle, G

2004-10-01

This work reports on the flagellate systematics and phylogeny, cytoskeleton, prokaryote-eukaryote cell junction organisation, and epibiotic bacteria identification. It confirms the pioneer 1964 study on Mixotricha paradoxa and supplies new information. Mixotricha paradoxa has a cresta structure specific to devescovinid parabasalid flagellates, a slightly modified recurrent flagellum, and an axostylar tube containing two lamina-shaped parabasal fibres. However, many parabasal profiles are distributed throughout the cell body. There is a conspicuous cortical microfibrillar network whose strands are related to cell junction structures subjacent to epibiotic bacteria. The supposed actin composition of this network could not be demonstrated with anti-actin antibodies or phalloidin labelling. Four types of epibiotic bacteria were described. Bacillus-shaped bacteria with a Gram-negative organisation are nested in alternate rows on most of the surface of the protozoon. They induce a striated calyxlike junction structure beneath the adhesion zone linked to the cortical microfibrillar network. Slender spirochetes are attached by one differentiated end to the plasma membrane of the protozoon, forming knobs on the cell surface. Two very similar long rod-shaped bacteria are also attached on the knobs of the plasma membrane. A large spirochete attributed to the genus Canaleparolina is also attached to the protozoon. Observations on epibiotic bacteria and of their attachments are compared with several described epibiotic bacteria of symbiotic protozoa and with the results of the molecular identification of the epibiotic bacteria of M. paradoxa.

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

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.

PubMed

Cunningham, J A; Thomas, C-W; Bengtson, S; Marone, F; Stampanoni, M; Turner, F R; Bailey, J V; Raff, R A; Raff, E C; Donoghue, P C J

2012-05-07

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils

PubMed Central

Cunningham, J. A.; Thomas, C.-W.; Bengtson, S.; Marone, F.; Stampanoni, M.; Turner, F. R.; Bailey, J. V.; Raff, R. A.; Raff, E. C.; Donoghue, P. C. J.

2012-01-01

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains. PMID:22158954

A nanovehicle developed for treating deep-seated bacteria using low-dose X-ray.

PubMed

Pan, Chien-Lin; Chen, Ming-Hong; Tung, Fu-I; Liu, Tse-Ying

2017-01-01

needed for avoiding amputation. To date, several non-antibiotic approaches, such as Ag nanoparticles, graphene-based materials, photocatalysis, and photodynamic therapy have been proposed to inhibit and/or kill bacteria. However, the major challenges of photochemical strategies, specificity and limited penetration depth of light source, still remain for treating the deep-seated bacteria. To overcome these problems, we developed a novel nanovehicle that exerted toxic effects specifically on bacteria following activation by a deeply penetrative low-dose X-ray, without damaging normal cells. As such, it realizes a deeply photochemical route for treating the deep-seated bacteria. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Proteorhodopsin-bearing bacteria in Antarctic sea ice.

PubMed

Koh, Eileen Y; Atamna-Ismaeel, Nof; Martin, Andrew; Cowie, Rebecca O M; Beja, Oded; Davy, Simon K; Maas, Elizabeth W; Ryan, Ken G

2010-09-01

Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.

Clinical microbiology of coryneform bacteria.

PubMed Central

Funke, G; von Graevenitz, A; Clarridge, J E; Bernard, K A

1997-01-01

Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed. PMID:8993861

[Occurrence of bacteria of the Yersinia genus in surface water].

PubMed

Krogulska, B; Maleszewska, J

1992-01-01

The aim of the study was determination of the frequency of occurrence of Yersinia genus bacteria in surface waters polluted to various degrees with bacteria of the coliform and of fecal coli. For detection of Yersinia rods the previously elaborated medium Endo MLCe and the membrane filter method were applied. Samples of 42 surface waters were examined, including 26 from rivers and 16 from lakes, ponds and clay-pits. On the basis of sanitary bacteriological analysis 16 surface waters were classified to class I purity, 10 to class II, the remaining ones to class III or beyond classification. Yersinia rods were detected in 15 water bodies that is 35.7% of the examined waters. A total of 27 Yersinia strains were identified with dominance of Y. intermedia (14 strains) and Y. enterocolitica (10 strains). Three strains represented by the species Yersinia frederiksenii. Most of the Y. enterocolitica strains belonged to biotype 1, the particular strains being represented by various serotypes. Hence their different origin may be concluded. The pathogenic serotypes 0:3 and 0:9 of Yersinia enterocolitica were not detected.

Planktonic Marine Luminous Bacteria: Species Distribution in the Water Column

PubMed Central

Ruby, E. G.; Greenberg, E. P.; Hastings, J. W.

1980-01-01

Luminous bacteria were isolated from oceanic water samples taken throughout the upper 1,000 m and ranged in density from 0.4 to 30 colony-forming units per 100 ml. Generally, two peaks in abundance were detected: one in the upper 100 m of the water column, which consisted primarily of Beneckea spp.; and a second between 250 and 1,000 m, which consisted almost entirely of Photobacterium phosphoreum. The population of P. phosphoreum remained relatively stable in abundance at one station that was visited three times over a period of 6 months. However, the abundance of luminous Beneckea spp. isolated from the upper waters fluctuated considerably; they were, as high as 30 colony-forming units per 100 ml in the spring and were not detected in the winter. Water samples from depths of 4,000 to 7,000 m contained less than 0.1 luminous colony-forming unit per 100 ml. The apparent vertical stratification of two taxa of oceanic luminous bacteria may reflect not only differences in physiology, but also depth-related, species-specific symbiotic associations. PMID:16345502

A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria.

PubMed

Yang, Yunpeng; Zhang, Lu; Huang, He; Yang, Chen; Yang, Sheng; Gu, Yang; Jiang, Weihong

2017-01-24

Catabolite control protein A (CcpA) is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR) and carbon catabolite activation (CCA), two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt) consensus site that is called a catabolite response element (cre) within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named cre var , has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA). It was found that the length of the intervening spacer of cre var can affect CcpA binding affinity, and moreover, the core palindromic sequence of cre var is the key structure for regulation. Such a variable architecture of cre var shows potential importance for CcpA's diverse and fine regulation. A total of 103 potential cre var sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs), and 30 sites were confirmed to be bound by CcpA. These 30 cre var sites are associated with 27 genes involved in many important pathways. Also of significance, the cre var sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria. In Gram-positive bacteria, the global regulator CcpA controls a large number of important physiological and metabolic processes. Although a typical consensus CcpA-binding site, cre, has been identified, it remains

Freeing Water from Viruses and Bacteria

NASA Technical Reports Server (NTRS)

2004-01-01

Four years ago, Argonide Corporation, a company focused on the research, production, and marketing of specialty nano materials, was seeking to develop applications for its NanoCeram[R] fibers. Only 2 nanometers in diameter, these nano aluminum oxide fibers possessed unusual bio-adhesive properties. When formulated into a filter material, the electropositive fibers attracted and retained electro-negative particles such as bacteria and viruses in water-based solutions. This technology caught the interest of NASA as a possible solution for improved water filtration in space cabins. NASA's Johnson Space Center awarded Sanford, Florida-based Argonide a Phase I Small Business Innovation Research (SBIR) contract to determine the feasibility of using the company's filter for purifying recycled space cabin water. Since viruses and bacteria can be carried aboard space cabins by space crews, the ability to detect and remove these harmful substances is a concern for NASA. The Space Agency also desired an improved filter to polish the effluent from condensed and waste water, producing potable drinking water. During its Phase I partnership with NASA, Argonide developed a laboratory-size filter capable of removing greater than 99.9999 percent of bacteria and viruses from water at flow rates more than 200 times faster than virus-rated membranes that remove particles by sieving. Since the new filter s pore size is rather large compared to other membranes, it is also less susceptible to clogging by small particles. In September 2002, Argonide began a Phase II SBIR project with Johnson to develop a full-size cartridge capable of serving a full space crew. This effort, which is still ongoing, enabled the company to demonstrate that its filter media is an efficient absorbent for DNA and RNA.

Bacteria and wound healing.

PubMed

Edwards, Ruth; Harding, Keith G

2004-04-01

Wound healing is a complex process with many potential factors that can delay healing. There is increasing interest in the effects of bacteria on the processes of wound healing. All chronic wounds are colonized by bacteria, with low levels of bacteria being beneficial to the wound healing process. Wound infection is detrimental to wound healing, but the diagnosis and management of wound infection is controversial, and varies between clinicians. There is increasing recognition of the concept of critical colonization or local infection, when wound healing may be delayed in the absence of the typical clinical features of infection. The progression from wound colonization to infection depends not only on the bacterial count or the species present, but also on the host immune response, the number of different species present, the virulence of the organisms and synergistic interactions between the different species. There is increasing evidence that bacteria within chronic wounds live within biofilm communities, in which the bacteria are protected from host defences and develop resistance to antibiotic treatment. An appreciation of the factors affecting the progression from colonization to infection can help clinicians with the interpretation of clinical findings and microbiological investigations in patients with chronic wounds. An understanding of the physiology and interactions within multi-species biofilms may aid the development of more effective methods of treating infected and poorly healing wounds. The emergence of consensus guidelines has helped to optimize clinical management.

Application of a plasmid classification system to determine prevalence of replicon families among multidrug resistant enterococci

USDA-ARS?s Scientific Manuscript database

The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. However, prevalence of plasmids from commensal bacteria in food animals such as the enterococci remains largely unknown. In this study, the prevale...

Laser-Based Identification of Pathogenic Bacteria

ERIC Educational Resources Information Center

Rehse, Steven J.

2009-01-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the…

Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities.

PubMed

Alvarez-Pérez, Sergio; Herrera, Carlos M; de Vega, Clara

2012-06-01

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Bacteriological Assessment of Pneumonia Caused by Gram-Negative Bacteria in Patients Hospitalized in Intensive Care Unit.

PubMed

Guzek, A; Korzeniewski, K; Tomaszewski, D; Rybicki, Z; Zwolińska, E

2017-01-01

The article presents the results of 11-year study (2005-2015) of Gram-negative bacteria responsible for pneumonia in 2033 mechanically ventilated patients hospitalized in Intensive Care Unit. Of 8796 biological samples, consisting mainly of bronchial aspirate (97.9 %), 2056 bacterial strains were isolated and subjected to identification. VITEK 2 was used to determine drug susceptibility (classified according to the EUCAST criteria). ESBL, MBL and KPC-producing strains were identified by means of phenotypic methods using appropriate discs. The findings were that the predominant bacteria responsible for infections consisted of Enterobacteriaceae (42.0 %), Acinetobacter baumannii (37.2 %), Pseudomonas aeruginosa (16.1 %), and Stenotrophomonas maltophila (4.7 %). We observed a rise in the number of bacteria causing pneumonia throughout the study period, especially in S. maltophila and Enterobacteriaceae ESBL (+). Gram-negative bacilli were 100 % susceptible to colistin, apart from naturally resistant strains such as Proteus mirabilis, Serratia marcescens, whereas Enterobacteriaceae ESBL (+) were susceptible to imipenem and meropenem. Acinetobacter baumannii strains exhibited the lowest drug susceptibility. In conclusion, we report an increase in the prevalence of pneumonia associated with Gram-negative bacteria in mechanically ventilated intensive care patients. Colistin remains the most effective drug against the majority of Gram-negative bacteria. Therapeutic problems are common in the course of treatment of Acinetobacter baumannii infections.

Extracellular deoxyribonuclease production by periodontal bacteria.

PubMed

Palmer, L J; Chapple, I L C; Wright, H J; Roberts, A; Cooper, P R

2012-08-01

Whilst certain bacteria have long been known to secrete extracellular deoxyribonuclease (DNase), the purpose in microbial physiology was unclear. Recently, however, this enzyme has been demonstrated to confer enhanced virulence, enabling bacteria to evade the host's immune defence of extruded DNA/chromatin filaments, termed neutrophil extracellular traps (NETs). As NETs have recently been identified in infected periodontal tissue, the aim of this study was to screen periodontal bacteria for extracellular DNase activity. To determine whether DNase activity was membrane bound or secreted, 34 periodontal bacteria were cultured in broth and on agar plates. Pelleted bacteria and supernatants from broth cultures were analysed for their ability to degrade DNA, with relative activity levels determined using an agarose gel electrophoresis assay. Following culture on DNA-supplemented agar, expression was determined by the presence of a zone of hydrolysis and DNase activity related to colony size. Twenty-seven bacteria, including red and orange complex members Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, Parvimonas micra, Prevotella intermedia, Streptococcus constellatus, Campylobacter rectus and Prevotella nigrescens, were observed to express extracellular DNase activity. Differences in DNase activity were noted, however, when bacteria were assayed in different culture states. Analysis of the activity of secreted DNase from bacterial broth cultures confirmed their ability to degrade NETs. The present study demonstrates, for the first time, that DNase activity is a relatively common property of bacteria associated with advanced periodontal disease. Further work is required to determine the importance of this bacterial DNase activity in the pathogenesis of periodontitis. © 2011 John Wiley & Sons A/S.

Mineral deposition in bacteria-filled and bacteria-free calcium bodies in the crustacean Hyloniscus riparius (Isopoda: Oniscidea).

PubMed

Vittori, Miloš; Rozman, Alenka; Grdadolnik, Jože; Novak, Urban; Štrus, Jasna

2013-01-01

Crustacean calcium bodies are epithelial sacs which contain a mineralized matrix. The objectives of this study were to describe the microscopic anatomy of calcium bodies in the terrestrial isopod Hyloniscus riparius and to establish whether they undergo molt-related structural changes. We performed 3D reconstruction of the calcium bodies from paraffin sections and analyzed their structure with light and electron microscopy. In addition, we analyzed the chemical composition of their mineralized matrices with micro-Raman spectroscopy. Two pairs of these organs are present in H. riparius. One pair is filled with bacteria while the other pair is not. In non-molting animals, the bacteria-filled calcium bodies contain apatite crystals and the bacteria-free calcium bodies enclose CaCO3-containing concretions with little organic matrix. During preparation for molt, an additional matrix layer is deposited in both pairs of calcium bodies. In the bacteria-filled calcium bodies it contains a mixture of calcium carbonate and calcium phosphate, whereas only calcium carbonate is present in bacteria-free calcium bodies. After ecdysis, all mineral components in bacteria-free calcium bodies and the additional matrix layer in bacteria-filled calcium bodies are completely resorbed. During calcium resorption, the apical surface of the calcium body epithelium is deeply folded and electron dense granules are present in spaces between epithelial cells. Our results indicate that the presence of bacteria might be linked to calcium phosphate mineralization. Calcium bodies likely provide a source of calcium and potentially phosphate for the mineralization of the new cuticle after molt. Unlike other terrestrial isopods, H. riparius does not form sternal CaCO3 deposits and the bacteria-free calcium bodies might functionally replace them in this species.

Mineral Deposition in Bacteria-Filled and Bacteria-Free Calcium Bodies in the Crustacean Hyloniscus riparius (Isopoda: Oniscidea)

PubMed Central

Vittori, Miloš; Rozman, Alenka; Grdadolnik, Jože; Novak, Urban; Štrus, Jasna

2013-01-01

Crustacean calcium bodies are epithelial sacs which contain a mineralized matrix. The objectives of this study were to describe the microscopic anatomy of calcium bodies in the terrestrial isopod Hyloniscus riparius and to establish whether they undergo molt-related structural changes. We performed 3D reconstruction of the calcium bodies from paraffin sections and analyzed their structure with light and electron microscopy. In addition, we analyzed the chemical composition of their mineralized matrices with micro-Raman spectroscopy. Two pairs of these organs are present in H. riparius. One pair is filled with bacteria while the other pair is not. In non-molting animals, the bacteria-filled calcium bodies contain apatite crystals and the bacteria-free calcium bodies enclose CaCO3-containing concretions with little organic matrix. During preparation for molt, an additional matrix layer is deposited in both pairs of calcium bodies. In the bacteria-filled calcium bodies it contains a mixture of calcium carbonate and calcium phosphate, whereas only calcium carbonate is present in bacteria-free calcium bodies. After ecdysis, all mineral components in bacteria-free calcium bodies and the additional matrix layer in bacteria-filled calcium bodies are completely resorbed. During calcium resorption, the apical surface of the calcium body epithelium is deeply folded and electron dense granules are present in spaces between epithelial cells. Our results indicate that the presence of bacteria might be linked to calcium phosphate mineralization. Calcium bodies likely provide a source of calcium and potentially phosphate for the mineralization of the new cuticle after molt. Unlike other terrestrial isopods, H. riparius does not form sternal CaCO3 deposits and the bacteria-free calcium bodies might functionally replace them in this species. PMID:23554963

Soil-borne reservoirs of antibiotic-resistant bacteria are established following therapeutic treatment of dairy calves.

PubMed

Liu, Jinxin; Zhao, Zhe; Orfe, Lisa; Subbiah, Murugan; Call, Douglas R

2016-02-01

We determined if antibiotics residues that are excreted from treated animals can contribute to persistence of resistant bacteria in agricultural environments. Administration of ceftiofur, a third-generation cephalosporin, resulted in a ∼ 3 log increase in ceftiofur-resistant Escherichia coli found in the faeces and pen soils by day 10 (P = 0.005). This resistant population quickly subsided in faeces, but was sustained in the pen soil (∼ 4.5 log bacteria g(-1)) throughout the trial (1 month). Florfenicol treatment resulted in a similar pattern although the loss of florfenicol-resistant E. coli was slower for faeces and remained stable at ∼ 6 log bacteria g(-1) in the soil. Calves were treated in pens where eGFP-labelled E. coli were present in the bedding (∼ 2 log g(-1)) resulting in amplification of the eGFP E. coli population ∼ 2.1 log more than eGFP E. coli populations in pens with untreated calves (day 4; P < 0.005). Excreted residues accounted for > 10-fold greater contribution to the bedding reservoir compared with shedding of resistant bacteria in faeces. Treatment with therapeutic doses of ceftiofur or florfenicol resulted in 2-3 log g(-1) more bacteria than the estimated ID50 (2.83 CFU g(-1)), consistent with a soil-borne reservoir emerging after antibiotic treatment that can contribute to the long-term persistence of antibiotic resistance in animal agriculture. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Cable Bacteria in Freshwater Sediments

PubMed Central

Kristiansen, Michael; Frederiksen, Rasmus B.; Dittmer, Anders Lindequist; Bjerg, Jesper Tataru; Trojan, Daniela; Schreiber, Lars; Damgaard, Lars Riis; Schramm, Andreas; Nielsen, Lars Peter

2015-01-01

In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. PMID:26116678

BioNLP Shared Task--The Bacteria Track.

PubMed

Bossy, Robert; Jourde, Julien; Manine, Alain-Pierre; Veber, Philippe; Alphonse, Erick; van de Guchte, Maarten; Bessières, Philippe; Nédellec, Claire

2012-06-26

We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions. Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system. The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found common trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.

Storing drinking-water in copper pots kills contaminating diarrhoeagenic bacteria.

PubMed

Sudha, V B Preethi; Ganesan, Sheeba; Pazhani, G P; Ramamurthy, T; Nair, G B; Venkatasubramanian, Padma

2012-03-01

Microbially-unsafe water is still a major concern in most developing countries. Although many water-purification methods exist, these are expensive and beyond the reach of many people, especially in rural areas. Ayurveda recommends the use of copper for storing drinking-water. Therefore, the objective of this study was to evaluate the effect of copper pot on microbially-contaminated drinking-water. The antibacterial effect of copper pot against important diarrhoeagenic bacteria, including Vibrio cholerae O1, Shigella flexneri 2a, enterotoxigenic Escherichia coli, enteropathogenic E. coli, Salmonella enterica Typhi, and Salmonella Paratyphi is reported. When drinking-water (pH 7.83 +/- 0.4; source: ground) was contaminated with 500 CFU/mL of the above bacteria and stored in copper pots for 16 hours at room temperature, no bacteria could be recovered on the culture medium. Recovery failed even after resuscitation in enrichment broth, followed by plating on selective media, indicating loss of culturability. This is the first report on the effect of copper on S. flexneri 2a, enteropathogenic E. coli, and Salmonella Paratyphi. After 16 hours, there was a slight increase in the pH of water from 7.83 to 7.93 in the copper pots while the other physicochemical parameters remained unchanged. Copper content (177 +/- 16 ppb) in water stored in copper pots was well within the permissible limits of the World Health Organization. Copper holds promise as a point-of-use solution for microbial purification of drinking-water, especially in developing countries.

Bacteria Counter

NASA Technical Reports Server (NTRS)

1981-01-01

Science Applications, Inc.'s ATP Photometer makes a rapid and accurate count of the bacteria in a body fluid sample. Instrument provides information on the presence and quantity of bacteria by measuring the amount of light emitted by the reaction between two substances. Substances are ATP adenosine triphosphate and luciferase. The reactants are applied to a human body sample and the ATP Photometer observes the intensity of the light emitted displaying its findings in a numerical output. Total time lapse is usually less than 10 minutes, which represents a significant time savings in comparison of other techniques. Other applications are measuring organisms in fresh and ocean waters, determining bacterial contamination of foodstuffs, biological process control in the beverage industry, and in assay of activated sewage sludge.

Microbial Transformation of Dicarboxylic Acids by Airborne Bacteria

NASA Astrophysics Data System (ADS)

Cote, V.; Ariya, P.

2004-05-01

Organic aerosols are assumed to be key players in driving climatic changes and can cause health problems for human. Dicarboxylic acids (DCA) include a large fraction of identified important class of organic aerosols. In addition to direct sources, DCA are partly formed as the result of ozonolysis of terpenes and cyclic alkenes. Previous works in our laboratory show that airborne fungi collected from urban and suburban air play an important role in the transformation of severals organic aerosols such as DCA. Our present study focuses on understanding the potential chemical transformation induced by airborne bacteria and on identification of the transformation products. Airborne bacteria have been collected using a biosampler and cultivated on a solid media. Each bacterial colony is being tested by HPLC for their ability to transform DCA in liquid cultures. Also, GC-MS, SPME and NMR are being used to identify the metabolites generated from the transformation. We will present our preliminary results and we will discuss the application of bacterial activities on the chemical transformation of organics in atmosphere.

Work-related factors influencing home care nurse intent to remain employed.

PubMed

Tourangeau, Ann E; Patterson, Erin; Saari, Margaret; Thomson, Heather; Cranley, Lisa

Health care is shifting out of hospitals into community settings. In Ontario, Canada, home care organizations continue to experience challenges recruiting and retaining nurses. However, factors influencing home care nurse retention that can be modified remain largely unexplored. Several groups of factors have been identified as influencing home care nurse intent to remain employed including job characteristics, work structures, relationships and communication, work environment, responses to work, and conditions of employment. The aim of this study was to test and refine a model that identifies which factors are related to home care nurse intentions to remain employed for the next 5 years with their current home care employer organization. A cross-sectional survey design was implemented to test and refine a hypothesized model of home care nurse intent to remain employed. Logistic regression was used to determine which factors influence home care nurse intent to remain employed. Home care nurse intent to remain employed for the next 5 years was associated with increasing age, higher nurse-evaluated quality of care, having greater variety of patients, experiencing greater meaningfulness of work, having greater income stability, having greater continuity of client care, experiencing more positive relationships with supervisors, experiencing higher work-life balance, and being more satisfied with salary and benefits. Home care organizations can promote home care nurse intent to remain employed by (a) ensuring nurses have adequate training and resources to provide quality client care, (b) improving employment conditions to increase income stability and satisfaction with pay and benefits, (c) ensuring manageable workloads to facilitate improved work-life balance, and (d) ensuring leaders are accessible and competent.

Sponge-associated microbial Antarctic communities exhibiting antimicrobial activity against Burkholderia cepacia complex bacteria.

PubMed

Papaleo, Maria Cristiana; Fondi, Marco; Maida, Isabel; Perrin, Elena; Lo Giudice, Angelina; Michaud, Luigi; Mangano, Santina; Bartolucci, Gianluca; Romoli, Riccardo; Fani, Renato

2012-01-01

The aerobic heterotrophic bacterial communities isolated from three different Antarctic sponge species were analyzed for their ability to produce antimicrobial compounds active toward Cystic Fibrosis opportunistic pathogens belonging to the Burkholderia cepacia complex (Bcc). The phylogenetic analysis performed on the 16S rRNA genes affiliated the 140 bacterial strains analyzed to 15 genera. Just three of them (Psychrobacter, Pseudoalteromonas and Arthrobacter) were shared by the three sponges. The further Random Amplified Polymorphic DNA analysis allowed to demonstrate that microbial communities are highly sponge-specific and a very low degree of genus/species/strain sharing was detected. Data obtained revealed that most of these sponge-associated Antarctic bacteria and belonging to different genera were able to completely inhibit the growth of bacteria belonging to the Bcc. On the other hand, the same Antarctic strains did not have any effect on the growth of other pathogenic bacteria, strongly suggesting that the inhibition is specific for Bcc bacteria. Moreover, the antimicrobial compounds synthesized by the most active Antarctic bacteria are very likely Volatile Organic Compounds (VOCs), a finding that was confirmed by the SPME-GC-MS technique, which revealed the production of a large set of VOCs by a representative set of Antarctic bacteria. The synthesis of these VOCs appeared to be related neither to the presence of pks genes nor the presence of plasmid molecules. The whole body of data obtained in this work indicates that sponge-associated bacteria represent an untapped source for the identification of new antimicrobial compounds and are paving the way for the discovery of new drugs that can be efficiently and successfully used for the treatment of CF infections. Copyright © 2011 Elsevier Inc. All rights reserved.

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.

PubMed

Green, Hyatt C; Fisher, Jenny C; McLellan, Sandra L; Sogin, Mitchell L; Shanks, Orin C

2015-12-28

The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineation of host-microbe associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macroorganisms, but it remains unclear how the specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA genes amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). We investigated the interspecific abundance-occupancy relationship, where widespread taxa tend to be more abundant than narrowly distributed taxa, among operational taxonomic units (OTUs) within and among host species. In a separate analysis, we identified specialist OTUs that were highly abundant in a single host and rare in all other hosts by using a multinomial model without excluding undersampled OTUs a priori. We show that intestinal microbes in humans and other vertebrates display abundance-occupancy relationships, but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest that intestinal bacteria can be shared among diverse hosts in ways that resemble the distribution of "free-living" bacteria in the extraintestinal environment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Antibiotic management of lung infections in cystic fibrosis. II. Nontuberculous mycobacteria, anaerobic bacteria, and fungi.

PubMed

Chmiel, James F; Aksamit, Timothy R; Chotirmall, Sanjay H; Dasenbrook, Elliott C; Elborn, J Stuart; LiPuma, John J; Ranganathan, Sarath C; Waters, Valerie J; Ratjen, Felix A

2014-10-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy.

Antibiotic Management of Lung Infections in Cystic Fibrosis. II. Nontuberculous Mycobacteria, Anaerobic Bacteria, and Fungi

PubMed Central

Aksamit, Timothy R.; Chotirmall, Sanjay H.; Dasenbrook, Elliott C.; Elborn, J. Stuart; LiPuma, John J.; Ranganathan, Sarath C.; Waters, Valerie J.; Ratjen, Felix A.

2014-01-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy. PMID:25167882

Review on SERS of Bacteria

PubMed Central

Mosier-Boss, Pamela A.

2017-01-01

Surface enhanced Raman spectroscopy (SERS) has been widely used for chemical detection. Moreover, the inherent richness of the spectral data has made SERS attractive for use in detecting biological materials, including bacteria. This review discusses methods that have been used to obtain SERS spectra of bacteria. The kinds of SERS substrates employed to obtain SERS spectra are discussed as well as how bacteria interact with silver and gold nanoparticles. The roll of capping agents on Ag/Au NPs in obtaining SERS spectra is examined as well as the interpretation of the spectral data. PMID:29137201

Bacteriophage-based nanoprobes for rapid bacteria separation

NASA Astrophysics Data System (ADS)

Chen, Juhong; Duncan, Bradley; Wang, Ziyuan; Wang, Li-Sheng; Rotello, Vincent M.; Nugen, Sam R.

2015-10-01

The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying concentrations were determined. The results indicated a similar bacteria capture efficiency between the two nanoprobes.The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying

Quick Estimation Model for the Concentration of Indoor Airborne Culturable Bacteria: An Application of Machine Learning.

PubMed

Liu, Zhijian; Li, Hao; Cao, Guoqing

2017-07-30

Indoor airborne culturable bacteria are sometimes harmful to human health. Therefore, a quick estimation of their concentration is particularly necessary. However, measuring the indoor microorganism concentration (e.g., bacteria) usually requires a large amount of time, economic cost, and manpower. In this paper, we aim to provide a quick solution: using knowledge-based machine learning to provide quick estimation of the concentration of indoor airborne culturable bacteria only with the inputs of several measurable indoor environmental indicators, including: indoor particulate matter (PM 2.5 and PM 10 ), temperature, relative humidity, and CO₂ concentration. Our results show that a general regression neural network (GRNN) model can sufficiently provide a quick and decent estimation based on the model training and testing using an experimental database with 249 data groups.

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

PubMed

Ibarra-Arellano, Miguel A; Campos-González, Adrián I; Treviño-Quintanilla, Luis G; Tauch, Andreas; Freyre-González, Julio A

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy ( A: cross- BA: cteria SY: stems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing

Critical cell wall hole size for lysis in Gram-positive bacteria

NASA Astrophysics Data System (ADS)

Mitchell, Gabriel; Wiesenfeld, Kurt; Nelson, Daniel; Weitz, Joshua

2013-03-01

Gram-positive bacteria transport molecules necessary for their survival through holes in their cell wall. The holes in cell walls need to be large enough to let critical nutrients pass through. However, the cell wall must also function to prevent the bacteria's membrane from protruding through a large hole into the environment and lysing the cell. As such, we hypothesize that there exists a range of cell wall hole sizes that allow for molecule transport but prevent membrane protrusion. Here we develop and analyze a biophysical theory of the response of a Gram-positive cell's membrane to the formation of a hole in the cell wall. We predict a critical hole size in the range 15-24nm beyond which lysis occurs. To test our theory, we measured hole sizes in Streptococcus pyogenes cells undergoing enzymatic lysis via transmission electron microscopy. The measured hole sizes are in strong agreement with our theoretical prediction. Together, the theory and experiments provide a means to quantify the mechanisms of death of Gram-positive cells via enzymatically mediated lysis and provides insight into the range of cell wall hole sizes compatible with bacterial homeostasis.

Bacteremias in liver transplant recipients: shift toward gram-negative bacteria as predominant pathogens.

PubMed

Singh, Nina; Wagener, Marilyn M; Obman, Asia; Cacciarelli, Thomas V; de Vera, Michael E; Gayowski, Timothy

2004-07-01

During the 1990s, gram-positive bacteria emerged as major pathogens after liver transplantation. We sought to determine whether the pathogens associated with bacteremias in liver transplant recipients have changed. Patients included 233 liver transplant recipients transplanted between 1989 and 2003. The proportion of all infections due to bacteremias increased significantly over time (P <.0001). Of other major infections, a trend toward a decrease in fungal infections (P =.089) and a significant decrease in cytomegalovirus (CMV) disease (P =.0004) were documented. Whereas the proportion of bacteremias due to gram-negatives increased from 25% in the period of 1989-1993 to 51.8% in 1998-03, that of gram-positive bacteria decreased from 75% in the period of 1989-93 to 48.2% in the period of 1998-2003. Methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, and Pseudomonas aeruginosa were the most frequent pathogens in bacteremic patients. The incidence of bacteremias due to MRSA and Pseudomonas aeruginosa has remained unchanged (P <.20); however, that due to enteric gram-negative bacteria, particularly Klebsiella pneumoniae has increased (P =.02). Klebsiella pneumoniae isolates in the current quartile were not clonally related. In conclusion, bacteremias as a proportion of all infections in liver transplant recipients have increased significantly over time, due in part to a decline in infections due to other major pathogens, e.g., fungi, primarily Candida species, and CMV. Gram-negative bacteria have emerged as predominant pathogens in bacteremic liver transplant recipients.

Relationship between the burden of major periodontal bacteria and serum lipid profile in a cross-sectional Japanese study.

PubMed

Choi, Youn-Hee; Kosaka, Takayuki; Ojima, Miki; Sekine, Shinichi; Kokubo, Yoshihiro; Watanabe, Makoto; Miyamoto, Yoshihiro; Ono, Takahiro; Amano, Atsuo

2018-05-04

The association of periodontal bacteria with lipid profile alteration remains largely unknown, although it has been suggested that chronic periodontitis increases the atherosclerotic risk. This cross-sectional study investigated the relationship between the prevalence and total burden of periodontal bacteria and serum lipid profile. Saliva from enrolled participants was collected to detect 4 major periodontal bacteria (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Prevotella intermedia) using Polymerase Chain Reaction method. High-density lipoprotein (HDL) cholesterol, triglycerides (TG), and low-density lipoprotein cholesterol were assessed using blood samples. We compared the averages of each lipid in association with the prevalence of each bacterial species, their burden (low, moderate, and high), and the combination of bacterial burden and periodontal status, defined as periodontitis, using the Community Periodontal Index, after adjustment for other potential confounding factors, by employing general linear models with least square means. A total of 385 Japanese individuals (176 men, 209 women; mean age 69.2 years) were enrolled. The number of bacterial species and their co-existence with periodontitis were significantly related to a decrease in HDL (p for trend < 0.01) and increase in TG (p for trend = 0.04). The adjusted mean HDL levels (mg/dL) in individuals with low, moderate, and high levels of bacterial species were 66.1, 63.0, and 58.9, respectively, and those in the 6 groups defined by combination of the two factors were 67.9, 64.6, 64.3, 65.4, 61.5, and 54.7, respectively. Periodontal bacterial burden is suggested to be independently involved in lowering serum HDL level. Our findings suggest that bacterial tests in a clinical setting could be a useful approach for predicting the risk of HDL metabolism dysregulation.

The frequency of antibiotic-resistant bacteria in homes differing in their use of surface antibacterial agents.

PubMed

Marshall, Bonnie M; Robleto, Eduardo; Dumont, Theresa; Levy, Stuart B

2012-10-01

Antibacterial agents are common in household cleaning and personal care products, but their long-range impacts on commensal and pathogenic household bacteria are largely unknown. In a one-time survey of 38 households from Boston, MA [19] and Cincinnati, OH [18], 13 kitchen and bathroom sites were sampled for total aerobic bacteria and screened for gram phenotype and susceptibility to six antibiotic drug families. The overall bacterial titers of both user (2 or more antibacterial cleaning or personal care products) and non-user (0 or 1 product) rooms were similar with sponges and sink drains consistently showing the highest overall titers and relatively high titers of antibiotic-resistant bacteria. The mean frequency of resistant bacteria ranged from ≤20 % to as high as 45 % and multi-drug resistance was common. However, no significant differences were noted between biocide users and non-users. The frequency of pathogen recovery was similar in both user and non-user groups.

Where do those remains come from?

PubMed

Nociarová, Dominika; Adserias, M Jose; Malgosa, Assumpció; Galtés, Ignasi

2014-12-01

Part of the study of skeletal remains or corpses in advance decay located in the field involves determining their origin. They may be the result of criminal activity, accident, unearthed because of erosion, or they may also have originated from a cemetery. The discovery site, condition of the remains, and the associated artifacts, are factors that could be helpful for the forensic anthropologist to identify the origin of the remains. In order to contribute to this recognition, an analysis was made of the exhumations of 168 unclaimed human remains from the cemetery of Terrassa (Catalonia, Spain). This investigation presents a description of artifacts and conditions of remains that could indicate that the human remains may have originated from a cemetery. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Amoeba-Resisting Bacteria and Ventilator-Associated Pneumonia

PubMed Central

La Scola, Bernard; Boyadjiev, Ioanna; Greub, Gilbert; Khamis, Atieh; Martin, Claude

2003-01-01

To evaluate the role of amoeba-associated bacteria as agents of ventilator-associated pneumonia (VAP), we tested the water from an intensive care unit (ICU) every week for 6 months for such bacteria isolates; serum samples and bronchoalveolar lavage samples (BAL) were also obtained from 30 ICU patients. BAL samples were examined for amoeba-associated bacteria DNA by suicide-polymerase chain reaction, and serum samples were tested against ICU amoeba-associated bacteria. A total of 310 amoeba-associated bacteria from10 species were isolated. Twelve of 30 serum samples seroconverted to one amoeba-associated bacterium isolated in the ICU, mainly Legionella anisa and Bosea massiliensis, the most common isolates from water (p=0.021). Amoeba-associated bacteria DNA was detected in BAL samples from two patients whose samples later seroconverted. Seroconversion was significantly associated with VAP and systemic inflammatory response syndrome, especially in patients for whom no etiologic agent was found by usual microbiologic investigations. Amoeba-associated bacteria might be a cause of VAP in ICUs, especially when microbiologic investigations are negative. PMID:12890321

Protection from Staphylococcus aureus mastitis associated with poly-N-acetyl β-1,6 glucosamine specific antibody production using biofilm-embedded bacteria

PubMed Central

Pérez, M. M.; Prenafeta, A.; Valle, J.; Penadés, J.; Rota, C.; Solano, C.; Marco, J.; Grilló, M.J.; Lasa, I.; Irache, J.M.; Maira-Litran, T.; Jiménez-Barbero, J.; Costa, L.; Pier, G.B.; de Andrés, D.; Amorena, B.

2010-01-01

Staphylococcus aureus vaccines based on bacterins surrounded by slime, surface polysaccharides coupled to protein carriers and polysaccharides embedded in liposomes administered together with non-biofilm bacterins confer protection against mastitis. However, it remains unknown whether protective antibodies are directed to slime-associated known exopolysaccharides and could be produced in the absence of bacterin immunizations. Here, a sheep mastitis vaccination study was carried out using bacterins, crude bacterial extracts or a purified exopolysaccharide from biofilm bacteria delivered in different vehicles. This polysaccharide reacted specifically with antibodies to poly-N-acetyl-β-1,6-glucosamine (PNAG) and not with antibodies to other capsular antigens or bacterial components. Following intra-mammary challenge with biofilm-producing bacteria, antibody production against the polysaccharide, milk bacterial counts and mastitis lesions were determined. Bacterins from strong biofilm-producing bacteria triggered the highest production of antibodies to PNAG and conferred the highest protection against infection and mastitis, compared with weak biofilm-producing bacteria and non-cellular inocula. Thus, bacterins from strong biofilm bacteria, rather than purified polysaccharide, are proposed as a cost-efficient vaccination against S. aureus ruminant mastitis. PMID:19428854

Close Encounters of Lymphoid Cells and Bacteria

PubMed Central

Cruz-Adalia, Aranzazu; Veiga, Esteban

2016-01-01

During infections, the first reaction of the host against microbial pathogens is carried out by innate immune cells, which recognize conserved structures on pathogens, called pathogen-associated molecular patterns. Afterward, some of these innate cells can phagocytose and destroy the pathogens, secreting cytokines that would modulate the immune response to the challenge. This rapid response is normally followed by the adaptive immunity, more specific and essential for a complete pathogen clearance in many cases. Some innate immune cells, usually named antigen-presenting cells, such as macrophages or dendritic cells, are able to process internalized invaders and present their antigens to lymphocytes, triggering the adaptive immune response. Nevertheless, the traditional boundary of separated roles between innate and adaptive immunity has been blurred by several studies, showing that very specialized populations of lymphocytes (cells of the adaptive immunity) behave similarly to cells of the innate immunity. These “innate-like” lymphocytes include γδ T cells, invariant NKT cells, B-1 cells, mucosal-associated invariant T cells, marginal zone B cells, and innate response activator cells, and together with the newly described innate lymphoid cells are able to rapidly respond to bacterial infections. Strikingly, our recent data suggest that conventional CD4+ T cells, the paradigm of cells of the adaptive immunity, also present innate-like behavior, capturing bacteria in a process called transinfection. Transinfected CD4+ T cells digest internalized bacteria like professional phagocytes and secrete large amounts of proinflammatory cytokines, protecting for further bacterial challenges. In the present review, we will focus on the data showing such innate-like behavior of lymphocytes following bacteria encounter. PMID:27774092

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms.

PubMed

Ho, Van Thi Thuy; Fleet, Graham H; Zhao, Jian

2018-08-20

Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of the bean pulp by microorganisms is essential for developing the precursors of chocolate flavour. Currently, the cocoa fermentation is still conducted by an uncontrolled traditional process via a consortium of indigenous species of yeasts, lactic acid bacteria and acetic acid bacteria. Although the essential contribution of yeasts to the production of good quality beans and, typical chocolate character is generally agreed, the roles of lactic acid bacteria and acetic acid bacteria are less certain. The objective of this study was to investigate the contribution of LAB and AAB in cocoa bean fermentation by conducting small scale laboratory fermentations under aseptic conditions, inoculated with different groups of microorganisms previously isolated from spontaneous cocoa fermentations. The inoculation protocols were: (1) four yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae; (2) four yeasts plus the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum; (3) four yeasts plus the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateuri and (4) four yeasts plus two lactic acid bacteria and two acetic acid bacteria. Only the inoculated species were detected in the microbiota of their respective fermentations. Beans from the inoculated fermentations showed no significant differences in colour, shell weights and concentrations of residual sugars, alcohols and esters (p>0.05), but they were slightly different in contents of lactic acid and acetic acid (p<0.05). All beans were fully brown and free of mould. Residual sugar levels were less than 2.6 mg/g while the shell contents and ethanol were in the range of 11-13.4% and 4.8-7 mg/g, respectively. Beans fermented in the presence of LAB contained higher levels of lactic acid (0.6-1.2 mg/g) whereas higher concentrations of acetic acid

Evolutionary tradeoffs in cellular composition across diverse bacteria

PubMed Central

Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

2016-01-01

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

Presence of Bacteria in Spontaneous Achilles Tendon Ruptures.

PubMed

Rolf, Christer G; Fu, Sai-Chuen; Hopkins, Chelsea; Luan, Ju; Ip, Margaret; Yung, Shu-Hang; Friman, Göran; Qin, Ling; Chan, Kai-Ming

2017-07-01

The structural pathology of Achilles tendon (AT) ruptures resembles tendinopathy, but the causes remain unknown. Recently, a number of diseases were found to be attributed to bacterial infections, resulting in low-grade inflammation and progressive matrix disturbance. The authors speculate that spontaneous AT ruptures may also be influenced by the presence of bacteria. Bacteria are present in ruptured ATs but not in healthy tendons. Cross-sectional study; Level of evidence, 3. Patients with spontaneous AT ruptures and patients undergoing anterior cruciate ligament (ACL) reconstruction were recruited for this study. During AT surgical repair, excised tendinopathic tissue was collected, and healthy tendon samples were obtained as controls from hamstring tendon grafts used in ACL reconstruction. Half of every sample was reserved for DNA extraction and the other half for histology. Polymerase chain reaction (PCR) was conducted using 16S rRNA gene universal primers, and the PCR products were sequenced for the identification of bacterial species. A histological examination was performed to compare tendinopathic changes in the case and control samples. Five of 20 AT rupture samples were positive for the presence of bacterial DNA, while none of the 23 hamstring tendon samples were positive. Sterile operating and experimental conditions and tests on samples, controlling for harvesting and processing procedures, ruled out the chance of postoperative bacterial contamination. The species identified predominantly belonged to the Staphylococcus genus. AT rupture samples exhibited histopathological features characteristic of tendinopathy, and most healthy hamstring tendon samples displayed normal tendon features. There were no apparent differences in histopathology between the bacterial DNA-positive and bacterial DNA-negative AT rupture samples. The authors have demonstrated the presence of bacterial DNA in ruptured AT samples. It may suggest the potential involvement of bacteria

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

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

Liu, Hualan; Price, Morgan N.; Waters, Robert Jordan

Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools.” Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. Tomore » identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylumBacteroidetes. IMPORTANCEMolecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA “parts,” we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.« less

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

DOE PAGES

Liu, Hualan; Price, Morgan N.; Waters, Robert Jordan; ...

2018-01-16

Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools.” Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. Tomore » identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylumBacteroidetes. IMPORTANCEMolecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA “parts,” we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.« less

Antibacterial Activities of Endophytic Bacteria Isolated from Taxus brevifolia Against Foodborne Pathogenic Bacteria.

PubMed

Islam, Nurul; Choi, Jaehyuk; Baek, Kwang-Hyun

2018-05-01

Endophytes are a potential source of novel bioactive compounds with medicinal properties. In this study, 41 endophytic bacteria (EB) were isolated from tissues of a medicinally important plant Taxus brevifolia (Pacific yew). The objective was to screen all the EB isolates for their antibacterial effects against five foodborne pathogenic bacteria: Bacillus cereus ATCC10876, Staphylococcus aureus ATCC12600, Listeria monocytogenes ATCC19115, Escherichia coli ATCC43890, and Salmonella Typhimurium ATCC19585. Among the EB isolates, T. brevifolia seed (TbS)-8, T. brevifolia fleshy part of fruit (TbFl)-10, T. brevifolia leaf (TbL)-22, TbS-29, and TbL-34 exerted significant antibacterial activity against the tested foodborne pathogens. Especially TbFl-10 showed the highest antibacterial activity against all the tested bacteria and was identified as Paenibacillus kribbensis (Pk). Furthermore, an ethyl acetate extract of Pk-TbFl-10 possessed antibacterial activities against the tested five foodborne pathogenic bacteria, with zones of inhibition from 15.71 ± 2.85 to 13.01 ± 2.12 mm. Scanning electron microscopy analysis revealed ruptured, lysed, shrunk, and swollen cells of all the tested foodborne pathogens treated with the ethyl acetate extract of Pk-TbFl-10, suggesting that a metabolite(s) of Pk-TbFl-10 penetrates the cell membrane and causes cell lysis leading to cell death. Our results indicate that Pk-TbFl-10 isolated from T. brevifolia can serve as a novel source of natural antibacterial agents against foodborne pathogenic bacteria, with potential applications in the pharmaceutical industry.

Using Fluorescent Viruses for Detecting Bacteria in Water

NASA Technical Reports Server (NTRS)

Tabacco, Mary Beth; Qian, Xiaohua; Russo, Jaimie A.

2009-01-01

A method of detecting water-borne pathogenic bacteria is based partly on established molecular-recognition and fluorescent-labeling concepts, according to which bacteria of a species of interest are labeled with fluorescent reporter molecules and the bacteria can then be detected by fluorescence spectroscopy. The novelty of the present method lies in the use of bacteriophages (viruses that infect bacteria) to deliver the fluorescent reporter molecules to the bacteria of the species of interest.

Strategies and ecological roles of algicidal bacteria.

PubMed

Meyer, Nils; Bigalke, Arite; Kaulfuß, Anett; Pohnert, Georg

2017-11-01

In both freshwater and marine ecosystems, phytoplankton are the most dominant primary producers, contributing substantially to aquatic food webs. Algicidal bacteria that can associate to microalgae from the phytoplankton have the capability to control the proliferation and even to lyse them. These bacteria thus play an important role in shaping species composition in pelagic environments. In this review, we discuss and categorise strategies used by algicidal bacteria for the attack on microalgae. We highlight the complex regulation of algicidal activity and defence responses that govern alga-bacteria interactions. We also discuss how algicidal bacteria impact algal physiology and metabolism and survey the existing algicidal metabolites and enzymes. The review illustrates that the ecological role of algicidal bacteria is not yet fully understood and critically discusses the challenges in obtaining ecologically relevant data. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Acetic acid bacteria: A group of bacteria with versatile biotechnological applications.

PubMed

Saichana, Natsaran; Matsushita, Kazunobu; Adachi, Osao; Frébort, Ivo; Frebortova, Jitka

2015-11-01

Acetic acid bacteria are gram-negative obligate aerobic bacteria assigned to the family Acetobacteraceae of Alphaproteobacteria. They are members of the genera Acetobacter, Gluconobacter, Gluconacetobacter, Acidomonas, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia, Granulibacter, Tanticharoenia, Ameyamaea, Neokomagataea, and Komagataeibacter. Many strains of Acetobacter and Komagataeibacter have been known to possess high acetic acid fermentation ability as well as the acetic acid and ethanol resistance, which are considered to be useful features for industrial production of acetic acid and vinegar, the commercial product. On the other hand, Gluconobacter strains have the ability to perform oxidative fermentation of various sugars, sugar alcohols, and sugar acids leading to the formation of several valuable products. Thermotolerant strains of acetic acid bacteria were isolated in order to serve as the new strains of choice for industrial fermentations, in which the cooling costs for maintaining optimum growth and production temperature in the fermentation vessels could be significantly reduced. Genetic modifications by adaptation and genetic engineering were also applied to improve their properties, such as productivity and heat resistance. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of kaolin silver complex on the control of populations of Brettanomyces and acetic acid bacteria in wine.

PubMed

Izquierdo-Cañas, P M; López-Martín, R; García-Romero, E; González-Arenzana, L; Mínguez-Sanz, S; Chatonnet, P; Palacios-García, A; Puig-Pujol, A

2018-05-01

In this work, the effects of kaolin silver complex (KAgC) have been evaluated to replace the use of SO 2 for the control of spoilage microorganisms in the winemaking process. The results showed that KAgC at a dose of 1 g/L provided effective control against the development of B. bruxellensis and acetic acid bacteria. In wines artificially contaminated with an initial population of B. bruxellensis at 10 4 CFU/mL, a concentration proven to produce off flavors in wine, only residual populations of the contaminating yeast remained after 24 days of contact with the additive. Populations of acetic bacteria inoculated into wine at concentrations of 10 2 and 10 4  CFU/mL were reduced to negligible levels after 72 h of treatment with KAgC. The antimicrobial effect of KAgC against B. bruxellensis and acetic bacteria was also demonstrated in a wine naturally contaminated by these microorganisms, decreasing their population in a similar way to a chitosan treatment. Related to this effect, wines with KAgC showed lower concentrations of acetic acid and 4-ethyl phenol than wines without KAgC. The silver concentration from KAgC that remained in the finished wines was below the legal limits. These results demonstrated the effectiveness of KAgC to reduce spoilage microorganisms in winemaking.

Graphene oxide-dependent growth and self-aggregation into a hydrogel complex of exoelectrogenic bacteria

PubMed Central

Yoshida, Naoko; Miyata, Yasushi; Doi, Kasumi; Goto, Yuko; Nagao, Yuji; Tero, Ryugo; Hiraishi, Akira

2016-01-01

Graphene oxide (GO) is reduced by certain exoelectrogenic bacteria, but its effects on bacterial growth and metabolism are a controversial issue. This study aimed to determine whether GO functions as the terminal electron acceptor to allow specific growth of and electricity production by exoelectrogenic bacteria. Cultivation of environmental samples with GO and acetate as the sole substrate could specifically enrich exoelectrogenic bacteria with Geobacter species predominating (51–68% of the total populations). Interestingly, bacteria in these cultures self-aggregated into a conductive hydrogel complex together with biologically reduced GO (rGO). A novel GO-respiring bacterium designated Geobacter sp. strain R4 was isolated from this hydrogel complex. This organism exhibited stable electricity production at >1000 μA/cm3 (at 200 mV vs Ag/AgCl) for more than 60 d via rGO while temporary electricity production using graphite felt. The better electricity production depends upon the characteristics of rGO such as a large surface area for biofilm growth, greater capacitance, and smaller internal resistance. This is the first report to demonstrate GO-dependent growth of exoelectrogenic bacteria while forming a conductive hydrogel complex with rGO. The simple put-and-wait process leading to the formation of hydrogel complexes of rGO and exoelectrogens will enable wider applications of GO to bioelectrochemical systems. PMID:26899353

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.

Detection of Escherichia Coli Bacteria in Wastewater by using Graphene as a Sensing Material

NASA Astrophysics Data System (ADS)

Wibowo, K. M.; Sahdan, M. Z.; Ramli, N. I.; Muslihati, A.; Rosni, N.; Tsen, V. H.; Saim, H.; Ahmad, S. A.; Sari, Y.; Mansor, Z.

2018-04-01

Graphene is a family of carbon bonded in hexagonal honeycomb crystalline structure that has many superior properties. It was very suitable to be applied on sensor application due to the superior properties on electrical, physical, and optical. Furthermore, graphene also provide a large detection area since it has 2D structure. In this research, we develop graphene as a nanosensor for detection of Escherichia coli (E. coli) bacteria. The sample E. coli bacteria were cultured from domestic wastewater by using plate culture method and then isolated to get pure single colony. The serial dilution was performed to create different concentration of bacteria. Field emission scanning electron microscope and biochemical test were performed to ensure the sample genuinely target E. coli that defined by the physical size and optical properties. Raman spectroscopy measurements were also performed on the grapheme films, and it was found that the ratio of G peak and D peak intensity changing do to the presence of E. coli. The electrical properties of graphene shows the increasing number of the bacteria 4 to 273 cfu result in decreasing the resistance from 4.371 to 3.903 ohm gradually.

Heterotrophic bacteria in drinking water distribution system: a review.

PubMed

Chowdhury, Shakhawat

2012-10-01

The microbiological quality of drinking water in municipal water distribution systems (WDS) depends on several factors. Free residual chlorine and/or chloramines are typically used to minimize bacterial recontamination and/or regrowth in WDS. Despite such preventive measures, regrowth of heterotrophic (HPC) and opportunistic bacteria in bulk water and biofilms has yet to be controlled completely. No approach has shown complete success in eliminating biofilms or HPC bacteria from bulk water and pipe surfaces. Biofilms can provide shelter for pathogenic bacteria and protect these bacteria from disinfectants. Some HPC bacteria may be associated with aesthetic and non-life threatening diseases. Research to date has achieved important success in understanding occurrence and regrowth of bacteria in bulk water and biofilms in WDS. To achieve comprehensive understanding and to provide efficient control against bacteria regrowth, future research on bacteria regrowth dynamics and their implications is warranted. In this study, a review was performed on the literature published in this area. The findings and limitations of these papers are summarized. Occurrences of bacteria in WDS, factors affecting bacteria regrowth in bulk water and biofilms, bacteria control strategies, sources of nutrients, human health risks from bacterial exposure, modelling of bacteria regrowth and methods of bacteria sampling and detection and quantification are investigated. Advances to date are noted, and future research needs are identified. Finally, research directions are proposed to effectively control HPC and opportunistic bacteria in bulk water and biofilms in WDS.

Spoilage bacteria of fresh broiler chicken carcasses.

PubMed

Russell, S M; Fletcher, D L; Cox, N A

1995-12-01

Studies were conducted to identify the bacteria responsible for spoilage of fresh broiler chicken carcasses and to characterize the off-odors these bacteria produce. Broiler carcasses were collected from processing plants in the northeast Georgia area, the southeastern U.S., Arkansas, California, and North Carolina. The carcasses were allowed to spoil under controlled conditions at 3 C and spoilage bacteria were isolated. Each spoilage bacterium was separately inoculated into a sterile chicken skin medium, incubated at 25 C for 48 h, and subjectively evaluated for odor. The bacteria isolated from spoiled carcasses that consistently produced off-odors in the chicken skin medium, regardless of the geographical location from which the chickens were obtained, were Shewanella putrefaciens A, B, and D, Pseudomonas fluorescens A, B, and D, and Pseudomonas fragi. These bacteria produced off-odors that resembled "sulfur", "dishrag", "ammonia", "wet dog", "skunk", "dirty socks", "rancid fish", "unspecified bad odor", or a sweet smell resembling "canned corn". Odors produced by the spoilage bacteria were varied; however, odors most associated with spoiled poultry, such as "dishraggy" odors, were produced by the bacteria that were most consistently isolated, such as S. putrefaciens and the pseudomonads.

Laser micropolishing of AISI 304 stainless steel surfaces for cleanability and bacteria removal capability

NASA Astrophysics Data System (ADS)

De Giorgi, Chiara; Furlan, Valentina; Demir, Ali Gökhan; Tallarita, Elena; Candiani, Gabriele; Previtali, Barbara

2017-06-01

In this work, laser micropolishing (LμP) was employed to reduce the surface roughness and waviness of cold-rolled AISI 304 stainless steel sheets. A pulsed fibre laser operating in the ns regime was used and the influence of laser parameters in a N2-controlled atmospheres was evaluated. In the optimal conditions, the surface remelting induced by the process allowed to reduce the surface roughness by closing cracks and defects formed during the rolling process. Other conditions that did not improve the surface quality were analysed for defect typology. Moreover, laser treatments allowed the production of more hydrophobic surfaces, and no surface chemistry modification was identified. Surface cleanability was investigated with Escherichia coli (E. coli), evaluating the number of residual bacteria adhering to the substrate after a washing procedure. These results showed that LμP is a suitable way to lower the average surface roughness by about 58% and average surface waviness by approximately 38%. The LμP process proved to be effective on the bacteria cleanability as approximately five times fewer bacteria remained on the surfaces treated with the optimized LμP parameters compared to the untreated surfaces.

Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria

USGS Publications Warehouse

Miller, L.G.; Kalin, Robert M.; McCauley, S.E.; Hamilton, John T.G.; Harper, D.B.; Millet, D.B.; Oremland, R.S.; Goldstein, Allen H.

2001-01-01

The largest biological fractionations of stable carbon isotopes observed in nature occur during production of methane by methanogenic archaea. These fractionations result in substantial (as much as ???70???) shifts in ??13C relative to the initial substrate. We now report that a stable carbon isotopic fractionation of comparable magnitude (up to 70???) occurs during oxidation of methyl halides by methylotrophic bacteria. We have demonstrated biological fractionation with whole Cells of three methylotrophs (strain IMB-1, strain CC495, and strain MB2) and, to a lesser extent, with the purified cobalamin-dependent methyltransferase enzyme obtained from strain CC495. Thus, the genetic similarities recently reported between methylotrophs, and methanogens with respect to their pathways for C1-unit metabolism are also reflected in the carbon isotopic fractionations achieved by these organisms. We found that only part of the observed fractionation of carbon isotopes could be accounted for by the activity of the corrinoid methyltransferase enzyme, suggesting fractionation by enzymes further along the degradation pathway. These observations are of potential biogeochemical significance in the application of stable carbon isotope ratios to constrain the tropospheric budgets for the ozone-depleting halocarbons, methyl bromide and methyl chloride.

Sunlight modulates the relative importance of heterotrophic bacteria and picophytoplankton in DMSP-sulphur uptake

PubMed Central

Ruiz-González, Clara; Simó, Rafel; Vila-Costa, Maria; Sommaruga, Ruben; Gasol, Josep M

2012-01-01

There is a large body of evidence supporting a major role of heterotrophic bacteria in dimethylsulphoniopropionate (DMSP) utilisation as a source of reduced sulphur. However, a role for phototrophic microorganisms has been only recently described and little is known about their contribution to DMSP consumption and the potential modulating effects of sunlight. In an attempt to ascertain the relative quantitative roles of heterotrophic bacteria and picophytoplankton in the osmoheterotrophic uptake of DMSP-sulphur upon exposure to natural sunlight conditions, we incubated northwestern Mediterranean waters under various optical filters and used an array of bulk and single-cell activity methods to trace the fate of added 35S-DMSP. Flow cytometry cell sorting confirmed dark 35S uptake by Prochlorococcus, Synechococcus and heterotrophic bacteria, the latter being the most efficient in terms of uptake on a cell volume basis. Under exposure to full sunlight, however, the relative contribution of Synechococcus was significantly enhanced, mainly because of the inhibition of heterotrophic bacteria. Microautoradiography showed a strong increase in the proportion of Synechococcus cells actively taking up 35S-DMSP, which, after full sunlight exposure, made up to 15% of total active Bacteria. Parallel incubations with 3H-leucine generally showed no clear responses to light. Finally, size-fractionated assimilation experiments showed greater relative cyanobacterial assimilation during the day than at night compared with that of heterotrophic bacteria. Our results show for the first time a major influence of sunlight in regulating the competition among autotrophic and heterotrophic picoplankton for DMSP uptake at both the daily and seasonal time scales. PMID:21955992

Quick Estimation Model for the Concentration of Indoor Airborne Culturable Bacteria: An Application of Machine Learning

PubMed Central

Liu, Zhijian; Li, Hao; Cao, Guoqing

2017-01-01

Indoor airborne culturable bacteria are sometimes harmful to human health. Therefore, a quick estimation of their concentration is particularly necessary. However, measuring the indoor microorganism concentration (e.g., bacteria) usually requires a large amount of time, economic cost, and manpower. In this paper, we aim to provide a quick solution: using knowledge-based machine learning to provide quick estimation of the concentration of indoor airborne culturable bacteria only with the inputs of several measurable indoor environmental indicators, including: indoor particulate matter (PM2.5 and PM10), temperature, relative humidity, and CO2 concentration. Our results show that a general regression neural network (GRNN) model can sufficiently provide a quick and decent estimation based on the model training and testing using an experimental database with 249 data groups. PMID:28758941

Magnetic Bacteria.

ERIC Educational Resources Information Center

Nelson, Jane Bray; Nelson, Jim

1992-01-01

Describes the history of Richard Blakemore's discovery of magnetotaxic organisms. Discusses possible reasons why the magnetic response in bacteria developed. Proposes research experiments integrating biology and physics in which students investigate problems using cultures of magnetotaxic organisms. (MDH)

Bacteria associated with cysts of the soybean cyst nematode (Heterodera glycines).

PubMed

Nour, Sarah M; Lawrence, John R; Zhu, Hong; Swerhone, George D W; Welsh, Martha; Welacky, Tom W; Topp, Edward

2003-01-01

The soybean cyst nematode (SCN), Heterodera glycines, causes economically significant damage to soybeans (Glycine max) in many parts of the world. The cysts of this nematode can remain quiescent in soils for many years as a reservoir of infection for future crops. To investigate bacterial communities associated with SCN cysts, cysts were obtained from eight SCN-infested farms in southern Ontario, Canada, and analyzed by culture-dependent and -independent means. Confocal laser scanning microscopy observations of cyst contents revealed a microbial flora located on the cyst exterior, within a polymer plug region and within the cyst. Microscopic counts using 5-(4,6-dichlorotriazine-2-yl)aminofluorescein staining and in situ hybridization (EUB 338) indicated that the cysts contained (2.6 +/- 0.5) x 10(5) bacteria (mean +/- standard deviation) with various cellular morphologies. Filamentous fungi were also observed. Live-dead staining indicated that the majority of cyst bacteria were viable. The probe Nile red also bound to the interior polymer, indicating that it is lipid rich in nature. Bacterial community profiles determined by denaturing gradient gel electrophoresis analysis were simple in composition. Bands shared by all eight samples included the actinobacterium genera Actinomadura and STREPTOMYCES: A collection of 290 bacteria were obtained by plating macerated surface-sterilized cysts onto nutrient broth yeast extract agar or on actinomycete medium. These were clustered into groups of siblings by repetitive extragenic palindromic PCR fingerprinting, and representative isolates were tentatively identified on the basis of 16S rRNA gene sequence. Thirty phylotypes were detected, with the collection dominated by Lysobacter and Variovorax spp. This study has revealed the cysts of this important plant pathogen to be rich in a variety of bacteria, some of which could presumably play a role in the ecology of SCN or have potential as biocontrol agents.

Bacteria Associated with Cysts of the Soybean Cyst Nematode (Heterodera glycines)

PubMed Central

Nour, Sarah M.; Lawrence, John R.; Zhu, Hong; Swerhone, George D. W.; Welsh, Martha; Welacky, Tom W.; Topp, Edward

2003-01-01

The soybean cyst nematode (SCN), Heterodera glycines, causes economically significant damage to soybeans (Glycine max) in many parts of the world. The cysts of this nematode can remain quiescent in soils for many years as a reservoir of infection for future crops. To investigate bacterial communities associated with SCN cysts, cysts were obtained from eight SCN-infested farms in southern Ontario, Canada, and analyzed by culture-dependent and -independent means. Confocal laser scanning microscopy observations of cyst contents revealed a microbial flora located on the cyst exterior, within a polymer plug region and within the cyst. Microscopic counts using 5-(4,6-dichlorotriazine-2-yl)aminofluorescein staining and in situ hybridization (EUB 338) indicated that the cysts contained (2.6 ± 0.5) × 105 bacteria (mean ± standard deviation) with various cellular morphologies. Filamentous fungi were also observed. Live-dead staining indicated that the majority of cyst bacteria were viable. The probe Nile red also bound to the interior polymer, indicating that it is lipid rich in nature. Bacterial community profiles determined by denaturing gradient gel electrophoresis analysis were simple in composition. Bands shared by all eight samples included the actinobacterium genera Actinomadura and Streptomyces. A collection of 290 bacteria were obtained by plating macerated surface-sterilized cysts onto nutrient broth yeast extract agar or on actinomycete medium. These were clustered into groups of siblings by repetitive extragenic palindromic PCR fingerprinting, and representative isolates were tentatively identified on the basis of 16S rRNA gene sequence. Thirty phylotypes were detected, with the collection dominated by Lysobacter and Variovorax spp. This study has revealed the cysts of this important plant pathogen to be rich in a variety of bacteria, some of which could presumably play a role in the ecology of SCN or have potential as biocontrol agents. PMID:12514048

Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose.

PubMed

Yuki, Masahiro; Kuwahara, Hirokazu; Shintani, Masaki; Izawa, Kazuki; Sato, Tomoyuki; Starns, David; Hongoh, Yuichi; Ohkuma, Moriya

2015-12-01

Wood-feeding lower termites harbour symbiotic gut protists that support the termite nutritionally by degrading recalcitrant lignocellulose. These protists themselves host specific endo- and ectosymbiotic bacteria, functions of which remain largely unknown. Here, we present draft genomes of a dominant, uncultured ectosymbiont belonging to the order Bacteroidales, 'Candidatus Symbiothrix dinenymphae', which colonizes the cell surface of the cellulolytic gut protists Dinenympha spp. We analysed four single-cell genomes of Ca. S. dinenymphae, the highest genome completeness was estimated to be 81.6-82.3% with a predicted genome size of 4.28-4.31 Mb. The genome retains genes encoding large parts of the amino acid, cofactor and nucleotide biosynthetic pathways. In addition, the genome contains genes encoding various glycoside hydrolases such as endoglucanases and hemicellulases. The genome indicates that Ca. S. dinenymphae ferments lignocellulose-derived monosaccharides to acetate, a major carbon and energy source of the host termite. We suggest that the ectosymbiont digests lignocellulose and provides nutrients to the host termites, and hypothesize that the hydrolytic activity might also function as a pretreatment for the host protist to effectively decompose the crystalline cellulose components. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Protist-Bacteria Associations: Gammaproteobacteria and Alphaproteobacteria Are Prevalent as Digestion-Resistant Bacteria in Ciliated Protozoa

PubMed Central

Gong, Jun; Qing, Yao; Zou, Songbao; Fu, Rao; Su, Lei; Zhang, Xiaoli; Zhang, Qianqian

2016-01-01

Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. Here we report the phylogenetic identities of digestion-resistant bacteria (DRB) that could survive starvation and form relatively stable associations with 11 marine and one freshwater ciliate species. Using clone library and sequencing of 16S rRNA genes, we found that the protistan predators could host a high diversity of DRB, most of which represented novel bacterial taxa that have not been cultivated. The localization inside host cells, quantity, and viability of these bacteria were checked using fluorescence in situ hybridization. The DRB were affiliated with Actinobacteria, Bacteroidetes, Firmicutes, Parcubacteria (OD1), Planctomycetes, and Proteobacteria, with Gammaproteobacteria and Alphaproteobacteria being the most frequently occurring classes. The dominance of Gamma- and Alphaproteobacteria corresponds well to a previous study of Global Ocean Sampling metagenomic data showing the widespread types of bacterial type VI and IV secretion systems (T6SS and T4SS) in these two taxa, suggesting a putatively significant role of secretion systems in promoting marine protist-bacteria associations. In the DRB assemblages, opportunistic bacteria such as Alteromonadaceae, Pseudoalteromonadaceae, and Vibrionaceae often presented with high proportions, indicating these bacteria could evade protistan grazing thus persist and accumulate in the community, which, however, contrasts with their well-known rarity in nature. This begs the question whether viral lysis is significant in killing these indigestible bacteria in microbial communities. Taken together, our study on

Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes.

PubMed

Durso, Lisa M; Miller, Daniel N; Wienhold, Brian J

2012-01-01

There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

PubMed

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

2016-07-01

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. Copyright © 2016 The Author(s). Published by Elsevier GmbH.. All rights reserved.

Mechanisms of action of brief alcohol interventions remain largely unknown - a narrative review.

PubMed

Gaume, Jacques; McCambridge, Jim; Bertholet, Nicolas; Daeppen, Jean-Bernard

2014-01-01

A growing body of evidence has shown the efficacy of brief intervention (BI) for hazardous and harmful alcohol use in primary health care settings. Evidence for efficacy in other settings and effectiveness when implemented at larger scale are disappointing. Indeed, BI comprises varying content; exploring BI content and mechanisms of action may be a promising way to enhance efficacy and effectiveness. Medline and PsychInfo, as well as references of retrieved publications were searched for original research or review on active ingredients (components or mechanisms) of face-to-face BIs [and its subtypes, including brief advice and brief motivational interviewing (BMI)] for alcohol. Overall, BI active ingredients have been scarcely investigated, almost only within BMI, and mostly among patients in the emergency room, young adults, and US college students. This body of research has shown that personalized feedback may be an effective component; specific MI techniques showed mixed findings; decisional balance findings tended to suggest a potential detrimental effect; while change plan exercises, advice to reduce or stop drinking, presenting alternative change options, and moderation strategies are promising but need further study. Client change talk is a potential mediator of BMI effects; change in norm perceptions and enhanced discrepancy between current behavior and broader life goals and values have received preliminary support; readiness to change was only partially supported as a mediator; while enhanced awareness of drinking, perceived risks/benefits of alcohol use, alcohol treatment seeking, and self-efficacy were seldom studied and have as yet found no significant support as such. Research is obviously limited and has provided no clear and consistent evidence on the mechanisms of alcohol BI. How BI achieves the effects seen in randomized trials remains mostly unknown and should be investigated to inform the development of more effective interventions.

Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection.

PubMed

Zelenin, Sergey; Ramachandraiah, Harisha; Faridi, Asim; Russom, Aman

2017-01-01

Bacterial blood stream infection (BSI) potentially leads to life-threatening clinical conditions and medical emergencies such as severe sepsis, septic shock, and multi organ failure syndrome. Blood culturing is currently the gold standard for the identification of microorganisms and, although it has been automated over the decade, the process still requires 24-72 h to complete. This long turnaround time, especially for the identification of antimicrobial resistance, is driving the development of rapid molecular diagnostic methods. Rapid detection of microbial pathogens in blood related to bloodstream infections will allow the clinician to decide on or adjust the antimicrobial therapy potentially reducing the morbidity, mortality, and economic burden associated with BSI. For molecular-based methods, there is a lot to gain from an improved and straightforward method for isolation of bacteria from whole blood for downstream processing.We describe a microfluidic-based sample-preparation approach that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.

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.

Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion

PubMed Central

Hermes, Michiel; Schwarz-Linek, Jana; Poon, Wilson C. K.

2018-01-01

Understanding and controlling the surface adhesion of pathogenic bacteria is of urgent biomedical importance. However, many aspects of this process remain unclear (for example, microscopic details of the initial adhesion and possible variations between individual cells). Using a new high-throughput method, we identify and follow many single cells within a clonal population of Escherichia coli near a glass surface. We find strong phenotypic heterogeneities: A fraction of the cells remain in the free (planktonic) state, whereas others adhere with an adhesion strength that itself exhibits phenotypic heterogeneity. We explain our observations using a patchy colloid model; cells bind with localized, adhesive patches, and the strength of adhesion is determined by the number of patches: Nonadherers have no patches, weak adherers bind with a single patch only, and strong adherers bind via a single or multiple patches. We discuss possible implications of our results for controlling bacterial adhesion in biomedical and other applications. PMID:29719861

Persistent and susceptible bacteria with individual deaths.

PubMed

Zucca, Fabio

2014-02-21

The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are not sensitive to antibiotics. These bacteria, called persisters, are in a state called persistence and each bacterium can switch from this state to a non-persistent (or susceptible) state and back (with rates b and a respectively). Our models extend those introduced in Garet et al. (2012) by adding a random natural life cycle for each bacterium and by allowing bacteria in the susceptible state to escape the action of the antibiotic with a fixed probability 1-p (while every bacterium in a persistent state survives with probability 1). This last mechanism of survival to the antibiotics differs from the persistent state one (where reproduction is forbidden) since in this case the bacterium can replicate. We study two different models. In the first model we "inject" the antibiotics in the system at fixed, deterministic times while in the second one the time intervals are random. We show that, in order to kill eventually the whole bacterial population, these time intervals cannot be "too large". The maximum admissible length is increasing with respect to p; we see that even when p is close to 1, this interval length can be significantly smaller than in the case p=1. While in the case p=1 switching back and forth to the persistent state is the only chance of surviving for bacteria, when p<1 and the death rate in the persistent state, say dr, is positive then the situation is more complex. In this case our model suggests that if dr and b are positive (and fixed) then for higher values of p there is an interval for the rate a, say (0,ap) where switching to the persistent state is a good strategy while for a>ap the situation is less favorable than a=0. On the other hand, for smaller values of p the best strategy is a=0, that is, not switching. Finally, when dr=0, switching to the susceptible state is always a better strategy, from the

Laser-Based Identification of Pathogenic Bacteria

NASA Astrophysics Data System (ADS)

Rehse, Steven J.

2009-03-01

Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the last 10 years, however, several events have occurred that demand the attention of the general populace — including the ranks of physicists among them.

Storing Drinking-water in Copper pots Kills Contaminating Diarrhoeagenic Bacteria

PubMed Central

Sudha, V.B. Preethi; Ganesan, Sheeba; Pazhani, G.P.; Ramamurthy, T.; Nair, G.B.

2012-01-01

Microbially-unsafe water is still a major concern in most developing countries. Although many water-purification methods exist, these are expensive and beyond the reach of many people, especially in rural areas. Ayurveda recommends the use of copper for storing drinking-water. Therefore, the objective of this study was to evaluate the effect of copper pot on microbially-contaminated drinking-water. The antibacterial effect of copper pot against important diarrhoeagenic bacteria, including Vibrio cholerae O1, Shigella flexneri 2a, enterotoxigenic Escherichia coli, enteropathogenic E. coli, Salmonella enterica Typhi, and Salmonella Paratyphi is reported. When drinking-water (pH 7.83±0.4; source: ground) was contaminated with 500 CFU/mL of the above bacteria and stored in copper pots for 16 hours at room temperature, no bacteria could be recovered on the culture medium. Recovery failed even after resuscitation in enrichment broth, followed by plating on selective media, indicating loss of culturability. This is the first report on the effect of copper on S. flexneri 2a, enteropathogenic E. coli, and Salmonella Paratyphi. After 16 hours, there was a slight increase in the pH of water from 7.83 to 7.93 in the copper pots while the other physicochemical parameters remained unchanged. Copper content (177±16 ppb) in water stored in copper pots was well within the permissible limits of the World Health Organization. Copper holds promise as a point-of-use solution for microbial purification of drinking-water, especially in developing countries. PMID:22524115

Characterization of anaerobic heterotrophic bacteria isolated from freshwater lake sediments.

PubMed Central

Molongoski, J J; Klug, M J

1976-01-01

Strict anaerobic culture techniques were used to quantitatively and qualitatively evaluate the anaerobic heterotrophic bacteria present at the sediment-water interface of hyperutrophic Wintergreen Lake (Augusta, Mich.). Anaerobic plate counts remained constant from March through December, 1973, ranging from 2.4 X 10(6) to 5.7 X 10(6) organisms/g (dry weight) of sediment. The isolatable bacteria represented a small percentage of the total microbial community, which was shown by direct microscopic counts to be 2.0 X 10'' organisms/g (dry weight) of sediment during June and July. Bacteria of the genus Clostridium dominated the isolates obtained, accounting for 71.8% of the 960 isolates examined. A single species, Clostridium bifermentens, comprised 47.7% of the total. Additional bacterial groups and the percentage in which they were isolated included: Streptococcus sp. (10.8%), unidentified curved rods (9.5%y, gram-positive nonsporing rods (5.6%), and motile gram-negative rods (1.9%). Temperature growth studies demonstrated the ability of all the isolates to grow at in situ sediment temperatures. Gas-liqid radiochromatography was used to determine the soluble metabolic end products from [U-14C]glucose and a U-14C-labeled amino acid mixture by representative sedimentary clostridial isolates and by natural sediment microbial communities. At in situ temperatures the natural sediment microflora produced soluble fermentative end products characteristic of those elaborated by the clostridial isolates tested. These results are considered strong presumptive evidence that clostridia are actively metabolizing in the sediments of Wintergreen Lake. PMID:942211

New fossil remains of Homo naledi from the Lesedi Chamber, South Africa

PubMed Central

Hawks, John; Elliott, Marina; Schmid, Peter; Churchill, Steven E; de Ruiter, Darryl J; Roberts, Eric M; Hilbert-Wolf, Hannah; Garvin, Heather M; Williams, Scott A; Delezene, Lucas K; Feuerriegel, Elen M; Randolph-Quinney, Patrick; Kivell, Tracy L; Laird, Myra F; Tawane, Gaokgatlhe; DeSilva, Jeremy M; Bailey, Shara E; Brophy, Juliet K; Meyer, Marc R; Skinner, Matthew M; Tocheri, Matthew W; VanSickle, Caroline; Walker, Christopher S; Campbell, Timothy L; Kuhn, Brian; Kruger, Ashley; Tucker, Steven; Gurtov, Alia; Hlophe, Nompumelelo; Hunter, Rick; Morris, Hannah; Peixotto, Becca; Ramalepa, Maropeng; van Rooyen, Dirk; Tsikoane, Mathabela; Boshoff, Pedro; Dirks, Paul HGM; Berger, Lee R

2017-01-01

The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species. DOI: http://dx.doi.org/10.7554/eLife.24232.001 PMID:28483039

New fossil remains of Homo naledi from the Lesedi Chamber, South Africa.

PubMed

Hawks, John; Elliott, Marina; Schmid, Peter; Churchill, Steven E; Ruiter, Darryl J de; Roberts, Eric M; Hilbert-Wolf, Hannah; Garvin, Heather M; Williams, Scott A; Delezene, Lucas K; Feuerriegel, Elen M; Randolph-Quinney, Patrick; Kivell, Tracy L; Laird, Myra F; Tawane, Gaokgatlhe; DeSilva, Jeremy M; Bailey, Shara E; Brophy, Juliet K; Meyer, Marc R; Skinner, Matthew M; Tocheri, Matthew W; VanSickle, Caroline; Walker, Christopher S; Campbell, Timothy L; Kuhn, Brian; Kruger, Ashley; Tucker, Steven; Gurtov, Alia; Hlophe, Nompumelelo; Hunter, Rick; Morris, Hannah; Peixotto, Becca; Ramalepa, Maropeng; Rooyen, Dirk van; Tsikoane, Mathabela; Boshoff, Pedro; Dirks, Paul Hgm; Berger, Lee R

2017-05-09

The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi . Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi . Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi , and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species.

[A Case of Hyperammonemia Caused by Urinary Tract Infection Due to Urease-Producing Bacteria].

PubMed

Emura, Masahiro; Tsuchihashi, Kazunari; Shimizu, Yosuke; Kanamaru, Sojun; Matoba, Shun; Ito, Noriyuki

2016-08-01

We present here a rare case of hyperammonemia without liver dysfunction or portal-systemic shunting. The patient was an 80-year-old woman with a history of neurogenic bladder. She was admitted to a nearby hospital for vomiting, diarrhea and consciousness disturbance. Two days after admission, she was transferred to our hospital because of persistant consciousness disturbance. Laboratory data revealed hyperammonemia, but there was no indication of liver dysfunction. Moreover abdominal computed tomography did not reveal any clear finding of liver disease or portal-systemic shunting, but we noted multiple large bladder diverticula. Antibiotic therapy, tracheal intubation, ventilator management and bladder catheterization were performed. The patient's level of consciousness improved rapidly. Urinary culture revealed Bacteroides ureolyticus (urease-producing bacteria). The patient was diagnosed with hyperammonemia and a urinary tract infection due to urease-producing bacteria. Thus, physicians should be aware that obstructive urinary tract infections due to urease-producing bacteria can also be the cause of hyperammonemia.

Silver Colloids in Bacteria: A Study by Transmission Electron Microscopy, Absorption Spectroscopy and Elemental Analysis

DTIC Science & Technology

2002-07-01

study concentrates on other available techniques to elucidate the association of the inorganic colloids and the bacterial components in order to further...the treated bacteria. This is consistent with the strong attraction expected between the silvered cells (with a large Hamaker constant) and their

Quantification and Qualification of Bacteria Trapped in Chewed Gum

PubMed Central

Wessel, Stefan W.; van der Mei, Henny C.; Morando, David; Slomp, Anje M.; van de Belt-Gritter, Betsy; Maitra, Amarnath; Busscher, Henk J.

2015-01-01

Chewing of gum contributes to the maintenance of oral health. Many oral diseases, including caries and periodontal disease, are caused by bacteria. However, it is unknown whether chewing of gum can remove bacteria from the oral cavity. Here, we hypothesize that chewing of gum can trap bacteria and remove them from the oral cavity. To test this hypothesis, we developed two methods to quantify numbers of bacteria trapped in chewed gum. In the first method, known numbers of bacteria were finger-chewed into gum and chewed gums were molded to standard dimensions, sonicated and plated to determine numbers of colony-forming-units incorporated, yielding calibration curves of colony-forming-units retrieved versus finger-chewed in. In a second method, calibration curves were created by finger-chewing known numbers of bacteria into gum and subsequently dissolving the gum in a mixture of chloroform and tris-ethylenediaminetetraacetic-acid (TE)-buffer. The TE-buffer was analyzed using quantitative Polymerase-Chain-Reaction (qPCR), yielding calibration curves of total numbers of bacteria versus finger-chewed in. Next, five volunteers were requested to chew gum up to 10 min after which numbers of colony-forming-units and total numbers of bacteria trapped in chewed gum were determined using the above methods. The qPCR method, involving both dead and live bacteria yielded higher numbers of retrieved bacteria than plating, involving only viable bacteria. Numbers of trapped bacteria were maximal during initial chewing after which a slow decrease over time up to 10 min was observed. Around 108 bacteria were detected per gum piece depending on the method and gum considered. The number of species trapped in chewed gum increased with chewing time. Trapped bacteria were clearly visualized in chewed gum using scanning-electron-microscopy. Summarizing, using novel methods to quantify and qualify oral bacteria trapped in chewed gum, the hypothesis is confirmed that chewing of gum can trap

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution.

PubMed

McNally, Alan; Thomson, Nicholas R; Reuter, Sandra; Wren, Brendan W

2016-03-01

Pathogenic species in the Yersinia genus have historically been targets for research aimed at understanding how bacteria evolve into mammalian pathogens. The advent of large-scale population genomic studies has greatly accelerated the progress in this field, and Yersinia pestis, Yersinia pseudotuberculosis and Yersinia enterocolitica have once again acted as model organisms to help shape our understanding of the evolutionary processes involved in pathogenesis. In this Review, we highlight the gene gain, gene loss and genome rearrangement events that have been identified by genomic studies in pathogenic Yersinia species, and we discuss how these findings are changing our understanding of pathogen evolution. Finally, as these traits are also found in the genomes of other species in the Enterobacteriaceae, we suggest that they provide a blueprint for the evolution of enteropathogenic bacteria.

Porphyromonas gingivalis as a Model Organism for Assessing Interaction of Anaerobic Bacteria with Host Cells.

PubMed

Wunsch, Christopher M; Lewis, Janina P

2015-12-17

Anaerobic bacteria far outnumber aerobes in many human niches such as the gut, mouth, and vagina. Furthermore, anaerobic infections are common and frequently of indigenous origin. The ability of some anaerobic pathogens to invade human cells gives them adaptive measures to escape innate immunity as well as to modulate host cell behavior. However, ensuring that the anaerobic bacteria are live during experimental investigation of the events may pose challenges. Porphyromonas gingivalis, a Gram-negative anaerobe, is capable of invading a variety of eukaryotic non-phagocytic cells. This article outlines how to successfully culture and assess the ability of P. gingivalis to invade human umbilical vein endothelial cells (HUVECs). Two protocols were developed: one to measure bacteria that can successfully invade and survive within the host, and the other to visualize bacteria interacting with host cells. These techniques necessitate the use of an anaerobic chamber to supply P. gingivalis with an anaerobic environment for optimal growth. The first protocol is based on the antibiotic protection assay, which is largely used to study the invasion of host cells by bacteria. However, the antibiotic protection assay is limited; only intracellular bacteria that are culturable following antibiotic treatment and host cell lysis are measured. To assess all bacteria interacting with host cells, both live and dead, we developed a protocol that uses fluorescent microscopy to examine host-pathogen interaction. Bacteria are fluorescently labeled with 2',7'-Bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein acetoxymethyl ester (BCECF-AM) and used to infect eukaryotic cells under anaerobic conditions. Following fixing with paraformaldehyde and permeabilization with 0.2% Triton X-100, host cells are labeled with TRITC phalloidin and DAPI to label the cell cytoskeleton and nucleus, respectively. Multiple images taken at different focal points (Z-stack) are obtained for temporal

Porphyromonas gingivalis as a Model Organism for Assessing Interaction of Anaerobic Bacteria with Host Cells

PubMed Central

Wunsch, Christopher M.; Lewis, Janina P.

2015-01-01

Anaerobic bacteria far outnumber aerobes in many human niches such as the gut, mouth, and vagina. Furthermore, anaerobic infections are common and frequently of indigenous origin. The ability of some anaerobic pathogens to invade human cells gives them adaptive measures to escape innate immunity as well as to modulate host cell behavior. However, ensuring that the anaerobic bacteria are live during experimental investigation of the events may pose challenges. Porphyromonas gingivalis, a Gram-negative anaerobe, is capable of invading a variety of eukaryotic non-phagocytic cells. This article outlines how to successfully culture and assess the ability of P. gingivalis to invade human umbilical vein endothelial cells (HUVECs). Two protocols were developed: one to measure bacteria that can successfully invade and survive within the host, and the other to visualize bacteria interacting with host cells. These techniques necessitate the use of an anaerobic chamber to supply P. gingivalis with an anaerobic environment for optimal growth. The first protocol is based on the antibiotic protection assay, which is largely used to study the invasion of host cells by bacteria. However, the antibiotic protection assay is limited; only intracellular bacteria that are culturable following antibiotic treatment and host cell lysis are measured. To assess all bacteria interacting with host cells, both live and dead, we developed a protocol that uses fluorescent microscopy to examine host-pathogen interaction. Bacteria are fluorescently labeled with 2',7'-Bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein acetoxymethyl ester (BCECF-AM) and used to infect eukaryotic cells under anaerobic conditions. Following fixing with paraformaldehyde and permeabilization with 0.2% Triton X-100, host cells are labeled with TRITC phalloidin and DAPI to label the cell cytoskeleton and nucleus, respectively. Multiple images taken at different focal points (Z-stack) are obtained for temporal

Effect of bacteria and dissolved organics on mineral dissolution kinetics:

NASA Astrophysics Data System (ADS)

Pokrovsky, Oleg; Shirokova, Liudmila; Benezeth, Pascale; Zabelina, Svetlana

2010-05-01

Quantification of the effect of microorganisms and associated organic ligands on mineral dissolution rate is one among the last remaining challenges in modeling of water-rock interactions under earth surface and subsurface environments. This is especially true for deep underground settings within the context of CO2 capture, sequestration and storage. First, elevated CO2 pressures create numerous experimental difficulties for performing robust flow-through experiments at a given saturation state. Second, reactivity of main rock-forming minerals in abiotic systems at pCO2 >> 1 atm and circumneutral pH is still poorly constrained. And third, most of microbial habitats of the subsurface biosphere are not suitable for routine culturing in the laboratory, many of them are anaerobic and even strictly anaerobic, and many bacteria and archae cultures can live only in the consortium of microorganisms which is very hard to maintain at a controlled and stable biomass concentration. For experimental modeling of bio-mineral interactions in the laboratory, two other main conceptual challenges exist. Typical concentration of dissolved organic carbon that serves as a main nutrient for heterotrophic bacteria in underground waters rarely exceeds 3-5 mg/L. Typical concentration of DOC in nutrient media used for bacteria culturing is between 100 and 10,000 mg/L. Therefore, performing mineral-bacteria interactions in the laboratory under environmentally-sound conditions requires significant dilution of the nutrient media or the use of flow-through reactors. Concerning the effect of organic ligands and bacterial excudates on rock-forming mineral dissolution, at the present time, mostly empirical (phenomenological) approach can be used. Indeed, the pioneering studies of Stumm and co-workers have established a firm basis for modeling the catalyzing and inhibiting effects of ligands on metal oxide dissolution rate. This approach, very efficient for studying the interaction of organic and

Communication among Oral Bacteria

PubMed Central

Kolenbrander, Paul E.; Andersen, Roxanna N.; Blehert, David S.; Egland, Paul G.; Foster, Jamie S.; Palmer, Robert J.

2002-01-01

Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities. PMID:12209001

Alginate Beads as Synthetic Inoculant Carriers for Slow Release of Bacteria That Affect Plant Growth †‡

PubMed Central

Bashan, Yoav

1986-01-01

Uniform synthetic beads were developed as carriers for the bacterial inoculation of plants. The beads are made of sodium alginate and skim milk and contain a large reservoir of bacterial culture which releases the bacteria at a slow and constant rate. The beads are biodegradable and produce no environmental pollution. The strength of the beads, the rate of bacterial release, and the time of their survival in the soil can be controlled by several hardening treatments. The final product, lyophilized beads, is simple to use and is applied to the seeds concomitantly with sowing. The released bacteria are available for root colonization immediately at seed germination. Dry beads containing bacteria can be stored at ambient temperature over a long period without loss of bacterial content; storage requires a limited space, and the quality control of a number of bacteria in the bead is simple. The level of plant inoculation with beads was similar to that with previously used peat inoculants, but the former method yielded more consistent results, as the frequency of inoculated plants was much higher. The former method provides a different approach for inoculation of plants with beneficial rhizosphere bacteria. Images PMID:16347055

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.

Sweet scents from good bacteria: Case studies on bacterial volatile compounds for plant growth and immunity.

PubMed

Chung, Joon-hui; Song, Geun Cheol; Ryu, Choong-Min

2016-04-01

Beneficial bacteria produce diverse chemical compounds that affect the behavior of other organisms including plants. Bacterial volatile compounds (BVCs) contribute to triggering plant immunity and promoting plant growth. Previous studies investigated changes in plant physiology caused by in vitro application of the identified volatile compounds or the BVC-emitting bacteria. This review collates new information on BVC-mediated plant-bacteria airborne interactions, addresses unresolved questions about the biological relevance of BVCs, and summarizes data on recently identified BVCs that improve plant growth or protection. Recent explorations of bacterial metabolic engineering to alter BVC production using heterologous or endogenous genes are introduced. Molecular genetic approaches can expand the BVC repertoire of beneficial bacteria to target additional beneficial effects, or simply boost the production level of naturally occurring BVCs. The effects of direct BVC application in soil are reviewed and evaluated for potential large-scale field and agricultural applications. Our review of recent BVC data indicates that BVCs have great potential to serve as effective biostimulants and bioprotectants even under open-field conditions.

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

PubMed

Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

2017-04-08

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model

Regulation of Multiple Carbon Monoxide Consumption Pathways in Anaerobic Bacteria

PubMed Central

Techtmann, Stephen M.; Colman, Albert S.; Murphy, Michael B.; Schackwitz, Wendy S.; Goodwin, Lynne A.; Robb, Frank T.

2011-01-01

Carbon monoxide (CO), well known as a toxic gas, is increasingly recognized as a key metabolite and signaling molecule. Microbial utilization of CO is quite common, evidenced by the rapid escalation in description of new species of CO-utilizing bacteria and archaea. Carbon monoxide dehydrogenase (CODH), the protein complex that enables anaerobic CO-utilization, has been well-characterized from an increasing number of microorganisms, however the regulation of multiple CO-related gene clusters in single isolates remains unexplored. Many species are extraordinarily resistant to high CO concentrations, thriving under pure CO at more than one atmosphere. We hypothesized that, in strains that can grow exclusively on CO, both carbon acquisition via the CODH/acetyl CoA synthase complex and energy conservation via a CODH-linked hydrogenase must be differentially regulated in response to the availability of CO. The CO-sensing transcriptional activator, CooA is present in most CO-oxidizing bacteria. Here we present a genomic and phylogenetic survey of CODH operons and cooA genes found in CooA-containing bacteria. Two distinct groups of CooA homologs were found: one clade (CooA-1) is found in the majority of CooA-containing bacteria, whereas the other clade (CooA-2) is found only in genomes that encode multiple CODH clusters, suggesting that the CooA-2 might be important for cross-regulation of competing CODH operons. Recombinant CooA-1 and CooA-2 regulators from the prototypical CO-utilizing bacterium Carboxydothermus hydrogenoformans were purified, and promoter binding analyses revealed that CooA-1 specifically regulates the hydrogenase-linked CODH, whereas CooA-2 is able to regulate both the hydrogenase-linked CODH and the CODH/ACS operons. These studies point to the ability of dual CooA homologs to partition CO into divergent CO-utilizing pathways resulting in efficient consumption of a single limiting growth substrate available across a wide range of concentrations. PMID

Spectroscopic diagnostics for bacteria in biologic sample

DOEpatents

El-Sayed, Mostafa A.; El-Sayed, Ivan H.

2002-01-01

A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

DOE PAGES

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica; ...

2014-08-29

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning

PubMed Central

Wybouw, Nicky; Dermauw, Wannes; Tirry, Luc; Stevens, Christian; Grbić, Miodrag; Feyereisen, René; Van Leeuwen, Thomas

2014-01-01

Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the enzyme known to detoxify HCN to β-cyanoalanine in arthropods has remained enigmatic. Here we identify this enzyme by transcriptome analysis and functional expression. Phylogenetic analysis showed that the gene is a member of the cysteine synthase family horizontally transferred from bacteria to phytophagous mites and Lepidoptera. The recombinant mite enzyme had both β-cyanoalanine synthase and cysteine synthase activity but enzyme kinetics showed that cyanide detoxification activity was strongly favored. Our results therefore suggest that an ancient horizontal transfer of a gene originally involved in sulfur amino acid biosynthesis in bacteria was co-opted by herbivorous arthropods to detoxify plant produced cyanide. DOI: http://dx.doi.org/10.7554/eLife.02365.001 PMID:24843024

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens

PubMed Central

Zeng, Melody Y.; Cisalpino, Daniel; Varadarajan, Saranyaraajan; Hellman, Judith; Warren, H. Shaw; Cascalho, Marilia; Inohara, Naohiro; Núñez, Gabriel

2016-01-01

The gut microbiota is compartmentalized in the intestinal lumen and induces local immune responses, but it remains unknown whether the gut microbiota can induce systemic response and contribute to systemic immunity. We report that selective gut symbiotic gram-negative bacteria were able to disseminate systemically to induce immunoglobulin G (IgG) response, which primarily targeted gram-negative bacterial antigens and conferred protection against systemic infections by E. coli and Salmonella by directly coating bacteria to promote killing by phagocytes. T cells and Toll-like receptor 4 on B cells were important in the generation of microbiota-specific IgG. We identified murein lipoprotein (MLP), a highly conserved gram-negative outer membrane protein, as a major antigen that induced systemic IgG homeostatically in both mice and humans. Administration of anti-MLP IgG conferred crucial protection against systemic Salmonella infection. Thus, our findings reveal an important function for the gut microbiota in combating systemic infection through the induction of protective IgG. PMID:26944199

Ecological differentiation within a cosmopolitan group of planktonic freshwater bacteria (SOL cluster, Saprospiraceae, Bacteroidetes).

PubMed

Schauer, Michael; Kamenik, Christian; Hahn, Martin W

2005-10-01

Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats.

Development of bacteria-based bioassays for arsenic detection in natural waters.

PubMed

Diesel, Elizabeth; Schreiber, Madeline; van der Meer, Jan Roelof

2009-06-01

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.

Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

PubMed Central

Yamamoto, Hiroyuki; Hiraishi, Akira; Kato, Kenji; Chiura, Hiroshi X.; Maki, Yonosuke; Shimizu, Akira

1998-01-01