Bacterial Activity at −2 to −20°C in Arctic Wintertime Sea Ice

PubMed Central

Junge, Karen; Eicken, Hajo; Deming, Jody W.

2004-01-01

Arctic wintertime sea-ice cores, characterized by a temperature gradient of −2 to −20°C, were investigated to better understand constraints on bacterial abundance, activity, and diversity at subzero temperatures. With the fluorescent stains 4′,6′-diamidino-2-phenylindole 2HCl (DAPI) (for DNA) and 5-cyano-2,3-ditoyl tetrazolium chloride (CTC) (for O2-based respiration), the abundances of total, particle-associated (>3-μm), free-living, and actively respiring bacteria were determined for ice-core samples melted at their in situ temperatures (−2 to −20°C) and at the corresponding salinities of their brine inclusions (38 to 209 ppt). Fluorescence in situ hybridization was applied to determine the proportions of Bacteria, Cytophaga-Flavobacteria-Bacteroides (CFB), and Archaea. Microtome-prepared ice sections also were examined microscopically under in situ conditions to evaluate bacterial abundance (by DAPI staining) and particle associations within the brine-inclusion network of the ice. For both melted and intact ice sections, more than 50% of cells were found to be associated with particles or surfaces (sediment grains, detritus, and ice-crystal boundaries). CTC-active bacteria (0.5 to 4% of the total) and cells detectable by rRNA probes (18 to 86% of the total) were found in all ice samples, including the coldest (−20°C), where virtually all active cells were particle associated. The percentage of active bacteria associated with particles increased with decreasing temperature, as did the percentages of CFB (16 to 82% of Bacteria) and Archaea (0.0 to 3.4% of total cells). These results, combined with correlation analyses between bacterial variables and measures of particulate matter in the ice as well as the increase in CFB at lower temperatures, confirm the importance of particle or surface association to bacterial activity at subzero temperatures. Measuring activity down to −20°C adds to the concept that liquid inclusions in frozen environments provide an adequate habitat for active microbial populations on Earth and possibly elsewhere. PMID:14711687

Bacterial community assembly in activated sludge: mapping beta diversity across environmental variables.

PubMed

Isazadeh, Siavash; Jauffur, Shameem; Frigon, Dominic

2016-12-01

Effect of ecological variables on community assembly of heterotrophic bacteria at eight full-scale and two pilot-scale activated sludge wastewater treatment plants (AS-WWTPs) were explored by pyrosequencing of 16S rRNA gene amplicons. In total, 39 samples covering a range of abiotic factors spread over space and time were analyzed. A core bacterial community of 24 families detected in at least six of the eight AS-WWTPs was defined. In addition to the core families, plant-specific families (observed at <50% AS-WWTPs) were found to be also important in the community structure. Observed beta diversity was partitioned with respect to ecological variables. Specifically, the following variables were considered: influent wastewater characteristics, season (winter vs. summer), process operations (conventional, oxidation ditch, and sequence batch reactor), reactor sizes (pilot-scale vs. full-scale reactors), chemical stresses defined by ozonation of return activated sludge, interannual variation, and geographical locations. Among the assessed variables, influent wastewater characteristics and geographical locations contributed more in explaining the differences between AS-WWTP bacterial communities with a maximum of approximately 26% of the observed variations. Partitioning of beta diversity is necessary to interpret the inherent variability in microbial community assembly and identify the driving forces at play in engineered microbial ecosystem. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

PubMed Central

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

2012-01-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

PubMed

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

2012-05-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

Water Behavior in Bacterial Spores by Deuterium NMR Spectroscopy

PubMed Central

2015-01-01

Dormant bacterial spores are able to survive long periods of time without nutrients, withstand harsh environmental conditions, and germinate into metabolically active bacteria when conditions are favorable. Numerous factors influence this hardiness, including the spore structure and the presence of compounds to protect DNA from damage. It is known that the water content of the spore core plays a role in resistance to degradation, but the exact state of water inside the core is a subject of discussion. Two main theories present themselves: either the water in the spore core is mostly immobile and the core and its components are in a glassy state, or the core is a gel with mobile water around components which themselves have limited mobility. Using deuterium solid-state NMR experiments, we examine the nature of the water in the spore core. Our data show the presence of unbound water, bound water, and deuterated biomolecules that also contain labile deuterons. Deuterium–hydrogen exchange experiments show that most of these deuterons are inaccessible by external water. We believe that these unreachable deuterons are in a chemical bonding state that prevents exchange. Variable-temperature NMR results suggest that the spore core is more rigid than would be expected for a gel-like state. However, our rigid core interpretation may only apply to dried spores whereas a gel core may exist in aqueous suspension. Nonetheless, the gel core, if present, is inaccessible to external water. PMID:24950158

Analysis of the Cellular and Molecular Mechanisms Which Underlie Sensitivity to Bacterial Endotoxin and Early Tolerance

DTIC Science & Technology

1992-06-24

system, such as pneumococcal polysaccharide (Hiernaux et aI., 1989) or those that are presented by malignant tumors (O’Malley et ai., 1963). LPS...isolated the active ingredient, which they called ’’bacterial polysaccharide " (Shear and Andervont, 1936). The practice of inducing "therapeutic febrile...acylated, diphosphorylated, ~-1,6-linked D-glucosamine disaccharide (referred to as lipid A) which is attached covalently to a core polysaccharide that

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

DOE PAGES

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; ...

2015-04-30

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

PubMed Central

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

2015-01-01

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

Clavanin A-bioconjugated Fe3O4/Silane core-shell nanoparticles for thermal ablation of bacterial biofilms.

PubMed

Ribeiro, Kalline L; Frías, Isaac A M; Franco, Octavio L; Dias, Simoni C; Sousa-Junior, Ailton A; Silva, Osmar N; Bakuzis, Andris F; Oliveira, Maria D L; Andrade, Cesar A S

2018-04-27

The use of central venous catheters (CVC) is highly associated with nosocomial blood infections and its use largely requires a systematic assessment of benefits and risks. Bacterial contamination of these tubes is frequent and may result in development of microbial consortia also known as biofilm. The woven nature of biofilm provides a practical defense against antimicrobial agents, facilitating bacterial dissemination through the patient's body and development of antimicrobial resistance. In this work, the authors describe the modification of CVC tubing by immobilizing Fe 3 O 4 -aminosilane core-shell nanoparticles functionalized with antimicrobial peptide clavanin A (clavA) as an antimicrobial prophylactic towards Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Its anti-biofilm-attachment characteristic relies in clavA natural activity to disrupt the bacterial lipidic membrane. The aminosilane shell prevents iron leaching, which is an important nutrient for bacterial growth. Fe 3 O 4 -clavA-modified CVCs showed to decrease Gram-negative bacteria attachment up to 90% when compared to control clean CVC. Additionally, when hyperthermal treatment is triggered for 5 min at 80 °C in a tubing that already presents bacterial biofilm (CVC-BF), the viability of attached bacteria reduces up to 88%, providing an efficient solution to avoid changing catheter. Copyright © 2018 Elsevier B.V. All rights reserved.

Two-dimensional distribution of microbial activity and flow patterns within naturally fractured chalk.

PubMed

Arnon, Shai; Ronen, Zeev; Adar, Eilon; Yakirevich, Alexander; Nativ, Ronit

2005-10-01

The two-dimensional distribution of flow patterns and their dynamic change due to microbial activity were investigated in naturally fractured chalk cores. Long-term biodegradation experiments were conducted in two cores ( approximately 20 cm diameter, 31 and 44 cm long), intersected by a natural fracture. 2,4,6-tribromophenol (TBP) was used as a model contaminant and as the sole carbon source for aerobic microbial activity. The transmissivity of the fractures was continuously reduced due to biomass accumulation in the fracture concurrent with TBP biodegradation. From multi-tracer experiments conducted prior to and following the microbial activity, it was found that biomass accumulation causes redistribution of the preferential flow channels. Zones of slow flow near the fracture inlet were clogged, thus further diverting the flow through zones of fast flow, which were also partially clogged. Quantitative evaluation of biodegradation and bacterial counts supported the results of the multi-tracer tests, indicating that most of the bacterial activity occurs close to the inlet. The changing flow patterns, which control the nutrient supply, resulted in variations in the concentrations of the chemical constituents (TBP, bromide and oxygen), used as indicators of biodegradation.

Structure of bacterial lipopolysaccharides.

PubMed

Caroff, Martine; Karibian, Doris

2003-11-14

Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in "smooth-type" lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

Topological defects in a living nematic ensnare swimming bacteria [Linking bacterial motility and liquid crystallinity in a model of living nematic

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

Genkin, Mikhail Mikhailovich; Sokolov, Andrey; Lavrentovich, Oleg D.

Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement withmore » the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of +1/2 topological defects and depletion of bacteria in the cores of -1/2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Lastly, our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.« less

Topological defects in a living nematic ensnare swimming bacteria [Linking bacterial motility and liquid crystallinity in a model of living nematic

DOE PAGES

Genkin, Mikhail Mikhailovich; Sokolov, Andrey; Lavrentovich, Oleg D.; ...

2017-03-08

Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement withmore » the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of +1/2 topological defects and depletion of bacteria in the cores of -1/2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Lastly, our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.« less

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

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

PubMed Central

van Tonder, Andries J.; Mistry, Shilan; Bray, James E.; Hill, Dorothea M. C.; Cody, Alison J.; Farmer, Chris L.; Klugman, Keith P.; von Gottberg, Anne; Bentley, Stephen D.; Parkhill, Julian; Jolley, Keith A.; Maiden, Martin C. J.; Brueggemann, Angela B.

2014-01-01

The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance. PMID:25144616

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology.

PubMed

Datta, Manoshi S; Almada, Amalia A; Baumgartner, Mark F; Mincer, Tracy J; Tarrant, Ann M; Polz, Martin F

2018-06-06

Copepods harbor diverse bacterial communities, which collectively carry out key biogeochemical transformations in the ocean. However, bulk copepod sampling averages over the variability in their associated bacterial communities, thereby limiting our understanding of the nature and specificity of copepod-bacteria associations. Here, we characterize the bacterial communities associated with nearly 200 individual Calanus finmarchicus copepods transitioning from active growth to diapause. We find that all individual copepods sampled share a small set of "core" operational taxonomic units (OTUs), a subset of which have also been found associated with other marine copepod species in different geographic locations. However, most OTUs are patchily distributed across individual copepods, thereby driving community differences across individuals. Among patchily distributed OTUs, we identified groups of OTUs correlated with common ecological drivers. For instance, a group of OTUs positively correlated with recent copepod feeding served to differentiate largely active growing copepods from those entering diapause. Together, our results underscore the power of individual-level sampling for understanding host-microbiome relationships.

Thienopyrimidine-type compounds protect Arabidopsis plants against the hemibiotrophic fungal pathogen Colletotrichum higginsianum and bacterial pathogen Pseudomonas syringae pv. maculicola.

PubMed

Narusaka, Mari; Narusaka, Yoshihiro

2017-03-04

Plant activators activate systemic acquired resistance-like defense responses or induced systemic resistance, and thus protect plants from pathogens. We screened a chemical library composed of structurally diverse small molecules. We isolated six plant immune-inducing thienopyrimidine-type compounds and their analogous compounds. It was observed that the core structure of thienopyrimidine plays a role in induced resistance in plants. Furthermore, we highlight the protective effect of thienopyrimidine-type compounds against both hemibiotrophic fungal pathogen, Colletotrichum higginsianum, and bacterial pathogen, Pseudomonas syringae pv. maculicola, in Arabidopsis thaliana. We suggest that thienopyrimidine-type compounds could be potential lead compounds as novel plant activators, and can be useful and effective agrochemicals against various plant diseases.

Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.

PubMed

Cheng, Weixiao; Chen, Hong; Yan, ShuHai; Su, Jianqiang

2014-09-01

Short-chain fatty acids (SCFAs) can be produced by primary and waste activated sludge anaerobic fermentation. The yield and product spectrum distribution of SCFAs can be significantly affected by different initial pH values. However, most studies have focused on the physical and chemical aspects of SCFA production by waste activated sludge fermentation at different pH values. Information on the bacterial community structures during acidogenic fermentation is limited. In this study, comparisons of the bacterial communities during the co-substrate fermentation of food wastes and sewage sludge at different pH values were performed using the barcoded Illumina paired-end sequencing method. The results showed that different pH environments harbored a characteristic bacterial community, including sequences related to Lactobacillus, Prevotella, Mitsuokella, Treponema, Clostridium, and Ureibacillus. The most abundant bacterial operational taxonomic units in the different pH environments were those related to carbohydrate-degrading bacteria, which are associated with constituents of co-substrate fermentation. Further analyses showed that during organic matter fermentation, a core microbiota composed of Firmicutes, Proteobacteria, and Bacteroidetes existed. Comparison analyses revealed that the bacterial community during fermentation was significantly affected by the pH, and that the diverse product distribution was related to the shift in bacterial communities.

Computational model for living nematic

NASA Astrophysics Data System (ADS)

Genkin, Mikhail; Sokolov, Andrey; Lavrentovich, Oleg; Aranson, Igor

A realization of an active system has been conceived by combining swimming bacteria and a lyotropic nematic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics we developed a computational model describing intricate properties of such a living nematic. In faithful agreement with the experiment, the model reproduces the onset of periodic undulation of the nematic director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields testable prediction on the accumulation and transport of bacteria in the cores of +1/2 topological defects and depletion of bacteria in the cores of -1/2 defects. Our new experiment on motile bacteria suspended in a free-standing liquid crystalline film fully confirmed this prediction. This effect can be used to capture and manipulation of small amounts of bacteria.

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.

PubMed

Kahlke, Tim; Goesmann, Alexander; Hjerde, Erik; Willassen, Nils Peder; Haugen, Peik

2012-05-10

The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.

Annual Surveillance Summary: Methicillin-Resistant Staphylococcus aureus (MRSA) Infections in the Military Health System (MHS), 2016

DTIC Science & Technology

2017-06-01

associated exposures, Defense Manpower Data Center (DMDC) rosters to determine burden among Department of Defense (DOD) active duty (AD) service members... active duty (AD) population in 2016 were also below the weighted historic IRs. The DOD AD, Army, and Marine Corps populations reported a change of...surveillance- summaries.aspx. Published June 2017. Accessed 30 June 2017. 4. Centers for Disease Control and Prevention. 2015. Active bacterial core

Analysis of mutagenic activity of biohazardous organics in Kanawha River sediments. Technical completion report

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

White, A.R.; Waldron, M.C.

1988-01-01

Residual chemical contamination of Kanawha River sediments may constitute a health hazard. Sediment cores have been analyzed using a coupled bioassay/chemical fractionation procedure. Both bacterial mutagenicity and sister chromatid exchange (SCE) analyses were conducted on sediment samples. Pocatalico River sediments extracts showed no response in either bacterial mutagenicity assay or SCE assay. Extracts from Armour Creek and the Kanawha River induced mutagenicities in the presence of S9 enzymes. The same extracts produced a significant increase in human chromosomal cross-over events.

Bioavailability of pollutants in bacterial communities of Rodrigo de Freitas Lagoon, Rio de Janeiro, Brazil

PubMed Central

da Fonseca, E.M.; Neto, J.A. Baptista; McAlister, J.J.; Smith, B.J.; Crapez, M.A.C.

2014-01-01

Processes involving heavy metals and other contaminants continue to present unsolved environmental questions. To advance the understanding of geochemical processes that involve the bioavailability of contaminants, cores where collected in the Rodrigo de Freitas lagoon, and analyzed for bacterial activity and metal concentrations. Results would suggest an extremely reducing environment where organic substances seem to be the predominant agents responsible for this geochemical process. Analytical data showed sulphate reduction to be the main agent driving this process, since this kind of bacteria was found to be active in all of the samples analyzed. Esterase enzyme production did not signal the influence of heavy metals and hydrocarbon concentrations and heavy metals were found to be unavailable for biota. However, correlation between results for bacterial biomass and the potentially mobile percentage of the total Ni concentrations would suggest a negative impact. PMID:25477931

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

PubMed Central

D Ainsworth, Tracy; Krause, Lutz; Bridge, Thomas; Torda, Gergely; Raina, Jean-Baptise; Zakrzewski, Martha; Gates, Ruth D; Padilla-Gamiño, Jacqueline L; Spalding, Heather L; Smith, Celia; Woolsey, Erika S; Bourne, David G; Bongaerts, Pim; Hoegh-Guldberg, Ove; Leggat, William

2015-01-01

Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes. PMID:25885563

Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.

PubMed

Bolten, Marcel; Delley, Cyrille L; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad; Weber-Ban, Eilika

2016-12-06

Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex. Copyright © 2016 Elsevier Ltd. All rights reserved.

Melanization and Pathogenicity in the Insect, Tenebrio molitor, and the Crustacean, Pacifastacus leniusculus, by Aeromonas hydrophila AH-3

PubMed Central

Noonin, Chadanat; Jiravanichpaisal, Pikul; Söderhäll, Irene; Merino, Susana; Tomás, Juan M.; Söderhäll, Kenneth

2010-01-01

Aeromonas hydrophila is the most common Aeromonas species causing infections in human and other animals such as amphibians, reptiles, fish and crustaceans. Pathogenesis of Aeromonas species have been reported to be associated with virulence factors such as lipopolysaccharides (LPS), bacterial toxins, bacterial secretion systems, flagella, and other surface molecules. Several mutant strains of A. hydrophila AH-3 were initially used to study their virulence in two animal species, Pacifastacus leniusculus (crayfish) and Tenebrio molitor larvae (mealworm). The AH-3 strains used in this study have mutations in genes involving the synthesis of flagella, LPS structures, secretion systems, and some other factors, which have been reported to be involved in A. hydrophila pathogenicity. Our study shows that the LPS (O-antigen and external core) is the most determinant A. hydrophila AH-3 virulence factor in both animals. Furthermore, we studied the immune responses of these hosts to infection of virulent or non-virulent strains of A. hydrophila AH-3. The AH-3 wild type (WT) containing the complete LPS core is highly virulent and this bacterium strongly stimulated the prophenoloxidase activating system resulting in melanization in both crayfish and mealworm. In contrast, the ΔwaaE mutant which has LPS without O-antigen and external core was non-virulent and lost ability to stimulate this system and melanization in these two animals. The high phenoloxidase activity found in WT infected crayfish appears to result from a low expression of pacifastin, a prophenoloxidase activating enzyme inhibitor, and this gene expression was not changed in the ΔwaaE mutant infected animal and consequently phenoloxidase activity was not altered as compared to non-infected animals. Therefore we show that the virulence factors of A. hydrophila are the same regardless whether an insect or a crustacean is infected and the O-antigen and external core is essential for activation of the proPO system and as virulence factors for this bacterium. PMID:21206752

Aspartame-stabilized gold-silver bimetallic biocompatible nanostructures with plasmonic photothermal properties, antibacterial activity, and long-term stability.

PubMed

Fasciani, Chiara; Silvero, M Jazmin; Anghel, Maria Alexandra; Argüello, Gerardo A; Becerra, Maria Cecilia; Scaiano, Juan C

2014-12-17

Gold-silver core-shell nanoparticles stabilized with a common sweetener, aspartame (AuNP@Ag@Asm), combine the antimicrobial properties of silver with the photoinduced plasmon-mediated photothermal effects of gold. The particles were tested with several bacterial strains, while biocompatibility was verified with human dermal fibroblasts.

Discovery of novel bacterial RNA polymerase inhibitors: pharmacophore-based virtual screening and hit optimization.

PubMed

Hinsberger, Stefan; Hüsecken, Kristina; Groh, Matthias; Negri, Matthias; Haupenthal, Jörg; Hartmann, Rolf W

2013-11-14

The bacterial RNA polymerase (RNAP) is a validated target for broad spectrum antibiotics. However, the efficiency of drugs is reduced by resistance. To discover novel RNAP inhibitors, a pharmacophore based on the alignment of described inhibitors was used for virtual screening. In an optimization process of hit compounds, novel derivatives with improved in vitro potency were discovered. Investigations concerning the molecular mechanism of RNAP inhibition reveal that they prevent the protein-protein interaction (PPI) between σ(70) and the RNAP core enzyme. Besides of reducing RNA formation, the inhibitors were shown to interfere with bacterial lipid biosynthesis. The compounds were active against Gram-positive pathogens and revealed significantly lower resistance frequencies compared to clinically used rifampicin.

Bacteria in deep coastal plain sediments of Maryland: A possible source of CO2 to groundwater

NASA Astrophysics Data System (ADS)

Chapelle, Francis H.; Zelibor, Joseph L., Jr.; Grimes, D. Jay; Knobel, Leroy L.

1987-08-01

Nineteen cores of unconsolidated Coastal Plain sediments obtained from depths of 14 to 182 m below land surface near Waldorf, Maryland, were collected and examined for metabolically active bacteria. The age of the sediments cored range from Miocene to Early Cretaceous. Acridine orange direct counts of total (viable and nonviable) bacteria in core subsamples ranged from 108 to 104 bacteria/g of dry sediment. Direct counts of viable bacteria ranged from 106 to 103 bacteria/g of dry sediment. Three cores contained viable methanogenic bacteria, and seven cores contained viable sulfate-reducing bacteria. The observed presence of bacteria in these sediments suggest that heterotrophic bacterial metabolism, with lignitic organic material as the primary substrate, is a plausible source of CO2 to groundwater. However, the possibility that abiotic processes also produce CO2 cannot be ruled out. Estimated rates of CO2 production in the noncalcareous Magothy/Upper Patapsco and Lower Patapsco aquifers based on mass balance of dissolved inorganic carbon, groundwater flow rates, and flow path segment lengths are in the range 10-3 to 10-5 mmol L-1 yr-1. Isotope balance calculations suggest that aquifer-generated CO2 is much heavier isotopically (˜—10 to + 5 per mil) than lignite (˜-24 per mil) present in these sediments. This may reflect isotopic fractionation during methanogenesis and possibly other bacterially mediated processes.

Bacterial Community Composition and Extracellular Enzyme Activity in Temperate Streambed Sediment during Drying and Rewetting

PubMed Central

Pohlon, Elisabeth; Ochoa Fandino, Adriana; Marxsen, Jürgen

2013-01-01

Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after harsh desiccation, followed by loss of the specialized functions of specific groups of bacteria. PMID:24386188

Influence of diesel contamination on the benthic microbial/meiofaunal food web of a Louisiana salt marsh

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

Carman, K.R.; Fleeger, J.W.; Pomarico, S.

The authors studied the influence of diesel-contaminated sediments on the benthic microbial/meiofaunal food web from a Louisiana salt marsh. Diesel-contaminated sediment was added to microcosms (intact cores of marsh mud) in a range of doses, and a suite of microbial and meiofaunal responses were measured over a 28-day period. The authors measured bacterial and microalgal (Chl a) abundance, bacterial and microalgal activity using radiotracers ({sup 14}C-acetate and {sup 14}CO{sub 2}, respectively), meiofaunal grazing on microalgae, meiofaunal community structure, and meiofaunal physiological condition. Preliminary results indicate that diesel-contaminated sediments influence microalgal biomass and activity, as well as the life histories ofmore » benthic copepod species.« less

Bactericidal Dendritic Polycation Cloaked with Stealth Material via Lipase-Sensitive Intersegment Acquires Neutral Surface Charge without Losing Membrane-Disruptive Activity.

PubMed

Xu, Lulu; He, Chen; Hui, Liwei; Xie, Yuntao; Li, Jia-Min; He, Wei-Dong; Yang, Lihua

2015-12-23

Net cationicity of membrane-disruptive antimicrobials is necessary for their activity but may elicit immune attack when administered intravenously. By cloaking a dendritic polycation (G2) with poly(caprolactone-b-ethylene glycol) (PCL-b-PEG), we obtain a nanoparticle antimicrobial, G2-g-(PCL-b-PEG), which exhibits neutral surface charge but kills >99.9% of inoculated bacterial cells at ≤8 μg/mL. The observed activity may be attributed PCL's responsive degradation by bacterial lipase and the consequent exposure of the membrane-disruptive, bactericidal G2 core. Moreover, G2-g-(PCL-b-PEG) exhibits good colloidal stability in the presence of serum and insignificant hemolytic toxicity even at ≥2048 μg/mL. suggesting good blood compatibility required for intravenous administration.

Epidemiology of infant meningococcal disease in the United States, 2006-2012.

PubMed

MacNeil, Jessica R; Bennett, Nancy; Farley, Monica M; Harrison, Lee H; Lynfield, Ruth; Nichols, Megin; Petit, Sue; Reingold, Arthur; Schaffner, William; Thomas, Ann; Pondo, Tracy; Mayer, Leonard W; Clark, Thomas A; Cohn, Amanda C

2015-02-01

The incidence of meningococcal disease is currently at historic lows in the United States; however, incidence remains highest among infants aged <1 year. With routine use of Haemophilus influenzae type b and pneumococcal vaccines in infants and children in the United States, Neisseria meningitidis remains an important cause of bacterial meningitis in young children. Data were collected from active, population- and laboratory-based surveillance for N meningitidis conducted through Active Bacterial Core surveillance during 2006 through 2012. Expanded data collection forms were completed for infant cases identified in the surveillance area during 2006 through 2010. An estimated 113 cases of culture-confirmed meningococcal disease occurred annually among infants aged <1 year in the United States from 2006 through 2012, for an overall incidence of 2.74 per 100,000 infants. Among these cases, an estimated 6 deaths occurred. Serogroup B was responsible for 64%, serogroup C for 12%, and serogroup Y for 16% of infant cases. Based on the expanded data collection forms, a high proportion of infant cases (36/58, 62%) had a smoker in the household and the socioeconomic status of the census tracts where infant meningococcal cases resided was lower compared with the other Active Bacterial Core surveillance areas and the United States as a whole. The burden of meningococcal disease remains highest in young infants and serogroup B predominates. Vaccines that provide long-term protection early in life have the potential to reduce the burden of meningococcal disease, especially if they provide protection against serogroup B meningococcal disease. Copyright © 2015 by the American Academy of Pediatrics.

External Resistances Applied to MFC Affect Core Microbiome and Swine Manure Treatment Efficiencies

PubMed Central

Vilajeliu-Pons, Anna; Bañeras, Lluis; Puig, Sebastià; Molognoni, Daniele; Vilà-Rovira, Albert; Hernández-del Amo, Elena; Balaguer, Maria D.; Colprim, Jesús

2016-01-01

Microbial fuel cells (MFCs) can be designed to combine water treatment with concomitant electricity production. Animal manure treatment has been poorly explored using MFCs, and its implementation at full-scale primarily relies on the bacterial distribution and activity within the treatment cell. This study reports the bacterial community changes at four positions within the anode of two almost identically operated MFCs fed swine manure. Changes in the microbiome structure are described according to the MFC fluid dynamics and the application of a maximum power point tracking system (MPPT) compared to a fixed resistance system (Ref-MFC). Both external resistance and cell hydrodynamics are thought to heavily influence MFC performance. The microbiome was characterised both quantitatively (qPCR) and qualitatively (454-pyrosequencing) by targeting bacterial 16S rRNA genes. The diversity of the microbial community in the MFC biofilm was reduced and differed from the influent swine manure. The adopted electric condition (MPPT vs fixed resistance) was more relevant than the fluid dynamics in shaping the MFC microbiome. MPPT control positively affected bacterial abundance and promoted the selection of putatively exoelectrogenic bacteria in the MFC core microbiome (Sedimentibacter sp. and gammaproteobacteria). These differences in the microbiome may be responsible for the two-fold increase in power production achieved by the MPPT-MFC compared to the Ref-MFC. PMID:27701451

An antibacterial vaccination strategy based on a glycoconjugate containing the core lipopolysaccharide tetrasaccharide Hep2Kdo2

NASA Astrophysics Data System (ADS)

Kong, Lingbing; Vijayakrishnan, Balakumar; Kowarik, Michael; Park, Jin; Zakharova, Alexandra N.; Neiwert, Larissa; Faridmoayer, Amirreza; Davis, Benjamin G.

2016-03-01

Certain non-mammalian cell wall sugars are conserved across a variety of pathogenic bacteria. This conservation of structure, combined with their structural differences when compared with mammalian sugars, make them potentially powerful epitopes for immunization. Here, we report the synthesis of a glycoconjugate that displays the so-called ‘inner core’ sugars of Gram-negative bacterial cell walls. We also describe an antibacterial vaccination strategy based on immunization with the glycoconjugate and the subsequent administration of an inhibitor that uncovers the corresponding epitope in pathogenic bacteria. The core tetrasaccharide, Hep2Kdo2, a common motif in bacterial lipopolysaccharides, was synthesized and attached via a chain linker to a diphtheria toxin mutant carrier protein. This glycoconjugate generated titres of antibodies towards the inner core tetrasaccharide of the lipopolysaccharide, which were capable of binding the cell-surface sugars of bacterial pathogenic strains including Neisseria meningitidis, Pseudomonas aeruginosa and Escherichia coli. Exposure of bacterial lipopolysaccharide in in vitro experiments, using an inhibitor of capsular polysaccharide transport, enabled potent bacterial killing with antiserum.

FlpS, the FNR-Like Protein of Streptococcus suis Is an Essential, Oxygen-Sensing Activator of the Arginine Deiminase System.

PubMed

Willenborg, Jörg; Koczula, Anna; Fulde, Marcus; de Greeff, Astrid; Beineke, Andreas; Eisenreich, Wolfgang; Huber, Claudia; Seitz, Maren; Valentin-Weigand, Peter; Goethe, Ralph

2016-07-21

Streptococcus (S.) suis is a zoonotic pathogen causing septicemia and meningitis in pigs and humans. During infection S. suis must metabolically adapt to extremely diverse environments of the host. CcpA and the FNR family of bacterial transcriptional regulators are important for metabolic gene regulation in various bacteria. The role of CcpA in S. suis is well defined, but the function of the FNR-like protein of S. suis, FlpS, is yet unknown. Transcriptome analyses of wild-type S. suis and a flpS mutant strain suggested that FlpS is involved in the regulation of the central carbon, arginine degradation and nucleotide metabolism. However, isotopologue profiling revealed no substantial changes in the core carbon and amino acid de novo biosynthesis. FlpS was essential for the induction of the arcABC operon of the arginine degrading pathway under aerobic and anaerobic conditions. The arcABC-inducing activity of FlpS could be associated with the level of free oxygen in the culture medium. FlpS was necessary for arcABC-dependent intracellular bacterial survival but redundant in a mice infection model. Based on these results, we propose that the core function of S. suis FlpS is the oxygen-dependent activation of the arginine deiminase system.

FlpS, the FNR-Like Protein of Streptococcus suis Is an Essential, Oxygen-Sensing Activator of the Arginine Deiminase System

PubMed Central

Willenborg, Jörg; Koczula, Anna; Fulde, Marcus; de Greeff, Astrid; Beineke, Andreas; Eisenreich, Wolfgang; Huber, Claudia; Seitz, Maren; Valentin-Weigand, Peter; Goethe, Ralph

2016-01-01

Streptococcus (S.) suis is a zoonotic pathogen causing septicemia and meningitis in pigs and humans. During infection S. suis must metabolically adapt to extremely diverse environments of the host. CcpA and the FNR family of bacterial transcriptional regulators are important for metabolic gene regulation in various bacteria. The role of CcpA in S. suis is well defined, but the function of the FNR-like protein of S. suis, FlpS, is yet unknown. Transcriptome analyses of wild-type S. suis and a flpS mutant strain suggested that FlpS is involved in the regulation of the central carbon, arginine degradation and nucleotide metabolism. However, isotopologue profiling revealed no substantial changes in the core carbon and amino acid de novo biosynthesis. FlpS was essential for the induction of the arcABC operon of the arginine degrading pathway under aerobic and anaerobic conditions. The arcABC-inducing activity of FlpS could be associated with the level of free oxygen in the culture medium. FlpS was necessary for arcABC-dependent intracellular bacterial survival but redundant in a mice infection model. Based on these results, we propose that the core function of S. suis FlpS is the oxygen-dependent activation of the arginine deiminase system. PMID:27455333

Topological Defects in a Living Nematic Ensnare Swimming Bacteria

NASA Astrophysics Data System (ADS)

Genkin, Mikhail M.; Sokolov, Andrey; Lavrentovich, Oleg D.; Aranson, Igor S.

2017-01-01

Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement with the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of +1 /2 topological defects and depletion of bacteria in the cores of -1 /2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.

Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean

NASA Astrophysics Data System (ADS)

Obernosterer, Ingrid; Christaki, Urania; Lefèvre, Dominique; Catala, Philippe; Van Wambeke, France; Lebaron, Philippe

2008-03-01

The response of heterotrophic bacteria ( Bacteria and Archaea) to the spring phytoplankton bloom that occurs annually above the Kerguelen Plateau (Southern Ocean) due to natural iron fertilization was investigated during the KErguelen Ocean and Plateau compared Study (KEOPS) cruise in January-February 2005. In surface waters (upper 100 m) in the core of the phytoplankton bloom, heterotrophic bacteria were, on an average, 3-fold more abundant and revealed rates of production ([ 3H] leucine incorporation) and respiration (<0.8 μm size fraction) that exceeded those in surrounding high-nutrient low-chlorophyll (HNLC) waters by factors of 6 and 5, respectively. These differences in bacterial metabolic activities were attributable to high-nucleic-acid-containing cells that dominated (≈80% of total cell abundance) the heterotrophic bacterial community associated with the phytoplankton bloom. Bacterial growth efficiencies varied between 14% and 20% inside the bloom and were <10% in HNLC waters. Results from bottle-incubation experiments performed at the bloom station indicated that iron had no direct but an indirect effect on heterotrophic bacterial activity, due to the stimulation by phytoplankton-derived dissolved organic matter. Within the Kerguelen bloom, bacterial carbon demand accounted for roughly 45% of gross community production. These results indicate that heterotrophic bacteria processed a significant portion of primary production, with most of it being rapidly respired.

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

Chapelle, F.H.; Zelibor, J.L. Jr.; Grimes, D.J.

Nineteen cores of unconsolidated Coastal Plain sediments obtained from depths of 14 to 182 m below land surface near Waldorf, Maryland, were collected and examined for metabolically active bacteria. The age of the sediments cored range from Miocene to Early Cretaceous. Acridine orange direct counts of total (viable and nonviable) bacteria in core subsamples ranged from 10/sup 8/ to 10/sup 4/ bacteria/g of dry sediment. Direct counts of viable bacteria ranged from 10/sup 6/ to 10/sup 3/ bacteria/g of dry sediment. Three cores contained viable methanogenic bacteria, and seven cores contained viable sulfate-reducing bacteria. The observed presence of bacteria inmore » these sediments suggest that hetrotrophic bacterial metabolism, with lignitic organic material as the primary substrate, is a plausible source of CO/sub 2/ to ground water. However, the possibility that abiotic processes also produce CO/sub 2/ cannot be rules out. Estimated rates of CO/sub 2/ production in the noncalcareous Magothy/Upper Patapsco and Lower Patapsco aquifers based on mass balance of dissolved inorganic carbon, ground water flow rates, and flow path segment lengths are in the range 10/sup -3/ to 10/sup -5/ mmol L/sup -1/ yr/sup -1/. Isotope balance calculations suggest that aquifer-generated CO/sub 2/ is much heavier isotopically ( approx. - 10 to + 5 per mil) than lignite ( approx. - 24 per mil) present in these sediments. This may reflect isotopic fractionation during methanogenesis and possibly other bacterially mediated processes.« less

On the core bacterial flora of Ixodes persulcatus (Taiga tick).

PubMed

Sui, Shuo; Yang, Yu; Sun, Yi; Wang, Xumin; Wang, Guoliang; Shan, Guangle; Wang, Jiancheng; Yu, Jun

2017-01-01

Ixodes persulcatus is a predominant hard tick species that transmits a wide range of human and animal pathogens. Since bacterial flora of the tick dwelling in the wild always vary according to their hosts and the environment, it is highly desirable that species-associated microbiomes are fully determined by using next-generation sequencing and based on comparative metagenomics. Here, we examine such metagenomic changes of I. persulcatus starting with samples collected from the wild ticks and followed by the reared animals under pathogen-free laboratory conditions over multiple generations. Based on high-coverage genomic sequences from three experimental groups-wild, reared for a single generation or R1, and reared for eight generations or R8 -we identify the core bacterial flora of I. persulcatus, which contains 70 species that belong to 69 genera of 8 phyla; such a core is from the R8 group, which is reduced from 4625 species belonging to 1153 genera of 29 phyla in the wild group. Our study provides a novel example of tick core bacterial flora acquired based on wild-to-reared comparison, which paves a way for future research on tick metagenomics and tick-borne disease pandemics.

On the core bacterial flora of Ixodes persulcatus (Taiga tick)

PubMed Central

Sun, Yi; Wang, Xumin; Wang, Guoliang; Shan, Guangle; Wang, Jiancheng; Yu, Jun

2017-01-01

Ixodes persulcatus is a predominant hard tick species that transmits a wide range of human and animal pathogens. Since bacterial flora of the tick dwelling in the wild always vary according to their hosts and the environment, it is highly desirable that species-associated microbiomes are fully determined by using next-generation sequencing and based on comparative metagenomics. Here, we examine such metagenomic changes of I. persulcatus starting with samples collected from the wild ticks and followed by the reared animals under pathogen-free laboratory conditions over multiple generations. Based on high-coverage genomic sequences from three experimental groups–wild, reared for a single generation or R1, and reared for eight generations or R8 –we identify the core bacterial flora of I. persulcatus, which contains 70 species that belong to 69 genera of 8 phyla; such a core is from the R8 group, which is reduced from 4625 species belonging to 1153 genera of 29 phyla in the wild group. Our study provides a novel example of tick core bacterial flora acquired based on wild-to-reared comparison, which paves a way for future research on tick metagenomics and tick-borne disease pandemics. PMID:28692666

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

Spatial distribution of marine airborne bacterial communities

PubMed Central

Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

2015-01-01

The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter

USGS Publications Warehouse

Findlay, S.E.G.; Sinsabaugh, R. L.; Sobczak, W.V.; Hoostal, M.

2003-01-01

Hyporheic sediment bacterial communities were exposed to dissolved organic matter (DOM) from a variety of sources to assess the interdependence of bacterial metabolism and community composition. Experiments ranged from small-scale core perfusions with defined compounds (glucose, bovine serum albumin) to mesocosms receiving natural leaf leachate or water from different streams. Response variables included bacterial production, oxygen consumption, extracellular enzyme activity, and community similarity as manifest by changes in banding patterns of randomly amplified polymorphic DNA (RAPD). All DOM manipulations generated responses in at least one metabolic variable. Additions of both labile and recalcitrant materials increased either oxygen consumption, production, or both depending on background DOM. Enzyme activities were affected by both types of carbon addition with largest effects from the labile mixture. Cluster analysis of RAPD data showed strong divergence of communities exposed to labile versus recalcitrant DOM. Additions of leaf leachate to mesocosms representing hyporheic flow-paths caused increases in oxygen consumption and some enzyme activities with weaker effects on production. Community structure yeas strongly affected; samples from the leachate-amended mesocosms clustered separately from the control samples. In mesocosms receiving water from streams ranging in DOC (0.5-4.5 mg L-1), there were significant differences in bacterial growth, oxygen consumption, and enzyme activities. RAPD analysis showed strongest clustering of samples by stream type with more subtle effects of position along the flowpaths. Responses in community metabolism were always accompanied by shifts in community composition, suggesting carbon supply affects both functional and structural attributes of hyporheic bacterial communities.

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic.

PubMed

Singh, Purnima; Singh, Shiv Mohan; Roy, Utpal

2016-03-01

Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7)  cells ml(-1) (mean 3.12 × 10(6)  cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Defining the Core Microbiome in Corals' Microbial Soup.

PubMed

Hernandez-Agreda, Alejandra; Gates, Ruth D; Ainsworth, Tracy D

2017-02-01

Corals are considered one of the most complex microbial biospheres studied to date, hosting thousands of bacterial phylotypes in species-specific associations. There are, however, substantial knowledge gaps and challenges in understanding the functional significance of bacterial communities and bacterial symbioses of corals. The ubiquitous nature of some bacterial interactions has only recently been investigated and an accurate differentiation between the healthy (symbiotic) and unhealthy (dysbiotic) microbial state has not yet been determined. Here we review the complexity of the coral holobiont, coral microbiome diversity, and recently proposed bacterial symbioses of corals. We provide insight into coupling the core microbiome framework with community ecology principals, and draw on the theoretical insights from other complex systems, to build a framework to aid in deciphering ecologically significant microbes within a corals' microbial soup. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)

PubMed Central

Cariveau, Daniel P; Elijah Powell, J; Koch, Hauke; Winfree, Rachael; Moran, Nancy A

2014-01-01

Bacterial gut symbiont communities are critical for the health of many insect species. However, little is known about how microbial communities vary among host species or how they respond to anthropogenic disturbances. Bacterial communities that differ in richness or composition may vary in their ability to provide nutrients or defenses. We used deep sequencing to investigate gut microbiota of three species in the genus Bombus (bumble bees). Bombus are among the most economically and ecologically important non-managed pollinators. Some species have experienced dramatic declines, probably due to pathogens and land-use change. We examined variation within and across bee species and between semi-natural and conventional agricultural habitats. We categorized as ‘core bacteria' any operational taxonomic units (OTUs) with closest hits to sequences previously found exclusively or primarily in the guts of honey bees and bumble bees (genera Apis and Bombus). Microbial community composition differed among bee species. Richness, defined as number of bacterial OTUs, was highest for B. bimaculatus and B. impatiens. For B. bimaculatus, this was due to high richness of non-core bacteria. We found little effect of habitat on microbial communities. Richness of non-core bacteria was negatively associated with bacterial abundance in individual bees, possibly due to deeper sampling of non-core bacteria in bees with low populations of core bacteria. Infection by the gut parasite Crithidia was negatively associated with abundance of the core bacterium Gilliamella and positively associated with richness of non-core bacteria. Our results indicate that Bombus species have distinctive gut communities, and community-level variation is associated with pathogen infection. PMID:24763369

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant.

PubMed

Hou, Luanfeng; Zhou, Qin; Wu, Qingping; Gu, Qihui; Sun, Ming; Zhang, Jumei

2018-06-01

To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water. Both microbial activity and bacterial diversity during the treatment process showed obvious spatial variation, with higher levels observed during the dry season and lower levels during the wet season. Clustering analysis and principal component analysis indicated dramatic shifts in the bacterial community after chlorination, suggesting that chlorination was highly effective at influencing the bacterial community. The bacterial community structure of finished water primarily comprised Pseudomonas, Citrobacter, and Acinetobacter, and interestingly showed high similarity to biofilms on granular activated carbon. Additionally, the abundance of bacterial communities was relatively stable in finished water and did not change with the season. A large number of unique operational taxonomic units were shared during treatment steps, indicating the presence of a diverse core microbiome throughout the treatment process. Opportunistic pathogens, including Pseudomonas, Acinetobacter, Citrobacter, Mycobacterium, Salmonella, Staphylococcus, Legionella, Streptococcus and Enterococcus, were detected in water including finished water, suggesting a potential threat to drinking-water safety. We also detected bacteria isolated from each treatment step using the pure-culture method. In particular, two isolates, identified as Mycobacterium sp. and Blastococcus sp., which belong to the phylum Actinobacteria, were obtained from finished water during the dry season. Together, these results provided evidence of spatial and temporal variations in DWTPs and contributed to the beneficial manipulation of the drinking water microbiome. Copyright © 2017. Published by Elsevier B.V.

Nanoparticle targeting of Gram-positive and Gram-negative bacteria for magnetic-based separations of bacterial pathogens

NASA Astrophysics Data System (ADS)

Lu, Hoang D.; Yang, Shirley S.; Wilson, Brian K.; McManus, Simon A.; Chen, Christopher V. H.-H.; Prud'homme, Robert K.

2017-04-01

Antimicrobial resistance is a healthcare problem of increasing significance, and there is increasing interest in developing new tools to address bacterial infections. Bacteria-targeting nanoparticles hold promise to improve drug efficacy, compliance, and safety. In addition, nanoparticles can also be used for novel applications, such as bacterial imaging or bioseperations. We here present the use of a scalable block-copolymer-directed self-assembly process, Flash NanoPrecipitation, to form zinc(II)-bis(dipicolylamine) modified nanoparticles that bind to both Gram-positive and Gram-negative bacteria with specificity. Particles have tunable surface ligand densities that change particle avidity and binding efficacy. A variety of materials can be encapsulated into the core of the particles, such as optical dyes or iron oxide colloids, to produce imageable and magnetically active bacterial targeting constructs. As a proof-of-concept, these particles are used to bind and separate bacteria from solution in a magnetic column. Magnetic manipulation and separation would translate to a platform for pathogen identification or removal. These magnetic and targeted nanoparticles enable new methods to address bacterial infections.

Electrochemical Biosensor for Rapid and Sensitive Detection of Magnetically Extracted Bacterial Pathogens

PubMed Central

Setterington, Emma B.; Alocilja, Evangelyn C.

2012-01-01

Biological defense and security applications demand rapid, sensitive detection of bacterial pathogens. This work presents a novel qualitative electrochemical detection technique which is applied to two representative bacterial pathogens, Bacillus cereus (as a surrogate for B. anthracis) and Escherichia coli O157:H7, resulting in detection limits of 40 CFU/mL and 6 CFU/mL, respectively, from pure culture. Cyclic voltammetry is combined with immunomagnetic separation in a rapid method requiring approximately 1 h for presumptive positive/negative results. An immunofunctionalized magnetic/polyaniline core/shell nano-particle (c/sNP) is employed to extract target cells from the sample solution and magnetically position them on a screen-printed carbon electrode (SPCE) sensor. The presence of target cells significantly inhibits current flow between the electrically active c/sNPs and SPCE. This method has the potential to be adapted for a wide variety of target organisms and sample matrices, and to become a fully portable system for routine monitoring or emergency detection of bacterial pathogens. PMID:25585629

Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.

PubMed

Sabree, Zakee L; Hansen, Allison K; Moran, Nancy A

2012-01-01

Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012) Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear.

Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

NASA Astrophysics Data System (ADS)

Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

2016-04-01

Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

The core domain as the force sensor of the yeast mechanosensitive TRP channel.

PubMed

Su, Zhenwei; Anishkin, Andriy; Kung, Ching; Saimi, Yoshiro

2011-12-01

Stretch-activated conductances are commonly encountered in careful electric recordings. Those of known proteins (TRP, MscL, MscS, K(2p), Kv, etc.) all share a core, which houses the ion pathway and the gate, but no recognizable force-sensing domain. Like animal TRPs, the yeast TRPY1 is polymodal, activated by stretch force, Ca(2+), etc. To test whether its S5-S6 core senses the stretch force, we tried to uncouple it from the peripheral domains by strategic peptide insertions to block the covalent core-periphery interactions. Insertion of long unstructured peptides should distort, if not disrupt, protein structures that transmit force. Such insertions between S6 and the C-terminal tail largely removed Ca(2+) activation, showing their effectiveness. However, such insertions as well as those between S5 and the N-terminal region, which includes S1-S4, did not significantly alter mechanosensitivity. Even insertions at both locations flanking the S5-S6 core did not much alter mechanosensitivity. Tryptophan scanning mutations in S5 were also constructed to perturb possible noncovalent core-periphery contacts. The testable tryptophan mutations also have little or no effects on mechanosensitivity. Boltzmann fits of the wild-type force-response curves agree with a structural homology model for a stretch-induced core expansion of ~2 nm(2) upon opening. We hypothesize that membrane tension pulls on S5-S6, expanding the core and opening the TRPY1 gate. The core being the major force sensor offers the simplest, though not the only, explanation of why so many channels of disparate designs are mechanically sensitive. Compared with the bacterial MscL, TRPY1 is much less sensitive to force, befitting a polymodal channel that relies on multiple stimuli.

Combined scanning transmission X-ray and electron microscopy for the characterization of bacterial endospores.

PubMed

Jamroskovic, Jan; Shao, Paul P; Suvorova, Elena; Barak, Imrich; Bernier-Latmani, Rizlan

2014-09-01

Endospores (also referred to as bacterial spores) are bacterial structures formed by several bacterial species of the phylum Firmicutes. Spores form as a response to environmental stress. These structures exhibit remarkable resistance to harsh environmental conditions such as exposure to heat, desiccation, and chemical oxidants. The spores include several layers of protein and peptidoglycan that surround a core harboring DNA as well as high concentrations of calcium and dipicolinic acid (DPA). A combination of scanning transmission X-ray microscopy, scanning transmission electron microscopy, and energy dispersive spectroscopy was used for the direct quantitative characterization of bacterial spores. The concentration and localization of DPA, Ca(2+) , and other elements were determined and compared for the core and cortex of spores from two distinct genera: Bacillus subtilis and Desulfotomaculum reducens. This micro-spectroscopic approach is uniquely suited for the direct study of individual bacterial spores, while classical molecular and biochemical methods access only bulk characteristics. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Bacterially mediated mineralization of vaterite

NASA Astrophysics Data System (ADS)

Rodriguez-Navarro, Carlos; Jimenez-Lopez, Concepcion; Rodriguez-Navarro, Alejandro; Gonzalez-Muñoz, Maria Teresa; Rodriguez-Gallego, Manuel

2007-03-01

Myxococcus xanthus, a common soil bacterium, plays an active role in the formation of spheroidal vaterite. Bacterial production of CO 2 and NH 3 and the transformation of the NH 3 to NH4+ and OH -, thus increasing solution pH and carbonate alkalinity, set the physicochemical conditions (high supersaturation) leading to vaterite precipitation in the microenvironment around cells, and directly onto the surface of bacterial cells. In the latter case, fossilization of bacteria occurs. Vaterite crystals formed by aggregation of oriented nanocrystals with c-axis normal to the bacterial cell-wall, or to the core of the spherulite when bacteria were not encapsulated. While preferred orientation of vaterite c-axis appears to be determined by electrostatic affinity (ionotropic effect) between vaterite crystal (0001) planes and the negatively charged functional groups of organic molecules on the bacterium cell-wall or on extracellular polymeric substances (EPS), analysis of the changes in the culture medium chemistry as well as high resolution transmission electron microscopy (HRTEM) observations point to polymorph selection by physicochemical (kinetic) factors (high supersaturation) and stabilization by organics, both connected with bacterial activity. The latter is in agreement with inorganic precipitation of vaterite induced by NH 3 and CO 2 addition in the protein-rich sterile culture medium. Our results as well as recent studies on vaterite precipitation in the presence of different types of bacteria suggest that bacterially mediated vaterite precipitation is not strain-specific, and could be more common than previously thought.

Plant Proanthocyanidins Bind to and Neutralize Bacterial Lipopolysaccharides

DTIC Science & Technology

2008-01-01

2008 NRL REVIEW 101 Plant Proanthocyanidins Bind to and Neutralize Bacterial Lipopolysaccharides J.B. Delehanty,1 B.J. Johnson,1 T.E. Hickey,1 T...polymers derived from higher plants and they have recently been associated with several potential positive health benefits such as antibacterial...and 2) a core oligosaccharide region which gives rise to 3) the O-antigen, a branched polysaccharide that extends from the core oligosaccharide .2

Bacterial leakage through temporary fillings in core buildup composite material - an in vitro study.

PubMed

Rechenberg, Dan-Krister; Schriber, Martina; Attin, Thomas

2012-08-01

To evaluate the ability of the provisional filling material Cavit-W alone or in combination with different restorative materials to prevent bacterial leakage through simulated access cavities in a resin buildup material. LuxaCore resin cylinders were subdivided into 4 experimental groups (n = 30), plus a positive (n = 5) and a negative (n = 30) control group. One bore hole was drilled through each cylinder, except those in the negative control group (G1). The holes were filled with Cavit-W (G2), Cavit-W and Ketac-Molar (glassionomer cement, G3), Cavit-W and LuxaCore bonded with LuxaBond (G4), Cavit-W and LuxaCore (G5), or left empty (G6). Specimens were mounted in a two-chamber leakage setup. The upper chamber was inoculated with E. faecalis. An enterococci-selective broth was used in the lower chamber. Leakage was assessed for 60 days and compared using Fisher's exact test (α < 0.05) corrected for multiple testing. Bacteria penetrated specimens in the positive control group within 24 h. All specimens in the negative control group resisted bacterial leakage for 60 days. Twenty-seven specimens in G2, 26 in G3, and 16 specimens in G5 showed bacterial leakage by the end of the experiment. G4 prevented bacterial penetration completely. The statistical comparison revealed significant differences between G4 and all other experimental groups. Under the current conditions, Cavit-W alone or combined with a glass-ionomer cement did not prevent bacterial leakage through a resin buildup material for two months. In contrast, covering Cavit-W with a bonded resin material resulted in a bacteria-tight seal for two months.

Geomicrobiology of cores from Suruí Mangrove--Guanabara Bay--Brazil.

PubMed

Fontana, Luiz Francisco; Mendonça Filho, João Graciano; Netto, Annibal Duarte Pereira; Sabadini-Santos, Elisamara; de Figueiredo, Alberto Garcia; Crapez, Mirian Araújo Carlos

2010-10-01

The aim of this work was to quantify the biopolymers associated to esterase enzymes and identify bacterial respiratory activity in four cores collected in Suruí Mangrove, Guanabara Bay - RJ. Biopolymer concentration was 1000 times lower than previously reported in the literature, indicating the need for creating and establishing eutrophication indicative rates and records compatible with tropical coastal systems. The biochemical representative relationships in the cores were equivalent to those from studies on coastal marine environments made in the Northern Hemisphere. The esterase enzymes in the sediment proved efficient in the mineralization of biopolymers, even with preferentially anaerobic metabolic physiology. Despite the lack of incipient geomicrobiological studies, the results highlighted the possible application of microbiology to a better understanding of geological processes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Biochemical Characterization of a Mycobacteriophage Derived DnaB Ortholog Reveals New Insight into the Evolutionary Origin of DnaB Helicases

PubMed Central

Bhowmik, Priyanka; Das Gupta, Sujoy K.

2015-01-01

The bacterial replicative helicases known as DnaB are considered to be members of the RecA superfamily. All members of this superfamily, including DnaB, have a conserved C- terminal domain, known as the RecA core. We unearthed a series of mycobacteriophage encoded proteins in which the RecA core domain alone was present. These proteins were phylogenetically related to each other and formed a distinct clade within the RecA superfamily. A mycobacteriophage encoded protein, Wildcat Gp80 that roots deep in the DnaB family, was found to possess a core domain having significant sequence homology (Expect value < 10-5) with members of this novel cluster. This indicated that Wildcat Gp80, and by extrapolation, other members of the DnaB helicase family, may have evolved from a single domain RecA core polypeptide belonging to this novel group. Biochemical investigations confirmed that Wildcat Gp80 was a helicase. Surprisingly, our investigations also revealed that a thioredoxin tagged truncated version of the protein in which the N-terminal sequences were removed was fully capable of supporting helicase activity, although its ATP dependence properties were different. DnaB helicase activity is thus, primarily a function of the RecA core although additional N-terminal sequences may be necessary for fine tuning its activity and stability. Based on sequence comparison and biochemical studies we propose that DnaB helicases may have evolved from single domain RecA core proteins having helicase activities of their own, through the incorporation of additional N-terminal sequences. PMID:26237048

DNA activates human immune cells through a CpG sequence-dependent manner

PubMed Central

Bauer, M; Heeg, K; Wagner, H; Lipford, G B

1999-01-01

While bacterial DNA and cytosine–guanosine-dinucleotide-containing oligonucleotides (CpG ODN) are well described activators of murine immune cells, their effect on human cells is inconclusive. We investigated their properties on human peripheral blood mononuclear cells (PBMC) and subsets thereof, such as purified monocytes, T and B cells. Here we demonstrate that bacterial DNA and CpG ODN induce proliferation of B cells, while other subpopulations, such as monocytes and T cells, did not proliferate. PBMC mixed cell cultures, as well as purified monocytes, produced interleukin-6 (IL-6), IL-12 and tumour necrosis factor-α upon stimulation with bacterial DNA; however, only IL-6 and IL-12 secretion became induced upon CpG ODN stimulation. We conclude that monocytes, but not B or T cells, represent the prime source of cytokines. Monocytes up-regulated expression of antigen-presenting, major histocompatibility complex class I and class II molecules in response to CpG DNA. In addition, both monocytes and B cells up-regulate costimulatory CD86 and CD40 molecules. The activation by CpG ODN depended on sequence motifs containing the core dinucleotide CG since destruction of the motif strongly reduced immunostimulatory potential. PMID:10457226

Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem

PubMed Central

König, Sara; Worrich, Anja; Banitz, Thomas; Harms, Hauke; Kästner, Matthias; Miltner, Anja; Wick, Lukas Y.; Frank, Karin; Thullner, Martin; Centler, Florian

2018-01-01

Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass. PMID:29696013

DNA stabilization at the Bacillus subtilis PolX core—a binding model to coordinate polymerase, AP-endonuclease and 3′-5′ exonuclease activities

PubMed Central

Baños, Benito; Villar, Laurentino; Salas, Margarita; de Vega, Miguel

2012-01-01

Family X DNA polymerases (PolXs) are involved in DNA repair. Their binding to gapped DNAs relies on two conserved helix-hairpin-helix motifs, one located at the 8-kDa domain and the other at the fingers subdomain. Bacterial/archaeal PolXs have a specifically conserved third helix-hairpin-helix motif (GFGxK) at the fingers subdomain whose putative role in DNA binding had not been established. Here, mutagenesis at the corresponding residues of Bacillus subtilis PolX (PolXBs), Gly130, Gly132 and Lys134 produced enzymes with altered DNA binding properties affecting the three enzymatic activities of the protein: polymerization, located at the PolX core, 3′-5′ exonucleolysis and apurinic/apyrimidinic (AP)-endonucleolysis, placed at the so-called polymerase and histidinol phosphatase domain. Furthermore, we have changed Lys192 of PolXBs, a residue moderately conserved in the palm subdomain of bacterial PolXs and immediately preceding two catalytic aspartates of the polymerization reaction. The results point to a function of residue Lys192 in guaranteeing the right orientation of the DNA substrates at the polymerization and histidinol phosphatase active sites. The results presented here and the recently solved structures of other bacterial PolX ternary complexes lead us to propose a structural model to account for the appropriate coordination of the different catalytic activities of bacterial PolXs. PMID:22844091

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

PubMed Central

Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

2017-01-01

Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations. PMID:28071697

Activity and stability of a complex bacterial soil community under simulated Martian conditions

NASA Astrophysics Data System (ADS)

Hansen, Aviaja Anna; Merrison, Jonathan; Nørnberg, Per; Aagaard Lomstein, Bente; Finster, Kai

2005-04-01

A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

NASA Astrophysics Data System (ADS)

Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

2017-01-01

Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.

Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.

PubMed

Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

2009-04-01

The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.

Revealing the gut bacteriome of Dendroctonus bark beetles (Curculionidae: Scolytinae): diversity, core members and co-evolutionary patterns.

PubMed

Hernández-García, Juan Alfredo; Briones-Roblero, Carlos Iván; Rivera-Orduña, Flor N; Zúñiga, Gerardo

2017-10-24

Dendroctonus bark beetles comprise 20 taxonomically recognized species, which are one of the most destructive pine forest pests in North and Central America, and Eurasia. The aims of this study were to characterize the gut bacterial diversity, to determine the core bacteriome and to explore the ecological association between these bacteria and bark beetles. A total of five bacterial phyla were identified in the gut of 13 Dendroctonus species; Proteobacteria was the most abundant, followed by Firmicutes, Fusobacteria, Actinobacteria and Deinococcus-Thermus. The α-diversity was low as demonstrated in previous studies and significant differences in β-diversity were observed. The core bacteriome was composed of Enterobacter, Pantoea, Pseudomonas, Rahnella, Raoultella, and Serratia. The tanglegram between bacteria and bark beetles suggests that members of bacterial community are acquired from the environment, possibly from the host tree. These findings improve the knowledge about the bacterial community composition, and provide the bases to study the metabolic functions of these bacteria, as well as their interaction with these bark beetles.

Role of the σ 54 Activator Interacting Domain in Bacterial Transcription Initiation

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

Siegel, Alexander R.; Wemmer, David E.

Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing the members of the σ 54 family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA + ATPase that acts through conformational changes brought on by ATP hydrolysis. Contacts between the transcriptional activator and σ 54 are primarily made through anmore » N-terminal σ 54 activator interacting domain (AID). To better understand this mechanism of bacterial transcription initiation, we characterized the σ 54 AID by NMR spectroscopy and other biophysical methods and show that it is an intrinsically disordered domain in σ 54 alone. In this paper, we identified a minimal construct of the Aquifex aeolicus σ 54 AID that consists of two predicted helices and retains native-like binding affinity for the transcriptional activator NtrC1. Using the NtrC1 ATPase domain, bound with the non-hydrolyzable ATP analog ADP-beryllium fluoride, we studied the NtrC1–σ 54 AID complex using NMR spectroscopy. We show that the σ 54 AID becomes structured after associating with the core loops of the transcriptional activators in their ATP state and that the primary site of the interaction is the first predicted helix. Finally, understanding this complex, formed as the first step toward initiation, will help unravel the mechanism of σ 54 bacterial transcription initiation.« less

BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis.

PubMed

Omadjela, Okako; Narahari, Adishesh; Strumillo, Joanna; Mélida, Hugo; Mazur, Olga; Bulone, Vincent; Zimmer, Jochen

2013-10-29

Cellulose is a linear extracellular polysaccharide. It is synthesized by membrane-embedded glycosyltransferases that processively polymerize UDP-activated glucose. Polymer synthesis is coupled to membrane translocation through a channel formed by the cellulose synthase. Although eukaryotic cellulose synthases function in macromolecular complexes containing several different enzyme isoforms, prokaryotic synthases associate with additional subunits to bridge the periplasm and the outer membrane. In bacteria, cellulose synthesis and translocation is catalyzed by the inner membrane-associated bacterial cellulose synthase (Bcs)A and BcsB subunits. Similar to alginate and poly-β-1,6 N-acetylglucosamine, bacterial cellulose is implicated in the formation of sessile bacterial communities, termed biofilms, and its synthesis is likewise stimulated by cyclic-di-GMP. Biochemical studies of exopolysaccharide synthesis are hampered by difficulties in purifying and reconstituting functional enzymes. We demonstrate robust in vitro cellulose synthesis reconstituted from purified BcsA and BcsB proteins from Rhodobacter sphaeroides. Although BcsA is the catalytically active subunit, the membrane-anchored BcsB subunit is essential for catalysis. The purified BcsA-B complex produces cellulose chains of a degree of polymerization in the range 200-300. Catalytic activity critically depends on the presence of the allosteric activator cyclic-di-GMP, but is independent of lipid-linked reactants. Our data reveal feedback inhibition of cellulose synthase by UDP but not by the accumulating cellulose polymer and highlight the strict substrate specificity of cellulose synthase for UDP-glucose. A truncation analysis of BcsB localizes the region required for activity of BcsA within its C-terminal membrane-associated domain. The reconstituted reaction provides a foundation for the synthesis of biofilm exopolysaccharides, as well as its activation by cyclic-di-GMP.

BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis

PubMed Central

Omadjela, Okako; Narahari, Adishesh; Strumillo, Joanna; Mélida, Hugo; Mazur, Olga; Bulone, Vincent; Zimmer, Jochen

2013-01-01

Cellulose is a linear extracellular polysaccharide. It is synthesized by membrane-embedded glycosyltransferases that processively polymerize UDP-activated glucose. Polymer synthesis is coupled to membrane translocation through a channel formed by the cellulose synthase. Although eukaryotic cellulose synthases function in macromolecular complexes containing several different enzyme isoforms, prokaryotic synthases associate with additional subunits to bridge the periplasm and the outer membrane. In bacteria, cellulose synthesis and translocation is catalyzed by the inner membrane-associated bacterial cellulose synthase (Bcs)A and BcsB subunits. Similar to alginate and poly-β-1,6 N-acetylglucosamine, bacterial cellulose is implicated in the formation of sessile bacterial communities, termed biofilms, and its synthesis is likewise stimulated by cyclic-di-GMP. Biochemical studies of exopolysaccharide synthesis are hampered by difficulties in purifying and reconstituting functional enzymes. We demonstrate robust in vitro cellulose synthesis reconstituted from purified BcsA and BcsB proteins from Rhodobacter sphaeroides. Although BcsA is the catalytically active subunit, the membrane-anchored BcsB subunit is essential for catalysis. The purified BcsA-B complex produces cellulose chains of a degree of polymerization in the range 200–300. Catalytic activity critically depends on the presence of the allosteric activator cyclic-di-GMP, but is independent of lipid-linked reactants. Our data reveal feedback inhibition of cellulose synthase by UDP but not by the accumulating cellulose polymer and highlight the strict substrate specificity of cellulose synthase for UDP-glucose. A truncation analysis of BcsB localizes the region required for activity of BcsA within its C-terminal membrane-associated domain. The reconstituted reaction provides a foundation for the synthesis of biofilm exopolysaccharides, as well as its activation by cyclic-di-GMP. PMID:24127606

Lipopolysaccharide from Crypt-Specific Core Microbiota Modulates the Colonic Epithelial Proliferation-to-Differentiation Balance.

PubMed

Naito, Tomoaki; Mulet, Céline; De Castro, Cristina; Molinaro, Antonio; Saffarian, Azadeh; Nigro, Giulia; Bérard, Marion; Clerc, Mélanie; Pedersen, Amy B; Sansonetti, Philippe J; Pédron, Thierry

2017-10-17

We identified a crypt-specific core microbiota (CSCM) dominated by strictly aerobic, nonfermentative bacteria in murine cecal and proximal colonic (PC) crypts and hypothesized that, among its possible functions, it may affect epithelial regeneration. In the present work, we isolated representative CSCM strains using selective media based upon our initial 16S rRNA-based molecular identification (i.e., Acinetobacter , Delftia , and Stenotrophomonas ). Their tropism for the crypt was confirmed, and their influence on epithelial regeneration was demonstrated in vivo by monocolonization of germfree mice. We also showed that lipopolysaccharide (LPS), through its endotoxin activity, was the dominant bacterial agonist controlling proliferation. The relevant molecular mechanisms were analyzed using colonic crypt-derived organoids exposed to bacterial sonicates or highly purified LPS as agonists. We identified a Toll-like receptor 4 (TLR4)-dependent program affecting crypts at different stages of epithelial differentiation. LPS played a dual role: it repressed cell proliferation through RIPK3-mediated necroptosis of stem cells and cells of the transit-amplifying compartment and concurrently enhanced cell differentiation, particularly the goblet cell lineage. IMPORTANCE The LPS from crypt-specific core microbiota controls intestinal epithelium proliferation through necroptosis of stem cells and enhances cell differentiation, mainly the goblet cell lineage. Copyright © 2017 Naito et al.

Changes in Magnetic Mineralogy Through a Depth Sequence of Hydrocarbon Contaminated Sediments

NASA Astrophysics Data System (ADS)

Ameen, N. N.; Klüglein, N.; Appel, E.; Petrovsky, E.; Kappler, A.

2013-12-01

Sediments, soils and groundwater can act as a natural storage for many types of pollution. This study aims to investigate ferro(i)magnetic phase formation and transformation in the presence of organic contaminants (hydrocarbons) and its relation to bacterial activity, in particular in the zone of fluctuating water levels. The work extends previous studies conducted at the same site. The study area is a former military air base at Hradčany, Czech Republic (50°37'22.71"N, 14°45'2.24"E). Due to leaks in petroleum storage tanks and jet fuelling stations over years of active use the site was heavily contaminated with petroleum hydrocarbons, until the base was closed in 1991. This site is one of the most important sources of high quality groundwater in the Czech Republic. During remediation processes the groundwater level in the sediments fluctuated, driving the hydrocarbon contaminants to lower depth levels along with the groundwater and leading to magnetite formation (Rijal et al., Environ.Pollut., 158, 1756-1762, 2010). In our study we drilled triplicate cores at three locations which were studied earlier. Magnetic susceptibility (MS) profiles combined with other magnetic properties were analyzed to obtain the ferro(i)magnetic concentration distributions along the depth sections. Additionally the sediment properties, hydrocarbon content and bacterial activity were studied. The triplicate cores were used to statistically discriminate outliers and to recognize significant magnetic signatures with depth. The results show that the highest concentration of ferrimagnetic phases (interpreted as newly formed magnetite) exists at the probable top of the groundwater fluctuation (GWF) zone. For example at one of the sites this zone is found between 1.4-1.9 m depth (groundwater table at ~2.3 m depth). High S-ratio and the correlation of ARM with MS values confirm the contribution of magnetite for the ferro(i)magnetic enhancement in the GWF zone. In the previous studies the MS signals revealed small-scale isolated features, but with the use of triplicate cores significant trends of MS could be identified, showing an increase from the lowermost position of the groundwater table upward. Bacterial activity is likely responsible for magnetite formation in this depth range as indicated by most probable number (MPN) results of iron-reducing bacteria.

Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking.

PubMed

Fernandes, Catarina G; Plácido, Diana; Lousa, Diana; Brito, José A; Isidro, Anabela; Soares, Cláudio M; Pohl, Jan; Carrondo, Maria A; Archer, Margarida; Henriques, Adriano O

2015-09-22

Transglutaminases are best known for their ability to catalyze protein cross-linking reactions that impart chemical and physical resilience to cellular structures. Here, we report the crystal structure and characterization of Tgl, a transglutaminase from the bacterium Bacillus subtilis. Tgl is produced during sporulation and cross-links the surface of the highly resilient spore. Tgl-like proteins are found only in spore-forming bacteria of the Bacillus and Clostridia classes, indicating an ancient origin. Tgl is a single-domain protein, produced in active form, and the smallest transglutaminase characterized to date. We show that Tgl is structurally similar to bacterial cell wall endopeptidases and has an NlpC/P60 catalytic core, thought to represent the ancestral unit of the cysteine protease fold. We show that Tgl functions through a unique partially redundant catalytic dyad formed by Cys116 and Glu187 or Glu115. Strikingly, the catalytic Cys is insulated within a hydrophobic tunnel that traverses the molecule from side to side. The lack of similarity of Tgl to other transglutaminases together with its small size suggests that an NlpC/P60 catalytic core and insulation of the active site during catalysis may be essential requirements for protein cross-linking.

Bacterial community structure in the hyperarid core of the Atacama Desert, Chile

USGS Publications Warehouse

Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

2006-01-01

Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.

The impact of pollen consumption on honey bee (Apis mellifera) digestive physiology and carbohydrate metabolism.

PubMed

Ricigliano, Vincent A; Fitz, William; Copeland, Duan C; Mott, Brendon M; Maes, Patrick; Floyd, Amy S; Dockstader, Arnold; Anderson, Kirk E

2017-10-01

Carbohydrate-active enzymes play an important role in the honey bee (Apis mellifera) due to its dietary specialization on plant-based nutrition. Secretory glycoside hydrolases (GHs) produced in worker head glands aid in the processing of floral nectar into honey and are expressed in accordance with age-based division of labor. Pollen utilization by the honey bee has been investigated in considerable detail, but little is known about the metabolic fate of indigestible carbohydrates and glycosides in pollen biomass. Here, we demonstrate that pollen consumption stimulates the hydrolysis of sugars that are toxic to the bee (xylose, arabinose, mannose). GHs produced in the head accumulate in the midgut and persist in the hindgut that harbors a core microbial community composed of approximately 10 8 bacterial cells. Pollen consumption significantly impacted total and specific bacterial abundance in the digestive tract. Bacterial isolates representing major fermentative gut phylotypes exhibited primarily membrane-bound GH activities that may function in tandem with soluble host enzymes retained in the hindgut. Additionally, we found that plant-originating β-galactosidase activity in pollen may be sufficient, in some cases, for probable physiological activity in the gut. These findings emphasize the potential relative contributions of host, bacteria, and pollen enzyme activities to carbohydrate breakdown, which may be tied to gut microbiome dynamics and associated host nutrition. © 2017 Wiley Periodicals, Inc.

Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.

PubMed

Zeng, Yin-Xin; Yan, Ming; Yu, Yong; Li, Hui-Rong; He, Jian-Feng; Sun, Kun; Zhang, Fang

2013-05-01

Two 16S rRNA gene clone libraries Cores 1U and 2U were constructed using two ice core samples collected from Austre Lovénbreen glacier in Svalbard. The two libraries yielded a total of 262 clones belonging to 59 phylotypes. Sequences fell into 10 major lineages of the domain Bacteria, including Proteobacteria (alpha, beta, gamma and delta subdivisions), Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, Chloroflexi, Planctomycetes, Cyanobacteria and candidate division TM7. Among them, Bacteroidetes, Actinobacteria, Alphaproteobacteria and Cyanobacteria were most abundant. UniFrac data showed no significant differences in community composition between the two ice cores. A total of nineteen bacterial strains from the genera Pseudoalteromonas and Psychrobacter were isolated from the ice cores. Phylogenetic and phenotypic analyses revealed a close relationship between the ice core isolates and bacteria in marine environments, indicating a wide distribution of some bacterial phylotypes in both terrestrial and marine ecosystems.

Novel Imidazoline Antimicrobial Scaffold That Inhibits DNA Replication with Activity against Mycobacteria and Drug Resistant Gram-Positive Cocci

PubMed Central

2015-01-01

Bacterial antimicrobial resistance is an escalating public health threat, yet the current antimicrobial pipeline remains alarmingly depleted, making the development of new antimicrobials an urgent need. Here, we identify a novel, potent, imidazoline antimicrobial compound, SKI-356313, with bactericidal activity against Mycobacterium tuberculosis and Gram-positive cocci, including vancomycin-resistant Enterococcus faecium (VRE) and methicillin-resistant Staphylococcus aureus (MRSA). SKI-356313 is active in murine models of Streptococcus pneumoniae and MRSA infection and is potently bactericidal for both replicating and nonreplicating M. tuberculosis. Using a combination of genetics, whole genome sequencing, and a novel target ID approach using real time imaging of core macromolecular biosynthesis, we show that SKI-356313 inhibits DNA replication and displaces the replisome from the bacterial nucleoid. These results identify a new antimicrobial scaffold with a novel mechanism of action and potential therapeutic utility against nonreplicating M. tuberculosis and antibiotic resistant Gram-positive cocci. PMID:25222597

A novel site-specific recombination system derived from bacteriophage phiMR11.

PubMed

Rashel, Mohammad; Uchiyama, Jumpei; Ujihara, Takako; Takemura, Iyo; Hoshiba, Hiroshi; Matsuzaki, Shigenobu

2008-04-04

We report identification of a novel site-specific DNA recombination system that functions in both in vivo and in vitro, derived from lysogenic Staphylococcus aureus phage phiMR11. In silico analysis of the phiMR11 genome indicated orf1 as a putative integrase gene. Phage and bacterial attachment sites (attP and attB, respectively) and attachment junctions were determined and their nucleotide sequences decoded. Sequences of attP and attB were mostly different to each other except for a two bp common core that was the crossover point. We found several inverted repeats adjacent to the core sequence of attP as potential protein binding sites. The precise and efficient integration properties of phiMR11 integrase were shown on attP and attB in Escherichia coli and the minimum size of attP was found to be 34bp. In in vitro assays using crude or purified integrase, only buffer and substrate DNAs were required for the recombination reaction, indicating that other bacterially encoded factors are not essential for activity.

Lipopolysaccharide from Crypt-Specific Core Microbiota Modulates the Colonic Epithelial Proliferation-to-Differentiation Balance

PubMed Central

Naito, Tomoaki; Mulet, Céline; De Castro, Cristina; Molinaro, Antonio; Saffarian, Azadeh; Nigro, Giulia; Bérard, Marion; Clerc, Mélanie; Pedersen, Amy B.; Pédron, Thierry

2017-01-01

ABSTRACT We identified a crypt-specific core microbiota (CSCM) dominated by strictly aerobic, nonfermentative bacteria in murine cecal and proximal colonic (PC) crypts and hypothesized that, among its possible functions, it may affect epithelial regeneration. In the present work, we isolated representative CSCM strains using selective media based upon our initial 16S rRNA-based molecular identification (i.e., Acinetobacter, Delftia, and Stenotrophomonas). Their tropism for the crypt was confirmed, and their influence on epithelial regeneration was demonstrated in vivo by monocolonization of germfree mice. We also showed that lipopolysaccharide (LPS), through its endotoxin activity, was the dominant bacterial agonist controlling proliferation. The relevant molecular mechanisms were analyzed using colonic crypt-derived organoids exposed to bacterial sonicates or highly purified LPS as agonists. We identified a Toll-like receptor 4 (TLR4)-dependent program affecting crypts at different stages of epithelial differentiation. LPS played a dual role: it repressed cell proliferation through RIPK3-mediated necroptosis of stem cells and cells of the transit-amplifying compartment and concurrently enhanced cell differentiation, particularly the goblet cell lineage. PMID:29042502

Characterization of a xylose containing oligosaccharide, an inhibitor of multidrug resistance in Staphylococcus aureus, from Ipomoea pes-caprae.

PubMed

Escobedo-Martínez, Carolina; Cruz-Morales, Sara; Fragoso-Serrano, Mabel; Rahman, M Mukhlesur; Gibbons, Simon; Pereda-Miranda, Rogelio

2010-10-01

Pescaprein XVIII (1), a type of bacterial efflux pump inhibitor, was obtained from the CHCl(3)-soluble resin glycosides of beach morning glory (Ipomoea pes-caprae). The glycosidation sequence for pescaproside C, the glycosidic acid core of the lipophilic macrolactone 1 containing D-xylose and L-rhamnose, was characterized by means of several NMR techniques and FAB mass spectrometry. Recycling HPLC also yielded eight non-cytotoxic bacterial resistance modifiers, the two pescapreins XIX (2) and XX (3) as well as the known murucoidin VI (4), pecapreins II (6) and III (7), and stoloniferins III (5), IX (8) and X (9), all of which contain simonic acid B as their oligosaccharide core. Compounds 1-9 were tested for in vitro antibacterial and resistance-modifying activity against strains of Staphylococcus aureus possessing multidrug resistance efflux mechanisms. All of the pescapreins potentiated the action of norfloxacin against the NorA over-expressing strain by 4-fold (8 microg/mL from 32 microg/mL) at a concentration of 25 microg/mL. Copyright © 2010 Elsevier Ltd. All rights reserved.

Carbohydrate hydrogels with stabilized phage particles for bacterial biosensing: bacterium diffusion studies.

PubMed

Balcão, Victor M; Barreira, Sérgio V P; Nunes, Thiago M; Chaud, Marco V; Tubino, Matthieu; Vila, Marta M D C

2014-02-01

Bacteriophage particles have been reported as potentially useful in the development of diagnosis tools for pathogenic bacteria as they specifically recognize and lyse bacterial isolates thus confirming the presence of viable cells. One of the most representative microorganisms associated with health care services is the bacterium Pseudomonas aeruginosa, which alone is responsible for nearly 15% of all nosocomial infections. In this context, structural and functional stabilization of phage particles within biopolymeric hydrogels, aiming at producing cheap (chromogenic) bacterial biosensing devices, has been the goal of a previous research effort. For this, a detailed knowledge of the bacterial diffusion profile into the hydrogel core, where the phage particles lie, is of utmost importance. In the present research effort, the bacterial diffusion process into the biopolymeric hydrogel core was mathematically described and the theoretical simulations duly compared with experimental results, allowing determination of the effective diffusion coefficients of P. aeruginosa in the agar and calcium alginate hydrogels tested.

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage.

PubMed

Duniere, Lysiane; Xu, Shanwei; Long, Jin; Elekwachi, Chijioke; Wang, Yuxi; Turkington, Kelly; Forster, Robert; McAllister, Tim A

2017-03-03

Describing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively. All small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09 ± 0.28) and high levels of lactic acid (59.8 ± 14.59 mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure. Next Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.

Microbial community dynamics induced by rewetting dry soil: summer precipitation matters

NASA Astrophysics Data System (ADS)

Barnard, Romain; Osborne, Catherine; Firestone, Mary

2015-04-01

The massive soil CO2 efflux associated with rewetting dry soils after the dry summer period significantly contributes to the annual carbon budget of Mediterranean grasslands. Rapid reactivation of soil heterotrophic activity and available carbon are both required to fuel the CO2 pulse. Better understanding of the effects of altered summer precipitation on the metabolic state of indigenous microorganisms may be important in predicting future changes in carbon cycling. We investigated the effects of a controlled rewetting event on the soil CO2 efflux pulse and on the present (DNA-based) and potentially active (rRNA-based) soil bacterial and fungal communities in intact soil cores previously subjected to three different precipitation patterns over four months (full summer dry season, extended wet season, and absent dry season). Phylogenetic marker genes for bacteria (16S) and fungi (28S) were sequenced before and after rewetting, and the abundance of these genes and transcripts was measured. Even after having experienced markedly different antecedent water conditions, the potentially active bacterial communities showed a consistent wet-up response, reflecting contrasting life-strategies for different groups. Moreover, we found a significant positive relation between the extent of change in the structure of the potentially active bacterial community and the magnitude of the CO2 pulse upon rewetting dry soils. We suggest that the duration of severe dry conditions (predicted to change under future climate) is important in conditioning the response potential of the soil bacterial community to wet-up as well as in framing the magnitude of the associated CO2 pulse.

Changing Summer Precipitation Pattern Alters Microbial Community Response to Fall Wet-up in a Mediterranean Soil

NASA Astrophysics Data System (ADS)

Barnard, R. L.; Osborne, C. A.; Firestone, M. K.

2014-12-01

The large soil CO2 efflux associated with rewetting dry soils after the dry summer period significantly contributes to the annual carbon budget of Mediterranean grasslands. Rapid reactivation of soil heterotrophic activity and a pulse of available carbon are both required to fuel the CO2 pulse. Better understanding of the effects of altered summer precipitation on the metabolic state of indigenous microorganisms may be important in predicting future changes in carbon cycling. Here, we investigated the effects of a controlled rewetting event on the soil CO2 efflux pulse and on the present (DNA-based) and potentially active (rRNA-based) soil bacterial and fungal communities in intact soil cores previously subjected to three different precipitation patterns over four months (full summer dry season, extended wet season, and absent dry season). Phylogenetic marker genes for bacteria (16S) and fungi (28S) were sequenced before and after rewetting, and the abundance of these genes and transcripts was measured. Even after having experienced markedly different antecedent water conditions, the potentially active bacterial communities showed a consistent wet-up response. Moreover, we found a significant positive relation between the extent of change in the structure of the potentially active bacterial community and the magnitude of the CO2 pulse upon rewetting dry soils. We suggest that the duration of severe dry conditions (predicted to change under future climate) is important in conditioning the response potential of the soil bacterial community to wet-up as well as in framing the magnitude of the associated CO2 pulse.

Decontamination Of Bacterial Spores by a Peptide-Mimic

DTIC Science & Technology

2006-11-01

consisting of a thin cell wall and the outer cortex. The cell wall guarantees the maintenance of cellular integrity after germination. Lytic- enzymes ...percent of the water content of the vegetative cell. The enzymes contained in the core become active on germination. All minerals (mainly Ca2+, Mn2+ and...such as amino acids and sugars, by enzymes , by high hydrostatic pressure and by some non-nutrient chemicals such as dodecylamine (see next section

Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera)

PubMed Central

Mott, Brendon M.; Maes, Patrick; Snyder, Lucy; Schwan, Melissa R.; Walton, Alexander; Jones, Beryl M.; Corby-Harris, Vanessa

2013-01-01

Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility. PMID:24358254

Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera).

PubMed

Anderson, Kirk E; Sheehan, Timothy H; Mott, Brendon M; Maes, Patrick; Snyder, Lucy; Schwan, Melissa R; Walton, Alexander; Jones, Beryl M; Corby-Harris, Vanessa

2013-01-01

Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or "beebread"). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.

Sterilization Resistance of Bacterial Spores Explained with Water Chemistry.

PubMed

Friedline, Anthony W; Zachariah, Malcolm M; Middaugh, Amy N; Garimella, Ravindranath; Vaishampayan, Parag A; Rice, Charles V

2015-11-05

Bacterial spores can survive for long periods without nutrients and in harsh environmental conditions. This survival is influenced by the structure of the spore, the presence of protective compounds, and water retention. These compounds, and the physical state of water in particular, allow some species of bacterial spores to survive sterilization schemes with hydrogen peroxide and UV light. The chemical nature of the spore core and its water has been a subject of some contention and the chemical environment of the water impacts resistance paradigms. Either the spore has a glassy core, where water is immobilized along with other core components, or the core is gel-like with mobile water diffusion. These properties affect the movement of peroxide and radical species, and hence resistance. Deuterium solid-state NMR experiments are useful for examining the nature of the water inside the spore. Previous work in our lab with spores of Bacillus subtilis indicate that, for spores, the core water is in a more immobilized state than expected for the gel-like core theory, suggesting a glassy core environment. Here, we report deuterium solid-state NMR observations of the water within UV- and peroxide-resistant spores from Bacillus pumilus SAFR-032. Variable-temperature NMR experiments indicate no change in the line shape after heating to 50 °C, but an overall decrease in signal after heating to 100 °C. These results show glass-like core dynamics within B. pumilus SAFR-032 that may be the potential source of its known UV-resistance properties. The observed NMR traits can be attributed to the presence of an exosporium containing additional labile deuterons that can aid in the deactivation of sterilizing agents.

Gut bacterial diversity of the tribes of India and comparison with the worldwide data

PubMed Central

Dehingia, Madhusmita; Thangjam devi, Kanchal; Talukdar, Narayan C.; Talukdar, Rupjyoti; Reddy, Nageshwar; Mande, Sharmila S.; Deka, Manab; Khan, Mojibur R.

2015-01-01

The gut bacteria exert phenotypic traits to the host but the factors which determine the gut bacterial profile (GBP) is poorly understood. This study aimed to understand the effect of ethnicity and geography on GBP of Mongoloid and Proto-Australoid tribes of India. Fecal bacterial diversity was studied in fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) by DGGE followed by NGS analysis on Illumina MiSeq platform. Geography and diet had significant effect on GBP of the Indian tribes which was dominated by Prevotella. The effects were more prominent with lower taxonomic levels, indicating probable functional redundancy of the core GBP. A comparison with the worldwide data revealed that GBP of the Indian population was similar to the Mongolian population (Mongolia). The bacterial genera Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia were found to be core genera in the representative populations of the world. PMID:26689136

Crystal structure analysis of a bacterial aryl acylamidase belonging to the amidase signature enzyme family

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

Lee, Saeyoung; Park, Eun-Hye; Ko, Hyeok-Jin

2015-11-13

The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in complex with the analgesic acetanilide, p-acetaminophenol, at 1.70 Å and 1.73 Å resolutions, respectively. The overall structural fold of AAA was identified as an α/β fold class, exhibiting an open twisted β-sheet core surrounded by α-helices. The asymmetric unit contains one AAA molecule and the monomeric form is functionally active. The core structure enclosing the signature sequence region, including the canonical Ser-cisSer-Lys catalytic triad,more » is conserved in all members of the Amidase Signature enzyme family. The structure of AAA in a complex with its ligand reveals a unique organization in the substrate-binding pocket. The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence. We identified two residues (Tyr{sup 136} and Thr{sup 330}) that interact with the ligand via water molecules, and a hydrogen-bonding network that explains the catalytic affinity over various aryl acyl compounds. The optimum activity of AAA at pH > 10 suggests that the reaction mechanism employs Lys{sup 84} as the catalytic base to polarize the Ser{sup 187} nucleophile in the catalytic triad. - Highlights: • We determined the first structure of a bacterial aryl acylamidase (EC 3.5.1.13). • Structure revealed spatially distinct architecture of the substrate-binding pocket. • Hydrogen-bonding with Tyr{sup 136} and Thr{sup 330} mediates ligand-binding and substrate.« less

Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster

PubMed Central

2018-01-01

Host responses to infection encompass many processes in addition to activation of the immune system, including metabolic adaptations, stress responses, tissue repair, and other reactions. The response to bacterial infection in Drosophila melanogaster has been classically described in studies that focused on the immune response elicited by a small set of largely avirulent microbes. Thus, we have surprisingly limited knowledge of responses to infection that are outside the canonical immune response, of how the response to pathogenic infection differs from that to avirulent bacteria, or even of how generic the response to various microbes is and what regulates that core response. In this study, we addressed these questions by profiling the D. melanogaster transcriptomic response to 10 bacteria that span the spectrum of virulence. We found that each bacterium triggers a unique transcriptional response, with distinct genes making up to one third of the response elicited by highly virulent bacteria. We also identified a core set of 252 genes that are differentially expressed in response to the majority of bacteria tested. Among these, we determined that the transcription factor CrebA is a novel regulator of infection tolerance. Knock-down of CrebA significantly increased mortality from microbial infection without any concomitant change in bacterial number. Upon infection, CrebA is upregulated by both the Toll and Imd pathways in the fat body, where it is required to induce the expression of secretory pathway genes. Loss of CrebA during infection triggered endoplasmic reticulum (ER) stress and activated the unfolded protein response (UPR), which contributed to infection-induced mortality. Altogether, our study reveals essential features of the response to bacterial infection and elucidates the function of a novel regulator of infection tolerance. PMID:29394281

Differences in community composition of bacteria in four glaciers in western China

NASA Astrophysics Data System (ADS)

An, L. Z.; Chen, Y.; Xiang, S.-R.; Shang, T.-C.; Tian, L.-D.

2010-06-01

Microbial community patterns vary in glaciers worldwide, presenting unique responses to global climatic and environmental changes. Four bacterial clone libraries were established by 16S rRNA gene amplification from four ice layers along the 42-m-long ice core MuztB drilled from the Muztag Ata Glacier. A total of 151 bacterial sequences obtained from the ice core MuztB were phylogenetically compared with the 71 previously reported sequences from three ice cores extracted from ice caps Malan, Dunde, and Puruogangri. Six phylogenetic clusters Flavisolibacter, Flexibacter (Bacteroidetes), Acinetobacter, Enterobacter (Gammaproteobacteria), Planococcus/Anoxybacillus (Firmicutes), and Propionibacter/Luteococcus (Actinobacteria) frequently occurred along the Muztag Ata Glacier profile, and their proportion varied by seasons. Sequence analysis showed that most of the sequences from the ice core clustered with those from cold environments, and the sequence clusters from the same glacier more closely grouped together than those from the geographically isolated glaciers. Moreover, bacterial communities from the same location or similarly aged ice formed a cluster, and were clearly separate from those from other geographically isolated glaciers. In summary, the findings provide preliminary evidence of zonal distribution of microbial community, and suggest biogeography of microorganisms in glacier ice.

Differences in community composition of bacteria in four deep ice sheets in western China

NASA Astrophysics Data System (ADS)

An, L.; Chen, Y.; Xiang, S.-R.; Shang, T.-C.; Tian, L.-De

2010-02-01

Microbial community patterns vary in glaciers world wide, presenting unique responses to global climatic and environmental changes. Four bacterial clone libraries were established by 16S rRNA gene amplification from four ice layers along the 42-m-long ice core MuztB drilled from the Muztag Ata Glacier. A total of 152 bacterial sequences obtained from the ice core MuztB were phylogenetically compared with the 71 previously reported sequences from three ice cores extracted from ice caps Malan, Dunde, and Puruoganri. The six functional clusters Flavisolibacter, Flexibacter (Bacteroidetes), Acinetobacter, Enterobacter (Gammaproteobacteria), Planococcus/Anoxybacillus (Firmicutes), and Propionibacter/Luteococcus (Actinobacteria) frequently occurred along the Muztag Ata Glacier profile. Sequence analysis showed that most of the sequences from the ice core clustered with those from cold environments, and the sequences from the same glacier formed a distinct cluster. Moreover, bacterial communities from the same location or similarly aged ice formed a cluster, and were clearly separate from those from other geographically isolated glaciers. In a summary, the findings provide preliminary evidence of zone distribution of microbial community, support our hypothesis of the spatial and temporal biogeography of microorganisms in glacial ice.

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

PubMed

Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

2015-03-01

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Effect of exogenous inoculants on enhancing oil recovery and indigenous bacterial community dynamics in long-term field pilot of low permeability reservoir.

PubMed

Li, Jing; Xue, Shuwen; He, Chunqiu; Qi, Huixia; Chen, Fulin; Ma, Yanling

2018-03-20

Pseudomonas aeruginosa DN1 strain and Bacillus subtilis QHQ110 strain were chosen as rhamnolipid and lipopeptide producer respectively, to evaluate the efficiency of exogenous inoculants on enhancing oil recovery (EOR) and to explore the relationship between injected bacteria and indigenous bacterial community dynamics in long-term filed pilot of Hujianshan low permeability water-flooded reservoir for 26 months. Core-flooding tests showed that the oil displacement efficiency increased by 18.46% with addition of exogenous consortia. Bacterial community dynamics using quantitative PCR and high-throughput sequencing revealed that the exogenous inoculants survived and could live together with indigenous bacterial populations. They gradually became the dominant community after the initial activation, while their comparative advantage weakened continually after 3 months of the first injection. The bacterial populations did not exert an observable change in the process of the second injection of exogenous inoculants. On account of facilitating oil emulsification and accelerating bacterial growth with oil as the carbon source by the injection of exogenous consortia, γ-proteobacteria was finally the prominent bacterial community at class level varying from 25.55 to 32.67%, and the dominant bacterial populations were increased by 2-3 orders of magnitude during the whole processes. The content of organic acids and rhamnolipids in reservoir were promoted with the change of bacterial community diversity, respectively. Cumulative oil increments reached 26,190 barrels for 13 months after the first injection, and 55,947 barrels of oil had been accumulated in all of A20 wells block through two rounds of bacterial consortia injection. The performance of EOR has a cumulative improvement by the injection of exogenous inoculants without observable inhibitory effect on the indigenous bacterial populations, demonstrating the application potential in low permeability water-flooded reservoirs.

Development, Characterization, and Functional Activity of a Panel of Specific Monoclonal Antibodies to Inner Core Lipopolysaccharide Epitopes in Neisseria meningitidis

PubMed Central

Gidney, Margaret Anne J.; Plested, Joyce S.; Lacelle, Suzanne; Coull, Philip A.; Wright, J. Claire; Makepeace, Katherine; Brisson, Jean-Robert; Cox, Andrew D.; Moxon, E. Richard; Richards, James C.

2004-01-01

A panel of six murine monoclonal antibodies (MAbs) recognizing inner core lipopolysaccharide (LPS) epitopes of Neisseria meningitidis was prepared and characterized in order to determine the diversity of inner core LPS glycoforms among disease and carrier isolates. Two of these MAbs, L2-16 (immunoglobulin G2b [IgG2b]) and LPT3-1 (IgG2a), together with a third, previously described MAb, L3B5 (IgG3), showed reactivity, either individually or in combination, with all except 3 of 143 disease and carriage isolates (125 of 126 strains from blood, cerebrospinal fluid, or skin biopsy samples and 15 of 17 from nasopharyngeal cultures). MAbs L3B5, L2-16, and LPT3-1 were further characterized in an indirect immunofluorescence assay. All three MAbs bound to the bacterial cell surface, findings that correlated strongly with whole-cell enzyme-linked immunosorbent assay and immunodot blots. However, in contrast to our findings with L3B5, cell surface binding of L2-16 or LPT 3-1 did not correlate with functional activity as determined by bactericidal or infant rat passive protection assays against wild-type N. meningitidis strains. These findings are provocative with respect to the requirements for protective activity of antibodies and the development of inner core LPS vaccines against invasive meningococcal disease. PMID:14688137

Widespread bacterial populations at glacier beds and their relationship to rock weathering and carbon cycling

NASA Astrophysics Data System (ADS)

Sharp, Martin; Parkes, John; Cragg, Barry; Fairchild, Ian J.; Lamb, Helen; Tranter, Martyn

1999-02-01

Bacterial populations found in subglacial meltwaters and basal ice are comparable to those in the active layer of permafrost and orders of magnitude larger than those found in ice cores from large ice sheets. Populations increase with sediment concentration, and 5% 24% of the bacteria are dividing or have just divided, suggesting that the populations are active. These findings (1) support inferences from recent studies of basal ice and meltwater chemistry that microbially mediated redox reactions may be important at glacier beds, (2) challenge the view that chemical weathering in glacial environments arises from purely inorganic reactions, and (3) raise the possibilities that redox reactions are a major source of protons consumed in subglacial weathering and that these reactions may be the dominant proton source beneath ice sheets where meltwaters are isolated from an atmospheric source of CO2. Microbial mediation may increase the rate of sulfide oxidation under subglacial conditions, a suggestion supported by the results of simple weathering experiments. If subglacial bacterial populations can oxidize and ferment organic carbon, it is important to reconsider the fate of soil organic carbon accumulated under interglacial conditions in areas subsequently overridden by Pleistocene ice sheets.

Periodontal bacteria in human carotid atherothrombosis as a potential trigger for neutrophil activation.

PubMed

Rangé, Hélène; Labreuche, Julien; Louedec, Liliane; Rondeau, Philippe; Planesse, Cynthia; Sebbag, Uriel; Bourdon, Emmanuel; Michel, Jean-Baptiste; Bouchard, Philippe; Meilhac, Olivier

2014-10-01

Epidemiological, biological and clinical links between periodontal and cardiovascular diseases are now well established. Several human studies have detected bacterial DNA corresponding to periodontal pathogens in cardiovascular samples. Intraplaque hemorrhage has been associated with a higher risk of atherosclerotic plaque rupture, potentially mediated by neutrophil activation. In this study, we hypothesized that plaque composition may be related to periodontal pathogens. Carotid culprit plaque samples were collected from 157 patients. Macroscopic characterization was performed at the time of collection: presence of blood, lipid core, calcification and fibrosis. Markers of neutrophil activation released by carotid samples were quantified (myeloperoxidase or MPO, cell-free DNA and DNA-MPO complexes). PCR analysis using specific primers for Porphyromonas gingivalis, Aggregatibacter actinomycetemcommitans, Treponema denticola, Prevotella intermedia and Tannerella forsythia was used to detect DNA from periodontal pathogens in carotid tissues. In addition, bacterial lipopolysaccharide (LPS) and Immunoglobulins G against T. forsythia were quantified in atherosclerotic carotid conditioned medium. Intraplaque hemorrhage was present in 73/157 carotid samples and was associated with neutrophil activation, reflected by the release of MPO, cell-free DNA and MPO-DNA complexes. LPS levels were also linked to intraplaque hemorrhage but not with the neutrophil activation markers. Seventy-three percent of the carotid samples were positive for periodontal bacterial DNA. Furthermore, hemoglobin levels were associated with the detection of T. forsythia and neutrophil activation/inflammation markers. This study suggests a potential role of periodontal microorganisms, especially T. forsythia, in neutrophil activation within hemorrhagic atherosclerotic carotid plaques. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

bcgTree: automatized phylogenetic tree building from bacterial core genomes.

PubMed

Ankenbrand, Markus J; Keller, Alexander

2016-10-01

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).

The perturbation of tryptophan fluorescence by phenylalanine to alanine mutations identifies the hydrophobic core in a subset of bacterial Ig-like domains.

PubMed

Raman, Rajeev; Ptak, Christopher P; Hsieh, Ching-Lin; Oswald, Robert E; Chang, Yung-Fu; Sharma, Yogendra

2013-07-09

Many host-parasite interactions are mediated via surface-exposed proteins containing bacterial immunoglobulin-like (Big) domains. Here, we utilize the spectral properties of a conserved Trp to provide evidence that, along with a Phe, these residues are positioned within the hydrophobic core of a subset of Big_2 domains. The mutation of the Phe to Ala decreases Big_2 domain stability and impairs the ability of LigBCen2 to bind to the host protein, fibronectin.

The ARTT motif and a unified structural understanding of substraterecognition in ADP ribosylating bacterial toxins and eukaryotic ADPribosyltransferases

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

Han, S.; Tainer, J.A.

2001-08-01

ADP-ribosylation is a widely occurring and biologically critical covalent chemical modification process in pathogenic mechanisms, intracellular signaling systems, DNA repair, and cell division. The reaction is catalyzed by ADP-ribosyltransferases, which transfer the ADP-ribose moiety of NAD to a target protein with nicotinamide release. A family of bacterial toxins and eukaryotic enzymes has been termed the mono-ADP-ribosyltransferases, in distinction to the poly-ADP-ribosyltransferases, which catalyze the addition of multiple ADP-ribose groups to the carboxyl terminus of eukaryotic nucleoproteins. Despite the limited primary sequence homology among the different ADP-ribosyltransferases, a central cleft bearing NAD-binding pocket formed by the two perpendicular b-sheet core hasmore » been remarkably conserved between bacterial toxins and eukaryotic mono- and poly-ADP-ribosyltransferases. The majority of bacterial toxins and eukaryotic mono-ADP-ribosyltransferases are characterized by conserved His and catalytic Glu residues. In contrast, Diphtheria toxin, Pseudomonas exotoxin A, and eukaryotic poly-ADP-ribosyltransferases are characterized by conserved Arg and catalytic Glu residues. The NAD-binding core of a binary toxin and a C3-like toxin family identified an ARTT motif (ADP-ribosylating turn-turn motif) that is implicated in substrate specificity and recognition by structural and mutagenic studies. Here we apply structure-based sequence alignment and comparative structural analyses of all known structures of ADP-ribosyltransfeases to suggest that this ARTT motif is functionally important in many ADP-ribosylating enzymes that bear a NAD binding cleft as characterized by conserved Arg and catalytic Glu residues. Overall, structure-based sequence analysis reveals common core structures and conserved active sites of ADP-ribosyltransferases to support similar NAD binding mechanisms but differing mechanisms of target protein binding via sequence variations within the ARTT motif structural framework. Thus, we propose here that the ARTT motif represents an experimentally testable general recognition motif region for many ADP-ribosyltransferases and thereby potentially provides a unified structural understanding of substrate recognition in ADP-ribosylation processes.« less

Microbial Transport Mechanisms in Silty, Sandy Media as Inferred From Short Core Experiments Performed in the Field.

NASA Astrophysics Data System (ADS)

Mailloux, B.; Hall, j; Fuller, M.; Scheibe, T.; DeFlaun, M.; Onstott, T.

2001-12-01

A novel approach to examining the mechanisms controlling the velocity and attachment of bacteria in porous media was developed for the South Oyster Bacterial Transport Field Site. Instead of performing bacterial transport experiments in the lab using repacked materials and artificial water, samples of sediment core, 7 cm. in length, were connected to multi-level samplers at the field site, the groundwater from select levels in the aquifer was pumped through the cores, and an aliquot of cells stained with a viable, fluorescent dye was injected with Br into the influent end of the cores. The same cells, Br and groundwater were simultaneously passed through repacked cores composed of sieved sand of varying grain size fractions (100 to 600  diameter) and a single grain size fraction coated with Fe and Al synthetic oxides. The grain size of the coated sand and the Fe and Al concentrations of the coated sand (500 to 1000 ppm) were representative of the average value of the aquifer. By using this approach, the parameters that are difficult to reproduce in the lab, e.g., the dissolved gas concentrations, pH, temperature, dissolved organic matter, the indigenous bacterial and protist populations, could be replicated. One of the results derived from 29 short core experiments indicate that the enhanced velocity of adhesion deficient DA001 that has been reported in laboratory experiments was greatly reduced in the field experiments for the Fe and Al coated sands and greatly enhanced for the fine grained sands.

Variations in archaeal and bacterial diversity associated with the anaerobic oxidation of methane in the active mud volcanoes of the Canadian Beaufort Sea

NASA Astrophysics Data System (ADS)

Lee, Y. M.; Lee, D. H.; Hwang, K.; Hong, S. G.; Jin, Y. K.

2016-12-01

The prokaryotic microorganisms inhabiting Mud Volcanoes (MVs) play an important role for mitigation of methane (CH4) emission. Despite the identification of active MVs in the continental slope of the Canadian Beaufort Sea, little is known about the distribution and functions of prokaryotic community in this region. Hence, we investigated the prokaryotic diversity of four sediment cores (three from the active MVs and one from a non-methane influenced reference site) of the Canadian Beaufort Sea using 454-pyrosequencing of 16S rRNA genes as the first step to understand the prokaryotic roles in controlling outgassing methane. Bacterial and archaeal communities of MVs were distinctive from those of the reference site, and the communities of MVs were similar to each other at deeper depth levels. Chloroflexi, Actinobacteria, unclassified bacterial groups, and MCG_c of Crenarchaeota were predominant in the MVs, while Firmicutes, Deltaproteobacteria, and unclassified class of Thaumarchaeota were dominant in reference site. The relative abundance of dominant bacterial groups varied at sulfate-methane transition zone (SMTZ) of individual MVs. However, certain microbial taxa such as members of SAGMEG_o or Methanosarcinales of Euryarcheaota and Dehalococcoidales of Chloroflexi were predominant at SMTZs. Since they are not the classical representative taxa known to be involved in anaerobic oxidation of methane, their dominance implicates that they could be playing important roles in methane cycling using unrevealed mechanisms. We will further perform the phylogenetic and network analyses to infer mechanisms and interactions of dominant operational taxonomic units in controlling methane flux.

Evidence for microbial activity in the formation of carbonate-hosted Zn-Pb deposits

NASA Astrophysics Data System (ADS)

Kucha, H.; Raith, J.

2009-04-01

*Kucha H **Raith J *University of Mining and Metallurgy, Faculty of Geology, Geophysics and Environmental Protection, Mickiewicza 30, PL-30-059 Krakow, Poland. ** University of Leoben, Department of Applied Geosciences and Geophysics, A-8700 Leoben, Peter Tunner Str. 5, Austria Evidence for microbial activity in the formation of carbonate-hosted Zn-Pb deposits To date evaluation of bacterial processes in the formation of carbonate-hosted Zn-Pb deposits is largely based on sulphur isotope evidence. However, during a past few years, textural criteria, have been established, which support the bacterial origin of many of these deposits. This has received a strong support from micro-, and nano-textures of naturally growing bacterial films in a flooded tunnel within carbonates that host the Piquette Zn-Pb deposit (Druschel et al., 2002). Bacterial textures, micro- and nano textures found in carbonate-hosted Zn-Pb deposits are: i)wavy bacterial films up to a few mm thick to up to a few cm long composed of peloids, ii)semimassive agglomeration of peloids in the carbonate matrix, and iii)solitary peloids dispersed in the carbonate matrix. Peloids are usually composed of a distinct 50-90um core most often made up of Zn-bearing calcite surrounded by 30-60um thick dentate rim composed of ZnS. Etching of Zn-carbonate cores reveals 1 - 2um ZnS filaments, and numerous 15 to 90nm large ZnS nano-spheres (Kucha et al., 2005). In massive ore composite Zn-calcite - sphalerite peloids are entirely replaced by zinc sulphide, and form peloids ghosts within banded sulphide layers. Bacterially derived micro- and nano-textures have been observed in the following carbonate-hosted Zn-Pb deposits: 1)Irish-type Zn-Pb deposits. In the Navan deposit the basic sulphur is isotopically light bacteriogenic S (Fallick at al., 2001). This is corroborated by semimassive agglomerations of composite peloids (Zn-calcite-ZnS corona or ZnS core-melnikovite corona). Etching of Zn-calcite core reveals globular 0.5 to 1um large fossilised bacteria with some nano-size spheres as well (Kucha et al., 1990). In the Silvermines and Ballinalack ores wavy bacterial film-like textures composed of peloids made up of Zn-calcite or Zn-siderite cores and ZnS rims are known (Kucha et al., 1990). 2) Alpine Zn-Pb deposits. Bleiberg sulphides, Austria, Zn-Pb ores display the δ34S‰ values from -32 to -2 (n=284), with mean close to 20‰ (Schroll & Rantitsch, 2005). Cardita and Crest ores contain wavy bacterial films (-28.84 to -27.91‰). Semimassive globular sphalerite with globules varying in size from 90 to 180um is a basic ZnS type in the Bleiberg ores with light sulphur from (-30.49 to -26.4‰). Based on sulphur isotope data, um-sized bacterial filaments, and spherical nano-textures seen in etched ZnS globules, sulphate reducing bacteria (SRB) involvement is suggested (Kucha et al. 2005). ZnS globules were formed by replacement of original peloids (i.e. bacterial colonies) and/or by agglomeration of original 10-15nm ZnS spheres secreted by SRB. The growth of peloids was promoted by unbalanced electric charges on the surfaces of these ZnS nano-spheres. 3) Upper Silesian MVT Zn-Pb deposits. Sulphur isotopes vary between 2 and 12‰, (mean 5‰) for early stage sulphides, main stage sulphides are characterised by S signature -2 to -15‰. Redeposition of ZnS from the horst to graben structures produced "pulvery" sphalerite with -19‰ (Haranczyk, 1993). Sulphide stalactites containing oxysulphides have δS‰ vales of -23.7. Bacterial microtextures occur mainly within oxysulphides and at the contact between Fe-smithsonite replaced by banded sphalerite (Kucha et al., 1990). 4) La Calamine and Engis, Belgium, contain bacterial micro- and nano-textures in ores related to karst cavities, and paleoweathering crusts (Kucha et al., 1990). The biogenic textures are represented by clumps of peloids, and bacterial mats occurring in banded sphalerite composed of replaced peloids. Peloids are composed of Zn-calcite cores and ZnS rims, oxysulphides, thiosulphates, vaesite and chalcedonic silica. Bacterial microtextures in all of the above mentioned deposits are as a rule associated with oxysulphides i.e. compounds with mixed and intermediate sulphur valences (Kucha et al., 1989). The origin of oxysulphides is probably related either directly to incomplete bacterial reduction of the sulphatic sulphur, or reaction of bacterial H2S with sulphatic S present in the fluids. Some of peloids are composed of oxysulphides (Kucha & Stumpfl, 1992; Kucha, 2003). Therefore, an interpretation of the S isotopic signature of bacterial textures should consider not only microbial community structure, but also the oxidative part of the sulphur cycle proceeding through compounds with mixed sulphur valences. References Druschel GK, Labrenz M, Thomsen-Ebert T, Fowler DA, Banfield JF (2002) Geochemical modelling of ZnS in biofilms: An example of ore depositional processes. Economic Geology, v 97, 1319-1329. Fallick, AE, Ashton JH, Boyce AJ, Ellam RM, Russell MJ (2001) Bacteria were responsible fort he magnitude of the world-class hydrothermal base metal sulphide orebody at Navan, Ireland. Economic Geology, v 96, 885 - 890. Haranczyk Cz (1993) Sulphur isotope models of genesis of the Silesian-Cracov Zn-Pb ore deposits. Geological Quarterly, v 37, 307 - 322. Kucha H (1988) Biogenic and non-biogenic concentration of sulfur and metals in the carbonate-hosted Ballinalack Zn-Pb deposit, Ireland. Min. Pet., 38, 171-187. Kucha H, Wouters R, Arkens O (1989) Determination of sulfur and iron valence by microprobe. Scanning Microscopy, 3, no 1, 89-97. Kucha H, Van der Biest J, Viaene W (1990) Peloids in strata bound Zn-Pb deposits and their genetic importance. Min. Deposita, 25, 132-139. Kucha H, Stumpfl EF (1992) Thiosulphates as precursors of banded sphalerite and pyrite at Bleiberg, Austria. Min. Mag., 56, 165-172. Kucha H (2003) Mississippi Valley Type Zn-Pb deposits of Upper Silesia, Poland, 253-272. In: Kelly, J., G., Andrew, C., J., Ashton, J., H., Boland, M., B., Earls, E., Fusciardi, L., Stanley, G. (eds) Europe's Major Base Metal Deposits, Irish Association for Economic Geology, Printed by Colour Books Ltd, Dublin 2003, 551 pp. Kucha H, Schroll E, Stumpfl EF (2005) Fossil sulphate-reducing bacteria in the Bleiberg lead-zinc deposit, Austria. Mineralium Deposita, v 40, 123-126. Schroll E, Rantitsch G (2005) Sulfur isotope patterns in the Bleiberg deposit (Eastern Alps) and their implications for genetically affiliated. Mineralogy and Petrology 148: 1-18.

Thermal Unfolding Simulations of Bacterial Flagellin: Insight into its Refolding Before Assembly

PubMed Central

Chng, Choon-Peng; Kitao, Akio

2008-01-01

Flagellin is the subunit of the bacterial filament, the micrometer-long propeller of a bacterial flagellum. The protein is believed to undergo unfolding for transport through the channel of the filament and to refold in a chamber at the end of the channel before being assembled into the growing filament. We report a thermal unfolding simulation study of S. typhimurium flagellin in aqueous solution as an attempt to gain atomic-level insight into the refolding process. Each molecule comprises two filament-core domains {D0, D1} and two hypervariable-region domains {D2, D3}. D2 can be separated into subdomains D2a and D2b. We observed a similar unfolding order of the domains as reported in experimental thermal denaturation. D2a and D3 exhibited high thermal stability and contained persistent three-stranded β-sheets in the denatured state which could serve as folding cores to guide refolding. A recent mutagenesis study on flagellin stability seems to suggest the importance of the folding cores. Using crude size estimates, our data suggests that the chamber might be large enough for either denatured hypervariable-region domains or filament-core domains, but not whole flagellin; this implicates a two-staged refolding process. PMID:18263660

Physical and biological properties of U. S. standard endotoxin EC after exposure to ionizing radiation

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

Csako, G.; Elin, R.J.; Hochstein, H.D.

Techniques that reduce the toxicity of bacterial endotoxins are useful for studying the relationship between structure and biological activity. We used ionizing radiation to detoxify a highly refined endotoxin preparation. U.S. standard endotoxin EC. Dose-dependent changes occurred by exposure to /sup 60/Co-radiation in the physical properties and biological activities of the endotoxin. Sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis showed gradual loss of the polysaccharide components (O-side chain and R-core) from the endotoxin molecules. In contrast, although endotoxin revealed a complex absorption pattern in the UV range, radiation treatment failed to modify that pattern. Dose-related destruction of the primary toxic component,more » lipid A, was suggested by the results of activity tests: both the pyrogenicity and limulus reactivity of the endotoxin were destroyed by increasing doses of radiation. The results indicate that the detoxification is probably due to multiple effects of the ionizing radiation on bacterial lipopolysaccharides, and the action involves (i) the destruction of polysaccharide moieties and possibly (ii) the alteration of lipid A component of the endotoxin molecule.« less

Antarctic ice core samples: culturable bacterial diversity.

PubMed

Shivaji, Sisinthy; Begum, Zareena; Shiva Nageswara Rao, Singireesu Soma; Vishnu Vardhan Reddy, Puram V; Manasa, Poorna; Sailaja, Buddi; Prathiba, Mambatta S; Thamban, Meloth; Krishnan, Kottekkatu P; Singh, Shiv M; Srinivas, Tanuku N R

2013-01-01

Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 10(3) CFU ml(-1) of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2-100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

PubMed

Apprill, Amy; Robbins, Jooke; Eren, A Murat; Pack, Adam A; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M T; Mincer, Tracy J

2014-01-01

Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.

Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

PubMed Central

Apprill, Amy; Robbins, Jooke; Eren, A. Murat; Pack, Adam A.; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M. T.; Mincer, Tracy J.

2014-01-01

Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals. PMID:24671052

Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor l-arginine

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

Garnett, James A.; Baumberg, Simon; Stockley, Peter G.

2007-11-01

The crystal structure of the C-terminal domain hexameric core of AhrC, with bound corepressor (l-arginine), has been solved at 1.95 Å resolution. Binding of l-arginine results in a rotation between the two trimers of the hexamer, leading to the activation of the DNA-binding state. The arginine repressor/activator protein (AhrC) from Bacillus subtilis belongs to a large family of multifunctional transcription factors that are involved in the regulation of bacterial arginine metabolism. AhrC interacts with operator sites in the promoters of arginine biosynthetic and catabolic operons, acting as a transcriptional repressor at biosynthetic sites and an activator of transcription at catabolicmore » sites. AhrC is a hexamer of identical subunits, each having two domains. The C-terminal domains form the core of the protein and are involved in oligomerization and l-arginine binding. The N-terminal domains lie on the outside of the compact core and play a role in binding to 18 bp DNA operators called ARG boxes. The C-terminal domain of AhrC has been expressed, purified and characterized, and also crystallized as a hexamer with the bound corepressor l-arginine. Here, the crystal structure refined to 1.95 Å is presented.« less

Bacterial diversity among four healthcare-associated institutes in Taiwan.

PubMed

Chen, Chang-Hua; Lin, Yaw-Ling; Chen, Kuan-Hsueh; Chen, Wen-Pei; Chen, Zhao-Feng; Kuo, Han-Yueh; Hung, Hsueh-Fen; Tang, Chuan Yi; Liou, Ming-Li

2017-08-15

Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.

PubMed

de Araujo, Ademir Sergio Ferreira; Bezerra, Walderly Melgaço; Dos Santos, Vilma Maria; Rocha, Sandra Mara Barbosa; Carvalho, Nilza da Silva; de Lyra, Maria do Carmo Catanho Pereira; Figueiredo, Marcia do Vale Barreto; de Almeida Lopes, Ângela Celis; Melo, Vania Maria Maciel

2017-04-01

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Novel role of the LPS core glycosyltransferase WapH for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis.

PubMed

Benforte, Florencia C; Colonnella, Maria A; Ricardi, Martiniano M; Solar Venero, Esmeralda C; Lizarraga, Leonardo; López, Nancy I; Tribelli, Paula M

2018-01-01

Psychrotroph microorganisms have developed cellular mechanisms to cope with cold stress. Cell envelopes are key components for bacterial survival. Outer membrane is a constituent of Gram negative bacterial envelopes, consisting of several components, such as lipopolysaccharides (LPS). In this work we investigated the relevance of envelope characteristics for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis by analyzing a mini Tn5 wapH mutant strain, encoding a core LPS glycosyltransferase. Our results showed that wapH strain is impaired to grow under low temperature but not for cold survival. The mutation in wapH, provoked a strong aggregative phenotype and modifications of envelope nanomechanical properties such as lower flexibility and higher turgor pressure, cell permeability and surface area to volume ratio (S/V). Changes in these characteristics were also observed in the wild type strain grown at different temperatures, showing higher cell flexibility but lower turgor pressure under cold conditions. Cold shock experiments indicated that an acclimation period in the wild type is necessary for cell flexibility and S/V ratio adjustments. Alteration in cell-cell interaction capabilities was observed in wapH strain. Mixed cells of wild type and wapH strains, as well as those of the wild type strain grown at different temperatures, showed a mosaic pattern of aggregation. These results indicate that wapH mutation provoked marked envelope alterations showing that LPS core conservation appears as a novel essential feature for active growth under cold conditions.

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

PubMed Central

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

2016-01-01

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

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

USGS Publications Warehouse

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

2016-01-01

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

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

PubMed

Schürch, A C; Arredondo-Alonso, S; Willems, R J L; Goering, R V

2018-04-01

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Personal collection of relevant publications. When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

PubMed Central

Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa; Kaye, Maria E.; Udomwong, Piyachat; Shamsani, N. Jannah; Young, J. Peter W.; Bailly, Xavier

2015-01-01

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny. PMID:25589577

Characteristics of environmental correlations between iron (oxyhydr)oxide nanoparticles and microbial activity

NASA Astrophysics Data System (ADS)

Tamura, T.; Kyono, A.; Muratani, M.

2014-12-01

Nanoparticulate iron oxides and oxyhydroxides with large surface area and high chemical reactivity cause the immobilization of heavy metals and the provision of essential nutrients to organisms. Environmental correlations between microbial activity and nanomorphology of iron (oxyhydr)oxides are significantly important for earth surface processes. In this study, we characterize iron (oxyhydr)oxide nanoparticles and microorganisms in natural lake sediments and describe their association observed between particle nanostructures and microbial species. About 40 cm depth of boring core sample was collected from Lake Kasumigaura, Lake Ushiku, Kokai River and Lake Tega, Japan. To distinguish both iron nanoparticles and growing bacterial colonies with depths, boring core samples were divided into three to five pieces. Particle morphologies, size, aggregation states, mineral species, and microorganisms were observed by transmission electron microscopy (TEM), X-ray diffraction (XRD), and rRNA gene sequences. Redox potential and pH of the lake sediments were also measured. The core sample from top is mainly composed of quartz of coarse-grained materials, while that from bottom is of ferrihydrite of fine grained materials. The authors will show the results of experiments and discuss the interrelation between iron nanoparticles and microorganisms.

Anaerobic thermophilic bacteria isolated from a Venezuelan oil field and its potential use in microbial improved oil recovery

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

Trebbau, G.; Fernandez, B.; Marin, A.

1995-12-31

The objective of this work is to determine the ability of indigenous bacteria from a Venezuelan oil field to grow under reservoir conditions inside a porous media, and to produce metabolites capable of recovering residual crude oil. For this purpose, samples of formation waters from a central-eastern Venezuelan oil reservoir were enriched with different carbon sources and a mineral basal media. Formation water was used as a source of trace metals. The enrichments obtained were incubated at reservoir temperature (71{degrees}C), reservoir pressure (1,200 psi), and under anaerobic conditions for both outside and inside porous media (Berea core). Growth and metabolicmore » activity was followed outside porous media by measuring absorbance at 660 nm, increases in pressure, and decreases in pH. Inside porous media bacterial activity was determined by visual examination of the produced waters (gas bubbles and bacterial cells). All the carbohydrates tested outside porous media showed good growth at reservoir conditions. The pH was lowered, gases such as CO{sub 2} and CH{sub 4} were identified by GC. Surface tension was lowered in some enrichments by 30% when compared to controls. Growth was decreased inside porous media, but gases were produced and helped displace oil. In addition, 10% residual oil was recovered from the Berea core. Mathematical modeling was applied to the laboratory coreflood experiment to evaluate the reproducibility of the results obtained.« less

When a habitat freezes solid: Microorganisms over-winter within the ice column of a coastal Antarctic lake

USGS Publications Warehouse

Foreman, C.M.; Dieser, M.; Greenwood, M.; Cory, R.M.; Laybourn-Parry, J.; Lisle, J.T.; Jaros, C.; Miller, P.L.; Chin, Y.-P.; McKnight, Diane M.

2011-01-01

A major impediment to understanding the biology of microorganisms inhabiting Antarctic environments is the logistical constraint of conducting field work primarily during the summer season. However, organisms that persist throughout the year encounter severe environmental changes between seasons. In an attempt to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the biological and chemical processes that occurred during winter freezeup. The ice contained bacteria and virus-like particles, while flagellated algae and ciliates over-wintered in the form of inactive cysts and spores. Both bacteria and algae were metabolically active in the ice core melt water. Bacterial production ranged from 1.8 to 37.9??gCL-1day-1. Upon encountering favorable growth conditions in the melt water, primary production ranged from 51 to 931??gCL-1day-1. Because of the strong H2S odor and the presence of closely related anaerobic organisms assigned to Pony Lake bacterial 16S rRNA gene clones, we hypothesize that the microbial assemblage was strongly affected by oxygen gradients, which ultimately restricted the majority of phylotypes to distinct strata within the ice column. This study provides evidence that the microbial community over-winters in the ice column of Pony Lake and returns to a highly active metabolic state when spring melt is initiated. ?? 2011 Federation of European Microbiological Societies.

The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens.

PubMed

Rybakova, Daria; Mancinelli, Riccardo; Wikström, Mariann; Birch-Jensen, Ann-Sofie; Postma, Joeke; Ehlers, Ralf-Udo; Goertz, Simon; Berg, Gabriele

2017-09-01

Although the plant microbiome is crucial for plant health, little is known about the significance of the seed microbiome. Here, we studied indigenous bacterial communities associated with the seeds in different cultivars of oilseed rape and their interactions with symbiotic and pathogenic microorganisms. We found a high bacterial diversity expressed by tight bacterial co-occurrence networks within the rape seed microbiome, as identified by llumina MiSeq amplicon sequencing. In total, 8362 operational taxonomic units (OTUs) of 40 bacterial phyla with a predominance of Proteobacteria (56%) were found. The three cultivars that were analyzed shared only one third of the OTUs. The shared core of OTUs consisted mainly of Alphaproteobacteria (33%). Each cultivar was characterized by having its own unique bacterial structure, diversity, and proportion of unique microorganisms (25%). The cultivar with the lowest bacterial abundance, diversity, and the highest predicted bacterial metabolic activity rate contained the highest abundance of potential pathogens within the seed. This data corresponded with the observation that seedlings belonging to this cultivar responded more strongly to the seed treatments with bacterial inoculants than other cultivars. Cultivars containing higher indigenous diversity were characterized as having a higher colonization resistance against beneficial and pathogenic microorganisms. Our results were confirmed by microscopic images of the seed microbiota. The structure of the seed microbiome is an important factor in the development of colonization resistance against pathogens. It also has a strong influence on the response of seedlings to biological seed treatments. These novel insights into seed microbiome structure will enable the development of next generation strategies combining both biocontrol and breeding approaches to address world agricultural challenges.

Exploring the effects of photon correlations from thermal sources on bacterial photosynthesis

NASA Astrophysics Data System (ADS)

Manrique, Pedro D.; Caycedo-Soler, Felipe; De Mendoza, Adriana; Rodríguez, Ferney; Quiroga, Luis; Johnson, Neil F.

Thermal light sources can produce photons with strong spatial correlations. We study the role that these correlations might potentially play in bacterial photosynthesis. Our findings show a relationship between the transversal distance between consecutive absorptions and the efficiency of the photosynthetic process. Furthermore, membranes where the clustering of core complexes (so-called RC-LH1) is high, display a range where the organism profits maximally from the spatial correlation of the incoming light. By contrast, no maximum is found for membranes with low core-core clustering. We employ a detailed membrane model with state-of-the-art empirical inputs. Our results suggest that the organization of the membrane's antenna complexes may be well-suited to the spatial correlations present in an natural light source. Future experiments will be needed to test this prediction.

Human gut microbiome: the second genome of human body.

PubMed

Zhu, Baoli; Wang, Xin; Li, Lanjuan

2010-08-01

The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50-100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.

Metabolic labelling of the carbohydrate core in bacterial peptidoglycan and its applications

PubMed Central

Liang, Hai; DeMeester, Kristen E.; Hou, Ching-Wen; Parent, Michelle A.; Caplan, Jeffrey L.; Grimes, Catherine L.

2017-01-01

Bacterial cells are surrounded by a polymer known as peptidoglycan (PG), which protects the cell from changes in osmotic pressure and small molecule insults. A component of this material, N-acetyl-muramic acid (NAM), serves as a core structural element for innate immune recognition of PG fragments. We report the synthesis of modifiable NAM carbohydrate derivatives and the installation of these building blocks into the backbone of Gram-positive and Gram-negative bacterial PG utilizing metabolic cell wall recycling and biosynthetic machineries. Whole cells are labelled via click chemistry and visualized using super-resolution microscopy, revealing higher resolution PG structural details and allowing the cell wall biosynthesis, as well as its destruction in immune cells, to be tracked. This study will assist in the future identification of mechanisms that the immune system uses to recognize bacteria, glean information about fundamental cell wall architecture and aid in the design of novel antibiotics. PMID:28425464

The AvrE superfamily: ancestral type III effectors involved in suppression of pathogen-associated molecular pattern-triggered immunity.

PubMed

Degrave, Alexandre; Siamer, Sabrina; Boureau, Tristan; Barny, Marie-Anne

2015-10-01

The AvrE superfamily of type III effectors (T3Es) is widespread among type III-dependent phytobacteria and plays a crucial role during bacterial pathogenesis. Members of the AvrE superfamily are vertically inherited core effectors, indicating an ancestral acquisition of these effectors in bacterial plant pathogens. AvrE-T3Es contribute significantly to virulence by suppressing pathogen-associated molecular pattern (PAMP)-triggered immunity. They inhibit salicylic acid-mediated plant defences, interfere with vesicular trafficking and promote bacterial growth in planta. AvrE-T3Es elicit cell death in both host and non-host plants independent of any known plant resistance protein, suggesting an original interaction with the plant immune system. Recent studies in yeast have indicated that they activate protein phosphatase 2A and inhibit serine palmitoyl transferase, the first enzyme of the sphingolipid biosynthesis pathway. In this review, we describe the current picture that has emerged from studies of the different members of this fascinating large family. © 2015 BSPP AND JOHN WILEY & SONS LTD.

Determination of the Core of a Minimal Bacterial Gene Set†

PubMed Central

Gil, Rosario; Silva, Francisco J.; Peretó, Juli; Moya, Andrés

2004-01-01

The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed. PMID:15353568

Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China.

PubMed

Zhang, Manping; Luo, Yi; Lin, Li'an; Lin, Xiaolan; Hetharua, Buce; Zhao, Weijun; Zhou, Mengkai; Zhan, Qing; Xu, Hong; Zheng, Tianling; Tian, Yun

2018-03-01

Nitrite-dependent anaerobic methane oxidation (n-damo), which is mediated by "Candidatus Methylomirabilis oxyfera-like" bacteria, is unique in linking the carbon and nitrogen cycles. However, the niche and activity of n-damo bacteria in the mangrove ecosystem have not been confirmed. Here, we report the occurrence of the n-damo process in the mangrove wetland of the Zhangjiang Estuary, China. The widespread occurrence of n-damo bacteria in mangrove wetland was confirmed using real-time quantitative polymerase chain reaction (qPCR) assay, which showed that the abundance of Methylomirabilis oxyfera-like bacterial 16S rRNA and pmoA genes ranged from 2.43 × 10 6 to 2.09 × 10 7 and 2.07 × 10 6 to 3.38 × 10 7 copies per gram of dry soil in the examined sediment cores. The highest amount of targeting genes was all detected in the upper layer (0-20 cm). Phylogenetic analyses of n-damo bacterial 16S rRNA and pmoA genes illustrated the depth-specific distribution and high diversity of n-damo bacteria in the mangrove wetland. Stable isotope experiments further confirmed the occurrence of n-damo in the examined mangrove sediments, and the potential n-damo rates ranged from 25.93 to 704.08 nmol CO 2 per gram of dry soil per day at different depths of the sediment cores, with the n-damo being more active in the upper layer of the mangrove sediments. These results illustrate the existence of active M. oxyfera-like bacteria and indicate that the n-damo process is a previously overlooked microbial methane sink in the mangrove wetlands.

In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

PubMed

Czudnochowski, Nadine; Wang, Amy Liya; Finer-Moore, Janet; Stroud, Robert M

2013-10-23

Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA. Copyright © 2013 Elsevier Ltd. All rights reserved.

A structural role for the PHP domain in E. coli DNA polymerase III.

PubMed

Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

2013-05-14

In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

A Consistent and Predictable Commercial Broiler Chicken Bacterial Microbiota in Antibiotic-Free Production Displays Strong Correlations with Performance.

PubMed

Johnson, Timothy J; Youmans, Bonnie P; Noll, Sally; Cardona, Carol; Evans, Nicholas P; Karnezos, T Peter; Ngunjiri, John M; Abundo, Michael C; Lee, Chang-Won

2018-06-15

Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and Lactobacillus was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production. IMPORTANCE Multidrug-resistant bacterial pathogens are perhaps the greatest medical challenge we will face in the 21st century and beyond. Antibiotics are necessary in animal production to treat disease. As such, animal production is a contributor to the problem of antibiotic resistance. Efforts are underway to reduce antibiotic use in animal production. However, we are also challenged to feed the world's increasing population, and sustainable meat production is paramount to providing a safe and quality protein source for human consumption. In the absence of antibiotics, alternative approaches are needed to maintain health and prevent disease, and probiotics have great promise as one such approach. This work paves the way for the development of alternative approaches to raising poultry by increasing our understandings of what defines the poultry microbiome and of how it can potentially be modulated to improve animal health and performance. Copyright © 2018 American Society for Microbiology.

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period.

PubMed

Postec, Anne; Quéméneur, Marianne; Bes, Méline; Mei, Nan; Benaïssa, Fatma; Payri, Claude; Pelletier, Bernard; Monnin, Christophe; Guentas-Dombrowsky, Linda; Ollivier, Bernard; Gérard, Emmanuelle; Pisapia, Céline; Gérard, Martine; Ménez, Bénédicte; Erauso, Gaël

2015-01-01

Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems.

Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows.

PubMed

Jeon, Soo Jin; Cunha, Federico; Vieira-Neto, Achilles; Bicalho, Rodrigo C; Lima, Svetlana; Bicalho, Marcela L; Galvão, Klibs N

2017-08-25

Metritis is an inflammatory disease of the uterus caused by bacterial infection, particularly Bacteroides, Porphyromonas, and Fusobacterium. Bacteria from the environment, feces, or vagina are believed to be the only sources of uterine contamination. Blood seeps into the uterus after calving; therefore, we hypothesized that blood could also be a seeding source of uterine bacteria. Herein, we compared bacterial communities from blood, feces, and uterine samples from the same cows at 0 and 2 days postpartum using deep sequencing and qPCR. The vaginal microbiome 7 days before calving was also compared. There was a unique structure of bacterial communities by sample type. Principal coordinate analysis revealed two distinct clusters for blood and feces, whereas vaginal and uterine bacterial communities were more scattered, indicating greater variability. Cluster analysis indicated that uterine bacterial communities were more similar to fecal bacterial communities than vaginal and blood bacterial communities. Nonetheless, there were core genera shared by all blood, feces, vaginal, and uterine samples. Major uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium were part of the core genera in blood, feces, and vagina. Other uterine pathogens such as Prevotella and Helcococcus were not part of the core genera in vaginal samples. In addition, uterine pathogens showed a strong and significant interaction with each other in the network of blood microbiota, but not in feces or vagina. These microbial interactions in blood may be an important component of disease etiology. The copy number of total bacteria in blood and uterus was correlated; the same did not occur in other sites. Bacteroides heparinolyticus was more abundant in the uterus on day 0, and both B. heparinolyticus and Fusobacterium necrophorum were more abundant in the uterus than in the blood and feces on day 2. This indicates that B. heparinolyticus has a tropism for the uterus, whereas both pathogens thrive in the uterine environment early postpartum. Blood harbored a unique microbiome that contained the main uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium. The presence of these pathogens in blood shortly after calving shows the feasibility of hematogenous spread of uterine pathogens in cows.

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis).

PubMed

Ben Guerrero, Emiliano; Soria, Marcelo; Salvador, Ricardo; Ceja-Navarro, Javier A; Campos, Eleonora; Brodie, Eoin L; Talia, Paola

2016-01-01

Cotton boll weevils, Anthonomus grandis , are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis)

PubMed Central

Ben Guerrero, Emiliano; Soria, Marcelo; Salvador, Ricardo; Ceja-Navarro, Javier A.; Campos, Eleonora; Brodie, Eoin L.; Talia, Paola

2016-01-01

Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray–Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems. PMID:28082962

Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF.

PubMed

Sova, Matej; Kovac, Andreja; Turk, Samo; Hrast, Martina; Blanot, Didier; Gobec, Stanislav

2009-12-01

Enzymes involved in the biosynthesis of bacterial peptidoglycan represent important targets for development of new antibacterial drugs. Among them, Mur ligases (MurC to MurF) catalyze the formation of the final cytoplasmic precursor UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid. We present the design, synthesis and biological evaluation of a series of phosphorylated hydroxyethylamines as new type of small-molecule inhibitors of Mur ligases. We show that the phosphate group attached to the hydroxyl moiety of the hydroxyethylamine core is essential for good inhibitory activity. The IC(50) values of these inhibitors were in the micromolar range, which makes them a promising starting point for the development of multiple inhibitors of Mur ligases as potential antibacterial agents. In addition, 1-(4-methoxyphenylsulfonamido)-3-morpholinopropan-2-yl dihydrogen phosphate 7a was discovered as one of the best inhibitors of MurE described so far.

Structural differences in the bacterial flagellar motor among bacterial species.

PubMed

Terashima, Hiroyuki; Kawamoto, Akihiro; Morimoto, Yusuke V; Imada, Katsumi; Minamino, Tohru

2017-01-01

The bacterial flagellum is a supramolecular motility machine consisting of the basal body as a rotary motor, the hook as a universal joint, and the filament as a helical propeller. Intact structures of the bacterial flagella have been observed for different bacterial species by electron cryotomography and subtomogram averaging. The core structures of the basal body consisting of the C ring, the MS ring, the rod and the protein export apparatus, and their organization are well conserved, but novel and divergent structures have also been visualized to surround the conserved structure of the basal body. This suggests that the flagellar motors have adapted to function in various environments where bacteria live and survive. In this review, we will summarize our current findings on the divergent structures of the bacterial flagellar motor.

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability.

PubMed

Goldenzweig, Adi; Goldsmith, Moshe; Hill, Shannon E; Gertman, Or; Laurino, Paola; Ashani, Yacov; Dym, Orly; Unger, Tamar; Albeck, Shira; Prilusky, Jaime; Lieberman, Raquel L; Aharoni, Amir; Silman, Israel; Sussman, Joel L; Tawfik, Dan S; Fleishman, Sarel J

2016-07-21

Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic transmission, is a typical case of a human protein that necessitates mammalian systems to obtain functional expression. We developed a computational strategy and designed an AChE variant bearing 51 mutations that improved core packing, surface polarity, and backbone rigidity. This variant expressed at ∼2,000-fold higher levels in E. coli compared to wild-type hAChE and exhibited 20°C higher thermostability with no change in enzymatic properties or in the active-site configuration as determined by crystallography. To demonstrate broad utility, we similarly designed four other human and bacterial proteins. Testing at most three designs per protein, we obtained enhanced stability and/or higher yields of soluble and active protein in E. coli. Our algorithm requires only a 3D structure and several dozen sequences of naturally occurring homologs, and is available at http://pross.weizmann.ac.il. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China

PubMed Central

Chen, Yong; Li, Xiang-Kai; Si, Jing; Wu, Guang-Jian; Tian, Li-De; Xiang, Shu-Rong

2016-01-01

In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups. PMID:27847503

Characteristics of Pediatric Antimicrobial Stewardship Programs: Current Status of the Sharing Antimicrobial Reports for Pediatric Stewardship (SHARPS) Collaborative

PubMed Central

McPherson, Christopher; Lee, Brian R.; Terrill, Cindy; Hersh, Adam L.; Gerber, Jeffrey S.; Kronman, Matthew P.; Newland, Jason G.

2018-01-01

In response to the growing epidemic of antibiotic-resistant bacterial infections, antimicrobial stewardship programs (ASP) have been rapidly implemented in the United States (US). This study examines the prevalence of the Centers for Disease Control and Prevention’s (CDC) seven core elements of a successful ASP within a large subset of US Children’s Hospitals. In 2016, a survey was conducted of 52 pediatric hospitals assessing the presence of the seven core elements: leadership commitment, accountability, drug expertise, action, tracking, reporting, and education. Forty-nine hospitals (94%) had established ASPs and 41 hospitals (79%) included all seven core elements. Physician accountability (87%) and a dedicated ASP pharmacist or drug expert (88%) were present in the vast majority of hospitals. However, substantial variability existed in the financial support allotted to these positions. This variability did not predict program actions, tracking, reporting, and education. When compared with previous surveys, these results document a dramatic increase in the prevalence and resources of pediatric stewardship programs, although continued expansion is warranted. Further research is required to understand the feasibility of various core stewardship activities and the impact on patient outcomes in the setting of finite resources. PMID:29370071

Characteristics of Pediatric Antimicrobial Stewardship Programs: Current Status of the Sharing Antimicrobial Reports for Pediatric Stewardship (SHARPS) Collaborative.

PubMed

McPherson, Christopher; Lee, Brian R; Terrill, Cindy; Hersh, Adam L; Gerber, Jeffrey S; Kronman, Matthew P; Newland, Jason G

2018-01-25

In response to the growing epidemic of antibiotic-resistant bacterial infections, antimicrobial stewardship programs (ASP) have been rapidly implemented in the United States (US). This study examines the prevalence of the Centers for Disease Control and Prevention's (CDC) seven core elements of a successful ASP within a large subset of US Children's Hospitals. In 2016, a survey was conducted of 52 pediatric hospitals assessing the presence of the seven core elements: leadership commitment, accountability, drug expertise, action, tracking, reporting, and education. Forty-nine hospitals (94%) had established ASPs and 41 hospitals (79%) included all seven core elements. Physician accountability (87%) and a dedicated ASP pharmacist or drug expert (88%) were present in the vast majority of hospitals. However, substantial variability existed in the financial support allotted to these positions. This variability did not predict program actions, tracking, reporting, and education. When compared with previous surveys, these results document a dramatic increase in the prevalence and resources of pediatric stewardship programs, although continued expansion is warranted. Further research is required to understand the feasibility of various core stewardship activities and the impact on patient outcomes in the setting of finite resources.

Role of macropore flow in the transport of Escherichia coli cells in undisturbed cores of a brown leached soil.

PubMed

Martins, Jean M F; Majdalani, Samer; Vitorge, Elsa; Desaunay, Aurélien; Navel, Aline; Guiné, Véronique; Daïan, Jean François; Vince, Erwann; Denis, Hervé; Gaudet, Jean Paul

2013-02-01

The objective of this work was to evaluate the transport of Escherichia coli cells in undisturbed cores of a brown leached soil collected at La Côte St André (France). Two undisturbed soil cores subjected to repeated injections of bacterial cells and/or bromide tracer were used to investigate the effect of soil hydrodynamics and ionic strength on cell mobility. Under the tested experimental conditions, E. coli cells were shown to be transported at the water velocity (retardation factor close to 1) and their retention appeared almost insensitive to water flow and ionic strength variations, both factors being known to control bacterial transport in model saturated porous media. In contrast, E. coli breakthrough curves evolved significantly along with the repetition of the cell injections in each soil core, with a progressive acceleration of their transport. The evolution of E. coli cells BTCs was shown to be due to the evolution of the structure of soil hydraulic pathways caused by the repeated water infiltrations and drainage as may occur in the field. This evolution was demonstrated through mercury intrusion porosimetry (MIP) performed on soil aggregates before and after the repeated infiltrations of bacteria. MIP revealed a progressive and important reduction of the soil aggregate porosity, n, that decreased from approximately 0.5 to 0.3, along with a decrease of the soil percolating step from 27 to 2 μm. From this result a clear compaction of soil aggregates was evidenced that concerned preferentially the pores larger than 2 μm equivalent diameter, i.e. those allowing bacterial cell passage. Since no significant reduction of the global soil volume was observed at the core scale, this aggregate compaction was accompanied by macropore formation that became progressively the preferential hydraulic pathway in the soil cores, leading to transiently bi-modal bacterial BTCs. The evolution of the soil pore structure induced a modification of the main hydrodynamic processes, evolving from a matrix-dominant transfer of water and bacteria to a macropore-dominant transfer. This work points out the importance of using undisturbed natural soils to evaluate the mobility of bacteria in the field, since the evolving hydrodynamic properties of soils appeared to dominate most physicochemical factors.

The Effect of Lipopolysaccharide Core Oligosaccharide Size on the Electrostatic Binding of Antimicrobial Proteins to Models of the Gram Negative Bacterial Outer Membrane

PubMed Central

2016-01-01

Understanding the electrostatic interactions between bacterial membranes and exogenous proteins is crucial to designing effective antimicrobial agents against Gram-negative bacteria. Here we study, using neutron reflecometry under multiple isotopic contrast conditions, the role of the uncharged sugar groups in the outer core region of lipopolysaccharide (LPS) in protecting the phosphate-rich inner core region from electrostatic interactions with antimicrobial proteins. Models of the asymmetric Gram negative outer membrane on silicon were prepared with phopshatidylcholine (PC) in the inner leaflet (closest to the silicon), whereas rough LPS was used to form the outer leaflet (facing the bulk solution). We show how salt concentration can be used to reversibly alter the binding affinity of a protein antibiotic colicin N (ColN) to the anionic LPS confirming that the interaction is electrostatic in nature. By examining the interaction of ColN with two rough LPS types with different-sized core oligosaccharide regions we demonstrate the role of uncharged sugars in blocking short-range electrostatic interactions between the cationic antibiotics and the vulnerable anionic phosphate groups. PMID:27003358

The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331)

PubMed Central

Yanagawa, Katsunori; Nunoura, Takuro; McAllister, Sean M.; Hirai, Miho; Breuker, Anja; Brandt, Leah; House, Christopher H.; Moyer, Craig L.; Birrien, Jean-Louis; Aoike, Kan; Sunamura, Michinari; Urabe, Tetsuro; Mottl, Michael J.; Takai, Ken

2013-01-01

During the Integrated Ocean Drilling Program (IODP) Expedition 331 at the Iheya North hydrothermal system in the Mid-Okinawa Trough by the D/V Chikyu, we conducted microbiological contamination tests of the drilling and coring operations. The contamination from the drilling mud fluids was assessed using both perfluorocarbon tracers (PFT) and fluorescent microsphere beads. PFT infiltration was detected from the periphery of almost all whole round cores (WRCs). By contrast, fluorescent microspheres were not detected in hydrothermally active core samples, possibly due to thermal decomposition of the microspheres under high-temperature conditions. Microbial contamination from drilling mud fluids to the core interior subsamples was further characterized by molecular-based evaluation. The microbial 16S rRNA gene phylotype compositions in the drilling mud fluids were mainly composed of sequences of Beta- and Gammaproteobacteria, and Bacteroidetes and not archaeal sequences. The phylotypes that displayed more than 97% similarity to the sequences obtained from the drilling mud fluids were defined as possible contaminants in this study and were detected as minor components of the bacterial phylotype compositions in 13 of 37 core samples. The degree of microbiological contamination was consistent with that determined by the PFT and/or microsphere assessments. This study suggests a constructive approach for evaluation and eliminating microbial contamination during riser-less drilling and coring operations by the D/V Chikyu. PMID:24265628

The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331).

PubMed

Yanagawa, Katsunori; Nunoura, Takuro; McAllister, Sean M; Hirai, Miho; Breuker, Anja; Brandt, Leah; House, Christopher H; Moyer, Craig L; Birrien, Jean-Louis; Aoike, Kan; Sunamura, Michinari; Urabe, Tetsuro; Mottl, Michael J; Takai, Ken

2013-01-01

During the Integrated Ocean Drilling Program (IODP) Expedition 331 at the Iheya North hydrothermal system in the Mid-Okinawa Trough by the D/V Chikyu, we conducted microbiological contamination tests of the drilling and coring operations. The contamination from the drilling mud fluids was assessed using both perfluorocarbon tracers (PFT) and fluorescent microsphere beads. PFT infiltration was detected from the periphery of almost all whole round cores (WRCs). By contrast, fluorescent microspheres were not detected in hydrothermally active core samples, possibly due to thermal decomposition of the microspheres under high-temperature conditions. Microbial contamination from drilling mud fluids to the core interior subsamples was further characterized by molecular-based evaluation. The microbial 16S rRNA gene phylotype compositions in the drilling mud fluids were mainly composed of sequences of Beta- and Gammaproteobacteria, and Bacteroidetes and not archaeal sequences. The phylotypes that displayed more than 97% similarity to the sequences obtained from the drilling mud fluids were defined as possible contaminants in this study and were detected as minor components of the bacterial phylotype compositions in 13 of 37 core samples. The degree of microbiological contamination was consistent with that determined by the PFT and/or microsphere assessments. This study suggests a constructive approach for evaluation and eliminating microbial contamination during riser-less drilling and coring operations by the D/V Chikyu.

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

PubMed Central

Li, Fuyong

2017-01-01

ABSTRACT Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation. IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions. PMID:28235871

Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome

PubMed Central

Kellogg, Christina A.; Goldsmith, Dawn B.; Gray, Michael A.

2017-01-01

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4–V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75–96%). At the family level, 80–95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia, both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium, was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production. PMID:28522997

Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome.

PubMed

Kellogg, Christina A; Goldsmith, Dawn B; Gray, Michael A

2017-01-01

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa , a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4-V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75-96%). At the family level, 80-95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia , both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium , was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

Biogeographic comparison of Lophelia-associated bacterial communities in the Western Atlantic reveals conserved core microbiome

USGS Publications Warehouse

Kellogg, Christina A.; Goldsmith, Dawn; Gray, Michael A.

2017-01-01

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4–V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75–96%). At the family level, 80–95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia, both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium, was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

The development of permafrost bacterial communities under submarine conditions

NASA Astrophysics Data System (ADS)

Mitzscherling, Julia; Winkel, Matthias; Winterfeld, Maria; Horn, Fabian; Yang, Sizhong; Grigoriev, Mikhail N.; Wagner, Dirk; Overduin, Pier P.; Liebner, Susanne

2017-07-01

Submarine permafrost is more vulnerable to thawing than permafrost on land. Besides increased heat transfer from the ocean water, the penetration of salt lowers the freezing temperature and accelerates permafrost degradation. Microbial communities in thawing permafrost are expected to be stimulated by warming, but how they develop under submarine conditions is completely unknown. We used the unique records of two submarine permafrost cores from the Laptev Sea on the East Siberian Arctic Shelf, inundated about 540 and 2500 years ago, to trace how bacterial communities develop depending on duration of the marine influence and pore water chemistry. Combined with geochemical analysis, we quantified total cell numbers and bacterial gene copies and determined the community structure of bacteria using deep sequencing of the bacterial 16S rRNA gene. We show that submarine permafrost is an extreme habitat for microbial life deep below the seafloor with changing thermal and chemical conditions. Pore water chemistry revealed different pore water units reflecting the degree of marine influence and stages of permafrost thaw. Millennia after inundation by seawater, bacteria stratify into communities in permafrost, marine-affected permafrost, and seabed sediments. In contrast to pore water chemistry, the development of bacterial community structure, diversity, and abundance in submarine permafrost appears site specific, showing that both sedimentation and permafrost thaw histories strongly affect bacteria. Finally, highest microbial abundance was observed in the ice-bonded seawater unaffected but warmed permafrost of the longer inundated core, suggesting that permafrost bacterial communities exposed to submarine conditions start to proliferate millennia after warming.

Bacterial formate hydrogenlyase complex.

PubMed

McDowall, Jennifer S; Murphy, Bonnie J; Haumann, Michael; Palmer, Tracy; Armstrong, Fraser A; Sargent, Frank

2014-09-23

Under anaerobic conditions, Escherichia coli can carry out a mixed-acid fermentation that ultimately produces molecular hydrogen. The enzyme directly responsible for hydrogen production is the membrane-bound formate hydrogenlyase (FHL) complex, which links formate oxidation to proton reduction and has evolutionary links to Complex I, the NADH:quinone oxidoreductase. Although the genetics, maturation, and some biochemistry of FHL are understood, the protein complex has never been isolated in an intact form to allow biochemical analysis. In this work, genetic tools are reported that allow the facile isolation of FHL in a single chromatographic step. The core complex is shown to comprise HycE (a [NiFe] hydrogenase component termed Hyd-3), FdhF (the molybdenum-dependent formate dehydrogenase-H), and three iron-sulfur proteins: HycB, HycF, and HycG. A proportion of this core complex remains associated with HycC and HycD, which are polytopic integral membrane proteins believed to anchor the core complex to the cytoplasmic side of the membrane. As isolated, the FHL complex retains formate hydrogenlyase activity in vitro. Protein film electrochemistry experiments on Hyd-3 demonstrate that it has a unique ability among [NiFe] hydrogenases to catalyze production of H2 even at high partial pressures of H2. Understanding and harnessing the activity of the FHL complex is critical to advancing future biohydrogen research efforts.

Energy transfer in light-adapted photosynthetic membranes: from active to saturated photosynthesis.

PubMed

Fassioli, Francesca; Olaya-Castro, Alexandra; Scheuring, Simon; Sturgis, James N; Johnson, Neil F

2009-11-04

In bacterial photosynthesis light-harvesting complexes, LH2 and LH1 absorb sunlight energy and deliver it to reaction centers (RCs) with extraordinarily high efficiency. Submolecular resolution images have revealed that both the LH2:LH1 ratio, and the architecture of the photosynthetic membrane itself, adapt to light intensity. We investigate the functional implications of structural adaptations in the energy transfer performance in natural in vivo low- and high-light-adapted membrane architectures of Rhodospirillum photometricum. A model is presented to describe excitation migration across the full range of light intensities that cover states from active photosynthesis, where all RCs are available for charge separation, to saturated photosynthesis where all RCs are unavailable. Our study outlines three key findings. First, there is a critical light-energy density, below which the low-light adapted membrane is more efficient at absorbing photons and generating a charge separation at RCs, than the high-light-adapted membrane. Second, connectivity of core complexes is similar in both membranes, suggesting that, despite different growth conditions, a preferred transfer pathway is through core-core contacts. Third, there may be minimal subareas on the membrane which, containing the same LH2:LH1 ratio, behave as minimal functional units as far as excitation transfer efficiency is concerned.

Advanced Copper Composites Against Copper-Tolerant Xanthomonas perforans and Tomato Bacterial Spot.

PubMed

Strayer-Scherer, A; Liao, Y Y; Young, M; Ritchie, L; Vallad, G E; Santra, S; Freeman, J H; Clark, D; Jones, J B; Paret, M L

2018-02-01

Bacterial spot, caused by Xanthomonas spp., is a widespread and damaging bacterial disease of tomato (Solanum lycopersicum). For disease management, growers rely on copper bactericides, which are often ineffective due to the presence of copper-tolerant Xanthomonas strains. This study evaluated the antibacterial activity of the new copper composites core-shell copper (CS-Cu), multivalent copper (MV-Cu), and fixed quaternary ammonium copper (FQ-Cu) as potential alternatives to commercially available micron-sized copper bactericides for controlling copper-tolerant Xanthomonas perforans. In vitro, metallic copper from CS-Cu and FQ-Cu at 100 μg/ml killed the copper-tolerant X. perforans strain within 1 h of exposure. In contrast, none of the micron-sized copper rates (100 to 1,000 μg/ml) from Kocide 3000 significantly reduced copper-tolerant X. perforans populations after 48 h of exposure compared with the water control (P < 0.05). All copper-based treatments killed the copper-sensitive X. perforans strain within 1 h. Greenhouse studies demonstrated that all copper composites significantly reduced bacterial spot disease severity when compared with copper-mancozeb and water controls (P < 0.05). Although there was no significant impact on yield, copper composites significantly reduced disease severity when compared with water controls, using 80% less metallic copper in comparison with copper-mancozeb in field studies (P < 0.05). This study highlights the discovery that copper composites have the potential to manage copper-tolerant X. perforans and tomato bacterial spot.

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

PubMed Central

Lambowitz, Alan M.; Belfort, Marlene

2015-01-01

SUMMARY This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome’s small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns. PMID:25878921

Endoribonuclease type II toxin-antitoxin systems: functional or selfish?

PubMed

Ramisetty, Bhaskar Chandra Mohan; Santhosh, Ramachandran Sarojini

2017-07-01

Most bacterial genomes have multiple type II toxin-antitoxin systems (TAs) that encode two proteins which are referred to as a toxin and an antitoxin. Toxins inhibit a cellular process, while the interaction of the antitoxin with the toxin attenuates the toxin's activity. Endoribonuclease-encoding TAs cleave RNA in a sequence-dependent fashion, resulting in translational inhibition. To account for their prevalence and retention by bacterial genomes, TAs are credited with clinically significant phenomena, such as bacterial programmed cell death, persistence, biofilms and anti-addiction to plasmids. However, the programmed cell death and persistence hypotheses have been challenged because of conceptual, methodological and/or strain issues. In an alternative view, chromosomal TAs seem to be retained by virtue of addiction at two levels: via a poison-antidote combination (TA proteins) and via transcriptional reprogramming of the downstream core gene (due to integration). Any perturbation in the chromosomal TA operons could cause fitness loss due to polar effects on the downstream genes and hence be detrimental under natural conditions. The endoribonucleases encoding chromosomal TAs are most likely selfish DNA as they are retained by bacterial genomes, even though TAs do not confer a direct advantage via the TA proteins. TAs are likely used by various replicons as 'genetic arms' that allow the maintenance of themselves and associated genetic elements. TAs seem to be the 'selfish arms' that make the best use of the 'arms race' between bacterial genomes and plasmids.

Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.

PubMed

von der Weid, Irene; Korenblum, Elisa; Jurelevicius, Diogo; Rosado, Alexandre Soares; Dino, Rodolfo; Sebastian, Gina Vasquez; Seldin, Lucy

2008-01-01

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

Succession of bacterial and fungal communities within biofilms of a chlorinated drinking water distribution system.

PubMed

Douterelo, I; Fish, K E; Boxall, J B

2018-09-15

Understanding the temporal dynamics of multi-species biofilms in Drinking Water Distribution Systems (DWDS) is essential to ensure safe, high quality water reaches consumers after it passes through these high surface area reactors. This research studied the succession characteristics of fungal and bacterial communities under controlled environmental conditions fully representative of operational DWDS. Microbial communities were observed to increase in complexity after one month of biofilm development but they did not reach stability after three months. Changes in cell numbers were faster at the start of biofilm formation and tended to decrease over time, despite the continuing changes in bacterial community composition. Fungal diversity was markedly less than bacterial diversity and had a lag in responding to temporal dynamics. A core-mixed community of bacteria including Pseudomonas, Massillia and Sphingomonas and the fungi Acremonium and Neocosmopora were present constantly and consistently in the biofilms over time and conditions studied. Monitoring and managing biofilms and such ubiquitous core microbial communities are key control strategies to ensuring the delivery of safe drinking water via the current ageing DWDS infrastructure. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

A core gut microbiome in obese and lean twins.

PubMed

Turnbaugh, Peter J; Hamady, Micah; Yatsunenko, Tanya; Cantarel, Brandi L; Duncan, Alexis; Ley, Ruth E; Sogin, Mitchell L; Jones, William J; Roe, Bruce A; Affourtit, Jason P; Egholm, Michael; Henrissat, Bernard; Heath, Andrew C; Knight, Rob; Gordon, Jeffrey I

2009-01-22

The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

PubMed Central

Nowell, Reuben W.; Green, Sarah; Laue, Bridget E.; Sharp, Paul M.

2014-01-01

Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages. PMID:24923323

Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes.

PubMed

Dilucca, Maddalena; Cimini, Giulio; Giansanti, Andrea

2018-07-15

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli, we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development.

PubMed

Anderson, Kirk E; Rodrigues, Pedro A P; Mott, Brendon M; Maes, Patrick; Corby-Harris, Vanessa

2016-05-01

In many vertebrates, social interactions and nutrition can affect the colonization of gut symbionts across generations. In the highly social honey bee, it is unknown to what extent the hive environment and older worker individuals contribute to the generational transmission of core gut bacteria. We used high-throughput sequencing to investigate the effect of nest materials and social contact on the colonization and succession of core hindgut microbiota in workers. With only brief exposure to hive materials following natural eclosion, gut bacterial communities at 3 and 7 days contained phylotypes typically found in the guts of mature adults regardless of treatment. Continuous exposure to nest materials or direct social interactions with mature adults did not affect the diversity or abundance of gut bacterial communities at the scale examined. Similarly, a common pollen supplement fed by beekeepers during pollen dearth had no effect. A consideration of unique OTUs revealed extensive microbial succession independent of treatment. The dominant Lactobacillus strain at 3 days was largely replaced by a different strain at day 7, revealing the colonization signature of a pioneer species. Similar but less pronounced patterns were evident in less abundant OTU's, many of which may influence community succession via alteration of the gut environment. Our results indicate that the process of bacterial community colonization in the hindgut is resilient to changes in the nutritional, hive, and social environment. Greater taxonomic resolution is needed to accurately resolve questions of ecological succession and typical proportional variation within and between core members of the gut bacterial community.

[Correlation of infection with the physical and chemical characteristics of gall bladder contents].

PubMed

Sulaberidze, G T; Rachvelishvili, B Kh; Gelbakhiani, G P; Barbakadze, G G; Kapanadze, A G

2005-06-01

The aim of the study was to investigate pH and viscosity (h) of gall bladder contents during cholelithiasis and establishment of their correlation with bacterial and HBV infections. Seventy-eight patients undergone the planned cholecystectomy were investigated. 5 healthy persons (control group) were also involved into the study. In all cases the markers of HBV (Anti-HB core IgG, Anti-HB core IgM, HBsAg) in blood were detected, also bacteriological analysis of gall bladder tissue was performed. In 78 cases (I group) pH of gall bladder contents was measured, in 29 cases (II group), also viscosity of gall was studied. In the control group pH and viscosity were detected. Statistical analysis was performed using ANOVA method. Bacteriological study revealed presence of bacterial infection in gall bladder tissue in 34 cases (43,6%), in 30 patients Anti-HB core antibodies were found in the blood, in 13 cases (16,7%) coincidence of bacterial and HBV infection was documented. Mean indexes of pH and viscosity appeared to be significantly higher in the operated group (pH--7,30, h 2,1 mm(2)/sec), then in the control group (pH--6,74, h--1,34 mm(2)/sec); this indexes were highest in the infected patients. Thus, according to results of the study, changes of pH and viscosity of gall bladder contents could be considered as the useful indexes of initial stage of cholelithiasis and their values depend on the presence of bacterial or HBV infection of gall bladder.

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring

PubMed Central

Miller, Carolyn A.; Moore, Michael J.; Durban, John W.; Fearnbach, Holly; Barrett-Lennard, Lance G.

2017-01-01

ABSTRACT The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide. PMID:29034331

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring.

PubMed

Apprill, Amy; Miller, Carolyn A; Moore, Michael J; Durban, John W; Fearnbach, Holly; Barrett-Lennard, Lance G

2017-01-01

The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales ( Megaptera novaeangliae ), sampled in the Massachusetts coastal waters off Cape Cod ( n = 17) and coastal waters around Vancouver Island ( n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.

A structural role for the PHP domain in E. coli DNA polymerase III

PubMed Central

2013-01-01

Background In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Results Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. Conclusions While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase. PMID:23672456

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate.

PubMed

Barnard, Romain L; Osborne, Catherine A; Firestone, Mary K

2015-03-17

A large soil CO2 pulse is associated with rewetting soils after the dry summer period under a Mediterranean-type climate, significantly contributing to grasslands' annual carbon budget. Rapid reactivation of soil heterotrophs and a pulse of available carbon are both required to fuel the CO2 pulse. Understanding of the effects of altered summer precipitation on the metabolic state of indigenous microorganisms may be important in predicting changes in carbon cycling. Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event, by following the present (DNA-based) and potentially active (rRNA-based) soil bacterial and fungal communities in intact soil cores (from a California annual grassland) previously subjected to three different precipitation patterns over 4 months (full summer dry season, extended wet season and absent dry season). Phylogenetic marker genes for bacteria and fungi were sequenced before and after rewetting, and the abundance of these genes and transcripts was measured. After having experienced markedly different antecedent water conditions, the potentially active bacterial communities showed a consistent wet-up response. We found a significant positive relation between the extent of change in the structure of the potentially active bacterial community and the magnitude of the CO2 pulse upon rewetting dry soils. We suggest that the duration of severe dry summer conditions characteristic of the Mediterranean climate is important in conditioning the response potential of the soil microbial community to wet-up as well as in framing the magnitude of the associated CO2 pulse.

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

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

Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J. P.

Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulicmore » conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112-120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ 13C values (-67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ 13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO 3 -, or SO 4 2-. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situ bacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down hydrocarbons. As a result, identifying microorganisms involved in coal degradation and the ydrogeochemical conditions that promote their activity is crucial to understanding and improving in situ CBM production.« less

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

DOE PAGES

Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J. P.; ...

2016-05-04

Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulicmore » conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112-120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ 13C values (-67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ 13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO 3 -, or SO 4 2-. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situ bacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down hydrocarbons. As a result, identifying microorganisms involved in coal degradation and the ydrogeochemical conditions that promote their activity is crucial to understanding and improving in situ CBM production.« less

Discovery of MK-7655, a β-lactamase inhibitor for combination with Primaxin®

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

Blizzard, Timothy A.; Chen, Helen; Kim, Seongkon

2014-02-01

β-Lactamase inhibitors with a bicyclic urea core and a variety of heterocyclic side chains were prepared and evaluated as potential partners for combination with imipenem to overcome class A and C β-lactamase mediated antibiotic resistance. The piperidine analog 3 (MK-7655) inhibited both class A and C β-lactamases in vitro. It effectively restored imipenem’s activity against imipenem-resistant Pseudomonas and Klebsiella strains at clinically achievable concentrations. A combination of MK-7655 and Primaxin® is currently in phase II clinical trials for the treatment of Gram-negative bacterial infections.

An environmentally benign antimicrobial nanoparticle based ...

EPA Pesticide Factsheets

Silver nanoparticles have antibacterial properties but their use has been a cause for concern because they persist in the environment. Here we show that lignin nanoparticles infused with silver ions and coated with a cationic polyelectrolyte layer form a biodegradable and green alternative to silver nanoparticles. The polyelectrolyte layer promotes the adhesion of the particles to bacterial cell membranes and together with silver ions can kill a broad spectrum of bacteria, including Escherichia coli, Pseudomonas aeruginosa and quaternary-amine-resistant Ralstonia sp. Ion depletion studies showed that the bioactivity of these nanoparticles is time-limited because of the desorption of silver ions. High-throughput bioactivity screening did not reveal increased toxicity of the particles when compared to an equivalent mass of metallic silver nanoparticles or silver nitrate solution. Our results demonstrate that the application of green chemistry principles may allow the synthesis of nanoparticles with biodegradable cores that have higher antimicrobial activity and smaller environmental impact than metallic silver nanoparticles. Our results demonstrate that the application of green chemistry principles may allow the synthesis of nanoparticles with biodegradable cores that have higher antimicrobial activity and smaller environmental impact than metallic silver nanoparticles

Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs

PubMed Central

Merritt, Ethan A; Arakaki, Tracy L; Gillespie, J Robert; Larson, Eric T; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J; Kim, Jessica; Zhang, Li; Verlinde, Christophe L M J; Fan, Erkang; Zucker, Frank; Buckner, Frederick S; Van Voorhis, Wesley C; Hol, Wim G J

2010-01-01

Crystal structures of histidyl-tRNA synthetase from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme, and reveal differences from bacterial homologs. Histidyl-tRNA synthetases in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active site rearrangement upon histidine binding, but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme’s first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human histidyl-tRNA synthetases. The essentiality of the single histidyl-tRNA synthetase gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference. PMID:20132829

Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

NASA Astrophysics Data System (ADS)

Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

2015-12-01

Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi Canyon 118 before the Deepwater Horizon disaster

NASA Astrophysics Data System (ADS)

Underwood, Sarah; Lapham, Laura; Teske, Andreas; Lloyd, Karen G.

2016-07-01

The Deepwater Horizon disaster caused a shift in microbial communities in Gulf of Mexico seawater, but less is known about the baseline for microbial communities in the underlying sediments. We compared 16S rRNA and functional gene sequences deriving from DNA and RNA with geochemical profiles (sulfate and methane concentrations, δ13C of methane and carbon dioxide, and chloride concentrations) of a sediment gravity core from the upper continental slope of the northwestern Gulf of Mexico (MC118) in 2008, 15 km from the spill site. The highest number of archaeal sequences were ANME-1 and ANME-2 archaea in the sulfate-reducing upper core segments (12 and 42 cmbsf), ANME-1 and Methanomicrobiales in the middle methanogenic depths (200 and 235 cmbsf), and ANME-1 at the deepest depths (309, 400, and 424 cmbsf). The presence of mcrA gene transcripts showed that members of the ANME-1 group are active throughout the core and transcribe the mcrA gene, a key gene of methanogenesis and anaerobic methane oxidation. The bacterial community consists mostly of members of the Deltaproteobacteria, Chloroflexi, Cytophaga, Epsilonproteobacteria, and the Japan Sea Group 1 throughout the core. The commonly detected genera of gammaproteobacterial hydrocarbon-degrading bacteria in the water column are not found in this sediment survey, indicating that the benthic sediment is an unlikely reservoir for these aerobes. However, the sediments contain members of the sulfate-reducing families Desulfobulbaceae and Desulfobacteraceae, some members of which degrade and completely oxidize aromatic hydrocarbons and alkanes, and the Desulfobacterium anilini lineage of obligately aromatics-degrading sulfate reducers. Thus, the benthic sediments are the most likely reservoir for the active deltaproteobacterial populations that were observed repeatedly after the Deepwater Horizon spill in the fall of 2010.

Bacteriological evaluation of tonsillar microbial flora according to age and tonsillar size in recurrent tonsillitis.

PubMed

Develioglu, Omer Necati; Ipek, Havva Duru; Bahar, Hrisi; Can, Gunay; Kulekci, Mehmet; Aygun, Gokhan

2014-06-01

Although numerous studies based on the bacteriology of the tonsil have been carried out, none of them analyzed the variation of tonsillar flora with respect to both age and tonsillar size. The purpose of this study was to isolate the facultative and obligate anaerobes both from the surface and the core of tonsils in recurrent tonsillitis as well as to analyze the variation of isolated bacterial strains according to age and tonsillar size. A prospective study was performed on 111 patients who underwent tonsillectomy. We analyzed the differences between the bacterial pathogens in recurrent tonsillitis and semi-growth estimates with regard to age and tonsillar grade. Among 111 cases, 604 bacterial strains of 21 different from the tonsil superficial and core were isolated. The most common facultative anaerobic species isolated from the surface and core were Coagulase-negative staphylococci, Alpha-hemolytic streptococci and Diphtheroid bacilli in all subgroups except patients below 8 years old. The most commonly obligate anaerobic species isolated from the core were Propionibacterium acnes, Prevotella melaninogenica and Peptostreptococcus anaerobius. We found no significant difference in the cultured bacteria with respect to age and tonsillar size. The study subgroups did not differ in the occurrence of semiquantitative growth estimates of 3-4+. Our study demonstrates that there is polymicrobial aerobic and anaerobic flora in tonsils with regardless of patient's age and tonsillar size. This polymicrobial spectrum of bacteria may contribute to recurrence and to the failure of conservative treatment of these cases and therefore leads to surgical therapy.

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

PubMed Central

Callister, Stephen J.; McCue, Lee Ann; Turse, Joshua E.; Monroe, Matthew E.; Auberry, Kenneth J.; Smith, Richard D.; Adkins, Joshua N.; Lipton, Mary S.

2008-01-01

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits. PMID:18253490

Tailor-made Au@Ag core-shell nanoparticle 2D arrays on protein-coated graphene oxide with assembly enhanced antibacterial activity

NASA Astrophysics Data System (ADS)

Wang, Huiqiao; Liu, Jinbin; Wu, Xuan; Tong, Zhonghua; Deng, Zhaoxiang

2013-05-01

Water-dispersible two-dimensional (2D) assemblies of Au@Ag core-shell nanoparticles are obtained through a highly selective electroless silver deposition on pre-assembled gold nanoparticles on bovine serum albumin (BSA)-coated graphene oxide (BSA-GO). While neither BSA-GO nor AuNP-decorated BSA-GO shows any antibacterial ability, the silver-coated GO@Au nanosheets (namely GO@Au@Ag) exhibit an enhanced antibacterial activity against Gram-negative Escherichia coli (E. coli) bacteria, superior to unassembled Au@Ag nanoparticles and even ionic Ag. Such an improvement may be attributed to the increased local concentration of silver nanoparticles around a bacterium and a polyvalent interaction with the bacterial surface. In addition, the colloidal stability of this novel nano-antimicrobial against the formation of random nanoparticle aggregates guarantees a minimized activity loss of the Au@Ag nanoparticles. The antibacterial efficacy of GO@Au@Ag is less sensitive to the existence of Cl-, in comparison with silver ions, providing another advantage for wound dressing applications. Our research unambiguously reveals a strong and very specific interaction between the GO@Au@Ag nanoassembly and E. coli, which could be an important clue toward a rational design, synthesis and assembly of innovative and highly active antibacterial nanomaterials.

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period

PubMed Central

Postec, Anne; Quéméneur, Marianne; Bes, Méline; Mei, Nan; Benaïssa, Fatma; Payri, Claude; Pelletier, Bernard; Monnin, Christophe; Guentas-Dombrowsky, Linda; Ollivier, Bernard; Gérard, Emmanuelle; Pisapia, Céline; Gérard, Martine; Ménez, Bénédicte; Erauso, Gaël

2015-01-01

Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems. PMID:26379636

Kinetic and structural requirements for carbapenemase activity in GES-type β-lactamases

DOE PAGES

Stewart, Nichole K.; Smith, Clyde A.; Frase, Hilary; ...

2014-12-08

Carbapenems are the last resort antibiotics for treatment of life-threatening infections. The GES β-lactamases are important contributors to carbapenem resistance in clinical bacterial pathogens. A single amino acid difference at position 170 of the GES-1, GES-2, and GES-5 enzymes is responsible for the expansion of their substrate profile to include carbapenem antibiotics. This highlights the increasing need to understand the mechanisms by which the GES β-lactamases function to aid in development of novel therapeutics. We demonstrate that the catalytic efficiency of the enzymes with carbapenems meropenem, ertapenem, and doripenem progressively increases (100-fold) from GES-1 to -5, mainly due to anmore » increase in the rate of acylation. The data reveal that while acylation is rate limiting for GES-1 and GES-2 for all three carbapenems, acylation and deacylation are indistinguishable for GES-5. The ertapenem–GES-2 crystal structure shows that only the core structure of the antibiotic interacts with the active site of the GES-2 β-lactamase. The identical core structures of ertapenem, doripenem, and meropenem are likely responsible for the observed similarities in the kinetics with these carbapenems. The lack of a methyl group in the core structure of imipenem may provide a structural rationale for the increase in turnover of this carbapenem by the GES β-lactamases. As a result, our data also show that in GES-2 an extensive hydrogen-bonding network between the acyl-enzyme complex and the active site water attenuates activation of this water molecule, which results in poor deacylation by this enzyme.« less

Nitrogen loss by anaerobic ammonium oxidation in unconfined aquifer soils

NASA Astrophysics Data System (ADS)

Wang, Shanyun; Radny, Dirk; Huang, Shuangbing; Zhuang, Linjie; Zhao, Siyan; Berg, Michael; Jetten, Mike S. M.; Zhu, Guibing

2017-01-01

Anaerobic ammonium oxidation (anammox) is recognized as an important process for nitrogen cycling, yet little is known about its role in the subsurface biosphere. In this study, we investigated the presence, abundance, and role of anammox bacteria in upland soil cores from Tianjin, China (20 m depth) and Basel, Switzerland (10 m depth), using isotope-tracing techniques, (q)PCR assays, and 16 S rRNA & hzsB gene clone libraries, along with nutrient profiles of soil core samples. Anammox in the phreatic (water-saturated) zone contributed to 37.5-67.6% of the N-loss (up to 0.675 gN m-2 d-1), with anammox activities of 0.005-0.74 nmolN g-1 soil h-1, which were even higher than the denitrification rates. By contrast, no significant anammox was measured in the vadose zone. Higher anammox bacterial cell densities were observed (0.75-1.4 × 107 copies g-1 soil) in the phreatic zone, where ammonia-oxidizing bacteria (AOB) maybe the major source of nitrite for anammox bacteria. The anammox bacterial cells in soils of the vadose zone were all <103 copies g-1 soil. We suggest that the subsurface provides a favorable niche for anammox bacteria whose contribution to N cycling and groundwater nitrate removal seems considerably larger than previously known.

Nitrogen loss by anaerobic ammonium oxidation in unconfined aquifer soils

PubMed Central

Wang, Shanyun; Radny, Dirk; Huang, Shuangbing; Zhuang, Linjie; Zhao, Siyan; Berg, Michael; Jetten, Mike S. M.; Zhu, Guibing

2017-01-01

Anaerobic ammonium oxidation (anammox) is recognized as an important process for nitrogen cycling, yet little is known about its role in the subsurface biosphere. In this study, we investigated the presence, abundance, and role of anammox bacteria in upland soil cores from Tianjin, China (20 m depth) and Basel, Switzerland (10 m depth), using isotope-tracing techniques, (q)PCR assays, and 16 S rRNA & hzsB gene clone libraries, along with nutrient profiles of soil core samples. Anammox in the phreatic (water-saturated) zone contributed to 37.5–67.6% of the N-loss (up to 0.675 gN m−2 d−1), with anammox activities of 0.005–0.74 nmolN g−1 soil h−1, which were even higher than the denitrification rates. By contrast, no significant anammox was measured in the vadose zone. Higher anammox bacterial cell densities were observed (0.75–1.4 × 107 copies g−1 soil) in the phreatic zone, where ammonia-oxidizing bacteria (AOB) maybe the major source of nitrite for anammox bacteria. The anammox bacterial cells in soils of the vadose zone were all <103 copies g−1 soil. We suggest that the subsurface provides a favorable niche for anammox bacteria whose contribution to N cycling and groundwater nitrate removal seems considerably larger than previously known. PMID:28071702

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PubMed Central

Brown, Tanya; Otero, Christopher; Grajales, Alejandro; Rodriguez, Estefania

2017-01-01

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind. PMID:28533949

H-NS regulates the Vibrio parahaemolyticus type VI secretion system 1

PubMed Central

Salomon, Dor; Klimko, John A.

2014-01-01

The marine bacterium Vibrio parahaemolyticus, a major cause of food-borne gastroenteritis, employs a type VI secretion system 1 (T6SS1), a recently discovered protein secretion system, to combat competing bacteria. Environmental signals such as temperature, salinity, cell density and surface sensing, as well as the quorum-sensing master regulator OpaR, were previously reported to regulate T6SS1 activity and expression. In this work, we set out to identify additional transcription regulators that control the tightly regulated T6SS1 activity. To this end, we determined the effect of deletions in several known virulence regulators and in two regulators encoded within the T6SS1 gene cluster on expression and secretion of the core T6SS component Hcp1 and on T6SS1-mediated anti-bacterial activity. We report that VP1391 and VP1407, transcriptional regulators encoded within the T6SS1 gene cluster, are essential for T6SS1 activity. Moreover, we found that H-NS, a bacterial histone-like nucleoid structuring protein, which mediates transcription silencing of horizontally acquired genes, serves as a repressor of T6SS1. We also show that activation of surface sensing and high salt conditions alleviate the H-NS-mediated repression. Our results shed light on the complex network of environmental signals and transcription regulators that govern the tight regulation over T6SS1 activity. PMID:24987102

Distance-Dependent Plasmon-Enhanced Singlet Oxygen Production and Emission for Bacterial Inactivation.

PubMed

Planas, Oriol; Macia, Nicolas; Agut, Montserrat; Nonell, Santi; Heyne, Belinda

2016-03-02

Herein, we synthesized a series of 10 core-shell silver-silica nanoparticles with a photosensitizer, Rose Bengal, tethered to their surface. Each nanoparticle possesses an identical silver core of about 67 nm, but presents a different silica shell thickness ranging from 5 to 100 nm. These hybrid plasmonic nanoparticles thus afford a plasmonic nanostructure platform with a source of singlet oxygen ((1)O2) at a well-defined distance from the metallic core. Via time-resolved and steady state spectroscopic techniques, we demonstrate the silver core exerts a dual role of enhancing both the production of (1)O2, through enhanced absorption of light, and its radiative decay, which in turn boosts (1)O2 phosphorescence emission to a greater extent. Furthermore, we show both the production and emission of (1)O2 in vitro to be dependent on proximity to the plasmonic nanostructure. Our results clearly exhibit three distinct regimes as the plasmonic nanostructure moves apart from the (1)O2 source, with a greater enhancement for silica shell thicknesses ranging between 10 and 20 nm. Moreover, these hybrid plasmonic nanoparticles can be delivered to both Gram-positive and Gram-negative bacteria boosting both photoantibacterial activity and detection limit of (1)O2 in cells.

Construction of hybrid photosynthetic units using peripheral and core antennae from two different species of photosynthetic bacteria: detection of the energy transfer from bacteriochlorophyll a in LH2 to bacteriochlorophyll b in LH1.

PubMed

Fujii, Ritsuko; Shimonaka, Shozo; Uchida, Naoko; Gardiner, Alastair T; Cogdell, Richard J; Sugisaki, Mitsuru; Hashimoto, Hideki

2008-01-01

Typical purple bacterial photosynthetic units consist of supra-molecular arrays of peripheral (LH2) and core (LH1-RC) antenna complexes. Recent atomic force microscopy pictures of photosynthetic units in intact membranes have revealed that the architecture of these units is variable (Scheuring et al. (2005) Biochim Bhiophys Acta 1712:109-127). In this study, we describe methods for the construction of heterologous photosynthetic units in lipid-bilayers from mixtures of purified LH2 (from Rhodopseudomonas acidophila) and LH1-RC (from Rhodopseudomonas viridis) core complexes. The architecture of these reconstituted photosynthetic units can be varied by controlling ratio of added LH2 to core complexes. The arrangement of the complexes was visualized by electron-microscopy in combination with Fourier analysis. The regular trigonal array of the core complexes seen in the native photosynthetic membrane could be regenerated in the reconstituted membranes by temperature cycling. In the presence of added LH2 complexes, this trigonal symmetry was replaced with orthorhombic symmetry. The small lattice lengths for the latter suggest that the constituent unit of the orthorhombic lattice is the LH2. Fluorescence and fluorescence-excitation spectroscopy was applied to the set of the reconstituted membranes prepared with various proportions of LH2 to core complexes. Remarkably, even though the LH2 complexes contain bacteriochlorophyll a, and the core complexes contain bacteriochlorophyll b, it was possible to demonstrate energy transfer from LH2 to the core complexes. These experiments provide a first step along the path toward investigating how changing the architecture of purple bacterial photosynthetic units affects the overall efficiency of light-harvesting.

Nanoparticle (star polymer) delivery of nitric oxide effectively negates Pseudomonas aeruginosa biofilm formation.

PubMed

Duong, Hien T T; Jung, Kenward; Kutty, Samuel K; Agustina, Sri; Adnan, Nik Nik M; Basuki, Johan S; Kumar, Naresh; Davis, Thomas P; Barraud, Nicolas; Boyer, Cyrille

2014-07-14

Biofilms are increasingly recognized as playing a major role in human infectious diseases, as they can form on both living tissues and abiotic surfaces, with serious implications for applications that rely on prolonged exposure to the body such as implantable biomedical devices or catheters. Therefore, there is an urgent need to develop improved therapeutics to effectively eradicate unwanted biofilms. Recently, the biological signaling molecule nitric oxide (NO) was identified as a key regulator of dispersal events in biofilms. In this paper, we report a new class of core cross-linked star polymers designed to store and release nitric oxide, in a controlled way, for the dispersion of biofilms. First, core cross-linked star polymers were prepared by reversible addition-fragmentation chain transfer polymerization (RAFT) via an arm first approach. Poly(oligoethylene methoxy acrylate) chains were synthesized by RAFT polymerization, and then chain extended in the presence of 2-vinyl-4,4-dimethyl-5-oxazolone monomer (VDM) with N,N-methylenebis(acrylamide) employed as a cross-linker to yield functional core cross-linked star polymers. Spermine was successfully attached to the star core by reaction with VDM. Finally, the secondary amine groups were reacted with NO gas to yield NO-core cross-linked star polymers. The core cross-linked star polymers were found to release NO in a controlled, slow delivery in bacterial cultures showing great efficacy in preventing both cell attachment and biofilm formation in Pseudomonas aeruginosa over time via a nontoxic mechanism, confining bacterial growth to the suspended liquid.

Identifying the core microbial community in the gut of fungus-growing termites.

PubMed

Otani, Saria; Mikaelyan, Aram; Nobre, Tânia; Hansen, Lars H; Koné, N'Golo A; Sørensen, Søren J; Aanen, Duur K; Boomsma, Jacobus J; Brune, Andreas; Poulsen, Michael

2014-09-01

Gut microbes play a crucial role in decomposing lignocellulose to fuel termite societies, with protists in the lower termites and prokaryotes in the higher termites providing these services. However, a single basal subfamily of the higher termites, the Macrotermitinae, also domesticated a plant biomass-degrading fungus (Termitomyces), and how this symbiont acquisition has affected the fungus-growing termite gut microbiota has remained unclear. The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. Using 454-pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes. A set of 42 genus-level taxa was present in all termite species and accounted for 56-68% of the species-specific reads. Gut communities of termites from the same genus were more similar than distantly related species, suggesting that phylogenetic ancestry matters, possibly in connection with specific termite genus-level ecological niches. Finally, we show that gut communities of fungus-growing termites are similar to cockroaches, both at the bacterial phylum level and in a comparison of the core Macrotermitinae taxa abundances with representative cockroach, lower termite and higher nonfungus-growing termites. These results suggest that the obligate association with Termitomyces has forced the bacterial gut communities of the fungus-growing termites towards a relatively uniform composition with higher similarity to their omnivorous relatives than to more closely related termites. © 2014 John Wiley & Sons Ltd.

The nature of water within bacterial spores: protecting life in extreme environments

NASA Astrophysics Data System (ADS)

Rice, Charles V.; Friedline, Anthony; Johnson, Karen; Zachariah, Malcolm M.; Thomas, Kieth J., III

2011-10-01

The bacterial spore is a formidable container of life, protecting the vital contents from chemical attack, antimicrobial agents, heat damage, UV light degradation, and water dehydration. The exact role of the spore components remains in dispute. Nevertheless, water molecules are important in each of these processes. The physical state of water within the bacterial spore has been investigated since the early 1930's. The water is found two states, free or bound, in two different areas, core and non-core. It is established that free water is accessible to diffuse and exchange with deuterated water and that the diffusible water can access all areas of the spore. The presence of bound water has come under recent scrutiny and has been suggested the water within the core is mobile, rather than bound, based on the analysis of deuterium relaxation rates. Using an alternate method, deuterium quadrupole-echo spectroscopy, we are able to distinguish between mobile and immobile water molecules. In the absence of rapid motion, the deuterium spectrum of D2O is dominated by a broad line, whose line shape is used as a characteristic descriptor of molecular motion. The deuterium spectrum of bacterial spores reveals three distinct features: the broad peak of immobilized water, a narrow line of water in rapid motion, and a signal of intermediate width. This third signal is assigned this peak from partially deuterated proteins with the spore in which N-H groups have undergone exchange with water deuterons to form N-D species. As a result of these observations, the nature of water within the spore requires additional explanation to understand how the spore and its water preserve life.

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja

2016-11-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

L-arginine supplementation prevents increases in intestinal permeability and bacterial translocation in male Swiss mice subjected to physical exercise under environmental heat stress.

PubMed

Costa, Kátia Anunciação; Soares, Anne Danieli Nascimento; Wanner, Samuel Penna; Santos, Rosana das Graças Carvalho dos; Fernandes, Simone Odília Antunes; Martins, Flaviano dos Santos; Nicoli, Jacques Robert; Coimbra, Cândido Celso; Cardoso, Valbert Nascimento

2014-02-01

Dietary supplementation with l-arginine has been shown to improve the intestinal barrier in many experimental models. This study investigated the effects of arginine supplementation on the intestinal permeability and bacterial translocation (BT) induced by prolonged physical exercise under heat stress. Under anesthesia, male Swiss mice (5-wk-old) were implanted with an abdominal sensor to record their core body temperature (T(core)). After recovering from surgery, the mice were divided into 3 groups: a non-supplemented group that was fed the standard diet formulated by the American Institute of Nutrition (AIN-93G; control), a non-supplemented group that was fed the AIN-93G diet and subjected to exertional hyperthermia (H-NS), and a group supplemented with l-arginine at 2% and subjected to exertional hyperthermia (H-Arg). After 7 d of treatment, the H-NS and H-Arg mice were forced to run on a treadmill (60 min, 8 m/min) in a warm environment (34°C). The control mice remained at 24°C. Thirty min before the exercise or control trials, the mice received a diethylenetriamine pentaacetic acid (DTPA) solution labeled with technetium-99m ((99m)Tc-DTPA) or (99m)Tc-Escherichia coli by gavage to assess intestinal permeability and BT, respectively. The H-NS mice terminated the exercise with T(core) values of ∼40°C, and, 4 h later, presented a 12-fold increase in the blood uptake of (99m)Tc-DTPA and higher bacterial contents in the blood and liver than the control mice. Although supplementation with arginine did not change the exercise-induced increase in T(core), it prevented the increases in intestinal permeability and BT caused by exertional hyperthermia. Our results indicate that dietary l-arginine supplementation preserves the integrity of the intestinal epithelium during exercise under heat stress, acting through mechanisms that are independent of T(core) regulation.

Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes

PubMed Central

Benjamino, Jacquelynn; Graf, Joerg

2016-01-01

The hindgut of the termite Reticulitermes flavipes harbors a complex symbiotic community consisting of protists, bacteria, and archaea. These symbionts aid in the digestion of lignocellulose from the termite’s wood meal. Termite hindguts were sampled and the V4 hyper-variable region of the 16S rRNA gene was sequenced and analyzed from individual termites. The core microbiota of worker termites consisted of 69 OTUs at the 97% identity level, grouped into 16 taxa, and together accounted for 67.05% of the sequences from the bacterial community. The core was dominated by Treponema, which contained 36 different OTUs and accounted for ∼32% of the sequences, which suggests Treponema sp. have an important impact on the overall physiology in the hindgut. Bray–Curtis beta diversity metrics showed that hindgut samples from termites of the same colony were more similar to each other than to samples from other colonies despite possessing a core that accounted for the majority of the sequences. The specific tasks and dietary differences of the termite castes could have an effect on the composition of the microbial community. The hindgut microbiota of termites from the alate castes differed from the worker caste with significantly lower abundances of Treponema and Endomicrobia, which dominated the hindgut microbiota in workers and soldiers. Protist abundances were also quantified in the same samples using qPCR of the 18S rRNA gene. Parabasalia abundances dropped significantly in the winged alates and the Oxymonadida abundances dropped in both alate castes. These data suggest that the changes in diet or overall host physiology affected the protist and bacterial populations in the hindgut. The in-depth bacterial characterization and protist quantification in this study sheds light on the potential community dynamics within the R. flavipes hindgut and identified a large and complex core microbiota in termites obtained from multiple colonies and castes. PMID:26925043

Evolution of Bacterial Global Modulators: Role of a Novel H-NS Paralogue in the Enteroaggregative Escherichia coli Strain 042

PubMed Central

2018-01-01

ABSTRACT Bacterial genomes sometimes contain genes that code for homologues of global regulators, the function of which is unclear. In members of the family Enterobacteriaceae, cells express the global regulator H-NS and its paralogue StpA. In Escherichia coli, out of providing a molecular backup for H-NS, the role of StpA is poorly characterized. The enteroaggregative E. coli strain 042 carries, in addition to the hns and stpA genes, a third gene encoding an hns paralogue (hns2). We present in this paper information about its biological function. Transcriptomic analysis has shown that the H-NS2 protein targets a subset of the genes targeted by H-NS. Genes targeted by H-NS2 correspond mainly with horizontally transferred (HGT) genes and are also targeted by the Hha protein, a fine-tuner of H-NS activity. Compared with H-NS, H-NS2 expression levels are lower. In addition, H-NS2 expression exhibits specific features: it is sensitive to the growth temperature and to the nature of the culture medium. This novel H-NS paralogue is widespread within the Enterobacteriaceae. IMPORTANCE Global regulators such as H-NS play key relevant roles enabling bacterial cells to adapt to a changing environment. H-NS modulates both core and horizontally transferred (HGT) genes, but the mechanism by which H-NS can differentially regulate these genes remains to be elucidated. There are several instances of bacterial cells carrying genes that encode homologues of the global regulators. The question is what the roles of these proteins are. We noticed that the enteroaggregative E. coli strain 042 carries a new hitherto uncharacterized copy of the hns gene. We decided to investigate why this pathogenic E. coli strain requires an extra H-NS paralogue, termed H-NS2. In our work, we show that H-NS2 displays specific expression and regulatory properties. H-NS2 targets a subset of H-NS-specific genes and may help to differentially modulate core and HGT genes by the H-NS cellular pool. PMID:29577085

Evolution of Bacterial Global Modulators: Role of a Novel H-NS Paralogue in the Enteroaggregative Escherichia coli Strain 042.

PubMed

Prieto, A; Bernabeu, M; Aznar, S; Ruiz-Cruz, S; Bravo, A; Queiroz, M H; Juárez, A

2018-01-01

Bacterial genomes sometimes contain genes that code for homologues of global regulators, the function of which is unclear. In members of the family Enterobacteriaceae , cells express the global regulator H-NS and its paralogue StpA. In Escherichia coli , out of providing a molecular backup for H-NS, the role of StpA is poorly characterized. The enteroaggregative E. coli strain 042 carries, in addition to the hns and stpA genes, a third gene encoding an hns paralogue ( hns2 ). We present in this paper information about its biological function. Transcriptomic analysis has shown that the H-NS2 protein targets a subset of the genes targeted by H-NS. Genes targeted by H-NS2 correspond mainly with horizontally transferred (HGT) genes and are also targeted by the Hha protein, a fine-tuner of H-NS activity. Compared with H-NS, H-NS2 expression levels are lower. In addition, H-NS2 expression exhibits specific features: it is sensitive to the growth temperature and to the nature of the culture medium. This novel H-NS paralogue is widespread within the Enterobacteriaceae . IMPORTANCE Global regulators such as H-NS play key relevant roles enabling bacterial cells to adapt to a changing environment. H-NS modulates both core and horizontally transferred (HGT) genes, but the mechanism by which H-NS can differentially regulate these genes remains to be elucidated. There are several instances of bacterial cells carrying genes that encode homologues of the global regulators. The question is what the roles of these proteins are. We noticed that the enteroaggregative E. coli strain 042 carries a new hitherto uncharacterized copy of the hns gene. We decided to investigate why this pathogenic E. coli strain requires an extra H-NS paralogue, termed H-NS2. In our work, we show that H-NS2 displays specific expression and regulatory properties. H-NS2 targets a subset of H-NS-specific genes and may help to differentially modulate core and HGT genes by the H-NS cellular pool.

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

PubMed Central

Takami, Hideto; Noguchi, Hideki; Takaki, Yoshihiro; Uchiyama, Ikuo; Toyoda, Atsushi; Nishi, Shinro; Chee, Gab-Joo; Arai, Wataru; Nunoura, Takuro; Itoh, Takehiko; Hattori, Masahira; Takai, Ken

2012-01-01

A nearly complete genome sequence of Candidatus ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO2 fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H2-dependent acetogens and methanogenes living in hydrothermal environments. PMID:22303444

The chromosomal organization of horizontal gene transfer in bacteria.

PubMed

Oliveira, Pedro H; Touchon, Marie; Cury, Jean; Rocha, Eduardo P C

2017-10-10

Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

Hepatitis B virus core antigen: synthesis in Escherichia coli and application in diagnosis.

PubMed Central

Stahl, S; MacKay, P; Magazin, M; Bruce, S A; Murray, K

1982-01-01

Fragments of hepatitis B virus DNA cloned in plasmid pBR322 carrying the gene for the viral core antigen have been placed under the control of the lac promoter of Escherichia coli. Several of the new recombinants direct higher levels of synthesis of the antigen, but the degree of enhancement varies with the different structures of the plasmids and hence the mRNAs produced. The antigen in crude bacterial lysates is a satisfactory diagnostic reagent for antibodies to the core antigen in serum samples. Images PMID:7041126

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

PubMed Central

Sahl, Jason W.; Vazquez, Adam J.; Hall, Carina M.; Busch, Joseph D.; Tuanyok, Apichai; Mayo, Mark; Schupp, James M.; Lummis, Madeline; Pearson, Talima; Shippy, Kenzie; Allender, Christopher J.; Theobald, Vanessa; Hutcheson, Alex; Korlach, Jonas; LiPuma, John J.; Ladner, Jason; Lovett, Sean; Koroleva, Galina; Palacios, Gustavo; Limmathurotsakul, Direk; Wuthiekanun, Vanaporn; Wongsuwan, Gumphol; Currie, Bart J.

2016-01-01

ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. PMID:27651357

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

PubMed Central

Chopyk, Jessica; Allard, Sarah; Nasko, Daniel J.; Bui, Anthony; Mongodin, Emmanuel F.; Sapkota, Amy R.

2018-01-01

Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October–December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season. PMID:29740420

Gamma-irradiated bacterial preparation having anti-tumor activity

DOEpatents

Vass, Arpad A.; Tyndall, Richard L.; Terzaghi-Howe, Peggy

1999-01-01

A bacterial preparation from Pseudomonas species isolated #15 ATCC 55638 that has been exposed to gamma radiation exhibits cytotoxicity that is specific for neoplastic carcinoma cells. A method for obtaining a bacterial preparation having antitumor activity consists of suspending a bacterial isolate in media and exposing the suspension to gamma radiation. A bacterial preparation of an aged culture of an amoeba-associated bacteria exhibits anti-reverse transcriptase activity. A method for obtaining a bacterial preparation having anti-reverse transcriptase activity from an amoeba-associated bacterial isolate grown to stationary phase is disclosed.

Insights from 20 years of bacterial genome sequencing

DOE PAGES

Land, Miriam L.; Hauser, Loren; Jun, Se-Ran; ...

2015-02-27

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date,more » there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.« less

Insights from 20 years of bacterial genome sequencing

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

Land, Miriam L.; Hauser, Loren; Jun, Se-Ran

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date,more » there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.« less

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope

PubMed Central

Helmann, John D.

2016-01-01

Summary Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σW is most closely associated with membrane-active agents, σX with cationic antimicrobial peptide resistance, and σV with resistance to lysozyme. Here, I highlight the role of the σM regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics. PMID:26901131

Gamma-irradiated bacterial preparation having anti-tumor activity

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

Vass, A.A.; Tyndall, R.L.; Terzaghi-Howe, P.

1999-11-16

This application describes a bacterial preparation from Pseudomonas species isolated {number{underscore}sign}15 ATCC 55638 that has been exposed to gamma radiation exhibits cytotoxicity that is specific for neoplastic carcinoma cells. A method for obtaining a bacterial preparation having antitumor activity consists of suspending a bacterial isolate in media and exposing the suspension to gamma radiation. A bacterial preparation of an aged culture of an amoeba-associated bacteria exhibits anti-reverse transcriptase activity. A method for obtaining a bacterial preparation having anti-reverse transcriptase activity from an amoeba-associated bacterial isolate grown to stationary phase is disclosed.

Differential carbohydrate utilization and organic acid production by honey bee symbionts.

PubMed

Lee, Fredrick J; Miller, Kayla I; McKinlay, James B; Newton, Irene L G

2018-06-06

The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

Permeability of bacterial spores. IV. Water content, uptake, and distribution.

PubMed

BLACK, S H; GERHARDT, P

1962-05-01

Black, S. H. (The University of Michigan, Ann Arbor) and Philipp Gerhardt. Permeability of bacterial spores. IV. Water content, uptake, and distribution. J. Bacteriol. 83:960-967. 1962.-Dormant and germinated spores of Bacillus cereus strain terminalis were examined for water properties. Respectively, they exhibited a mean density of 1.28 and 1.11 g/ml, a water content of 64.8 and 73.0%, and a total water uptake of 66.6 and 75.6%, based on spore weight, or 86.0 and 83.9%, based on spore volume. The results confirmed a previous report that internal and external water are in virtually complete equilibrium, but refuted a prevailing hypothesis that heat resistance is attributable to a dry core. A model of spore ultrastructure that evolved from the cumulative results pictures a moist, dense, heteroporous core. A new hypothesis is formulated as an explanation for thermostability in spores and possibly in other instances; it postulates the occurrence of an insolubly gelled core with cross-linking between macromolecules through stable but reversible bonds so as to form a high-polymer matrix with entrapped free water.

The core faecal bacterial microbiome of Irish Thoroughbred racehorses.

PubMed

O' Donnell, M M; Harris, H M B; Jeffery, I B; Claesson, M J; Younge, B; O' Toole, P W; Ross, R P

2013-12-01

In this study, we characterized the gut microbiota in six healthy Irish thoroughbred racehorses and showed it to be dominated by the phyla Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Moreover, all the horses harboured Clostridium, Fibrobacter, Faecalibacterium, Ruminococcus, Eubacterium, Oscillospira, Blautia Anaerotruncus, Coprococcus, Treponema and Lactobacillus spp. Notwithstanding the sample size, it was noteworthy that the core microbiota species assignments identified Fibrobacter succinogenes, Eubacterium coprostanoligenes, Eubacterium hallii, Eubacterium ruminantium, Oscillospira guillermondii, Sporobacter termiditis, Lactobacillus equicursoris, Treponema parvum and Treponema porcinum in all the horses. This is the first study of the faecal microbiota in the Irish thoroughbred racehorse, a significant competitor in the global bloodstock industry. The information gathered in this pilot study provides a foundation for veterinarians and other equine health-associated professionals to begin to analyse the microbiome of performance of racehorses. This study and subsequent work may lead to alternate dietary approaches aimed at minimizing the risk of microbiota-related dysbiosis in these performance animals. Although Irish thoroughbreds are used nationally and internationally as performance animals, very little is known about the core faecal microbiota of these animals. This is the first study to characterize the bacterial microbiota present in the Irish thoroughbred racehorse faeces and elucidate a core microbiome irrespective of diet, animal management and geographical location. © 2013 The Society for Applied Microbiology.

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

Core Principles of Bacterial Autoinducer Systems

PubMed Central

2015-01-01

SUMMARY Autoinduction (AI), the response to self-produced chemical signals, is widespread in the bacterial world. This process controls vastly different target functions, such as luminescence, nutrient acquisition, and biofilm formation, in different ways and integrates additional environmental and physiological cues. This diversity raises questions about unifying principles that underlie all AI systems. Here, we suggest that such core principles exist. We argue that the general purpose of AI systems is the homeostatic control of costly cooperative behaviors, including, but not limited to, secreted public goods. First, costly behaviors require preassessment of their efficiency by cheaper AI signals, which we encapsulate in a hybrid “push-pull” model. The “push” factors cell density, diffusion, and spatial clustering determine when a behavior becomes effective. The relative importance of each factor depends on each species' individual ecological context and life history. In turn, “pull” factors, often stress cues that reduce the activation threshold, determine the cellular demand for the target behavior. Second, control is homeostatic because AI systems, either themselves or through accessory mechanisms, not only initiate but also maintain the efficiency of target behaviors. Third, AI-controlled behaviors, even seemingly noncooperative ones, are generally cooperative in nature, when interpreted in the appropriate ecological context. The escape of individual cells from biofilms, for example, may be viewed as an altruistic behavior that increases the fitness of the resident population by reducing starvation stress. The framework proposed here helps appropriately categorize AI-controlled behaviors and allows for a deeper understanding of their ecological and evolutionary functions. PMID:25694124

Identifying the core seed bank of a complex boreal bacterial metacommunity.

PubMed

Ruiz-González, Clara; Niño-García, Juan Pablo; Kembel, Steven W; Del Giorgio, Paul A

2017-09-01

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

Crl binds to domain 2 of σ(S) and confers a competitive advantage on a natural rpoS mutant of Salmonella enterica serovar Typhi.

PubMed

Monteil, Véronique; Kolb, Annie; Mayer, Claudine; Hoos, Sylviane; England, Patrick; Norel, Françoise

2010-12-01

The RpoS sigma factor (σ(S)) is the master regulator of the bacterial response to a variety of stresses. Mutants in rpoS arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. We characterized here one natural rpoS mutant of Salmonella enterica serovar Typhi (Ty19). We show that the rpoS allele of Ty19 (rpoS(Ty19)) led to the synthesis of a σ(S)(Ty19) protein carrying a single glycine-to-valine substitution at position 282 in σ(S) domain 4, which was much more dependent than the wild-type σ(S) protein on activation by Crl, a chaperone-like protein that increases the affinity of σ(S) for the RNA polymerase core enzyme (E). We used the bacterial adenylate cyclase two-hybrid system to demonstrate that Crl bound to residues 72 to 167 of σ(S) domain 2 and that G282V substitution did not directly affect Crl binding. However, this substitution drastically reduced the ability of σ(S)(Ty19) to bind E in a surface plasmon resonance assay, a defect partially rescued by Crl. The modeled structure of the Eσ(S) holoenzyme suggested that substitution G282V could directly disrupt a favorable interaction between σ(S) and E. The rpoS(Ty19) allele conferred a competitive fitness when the bacterial population was wild type for crl but was outcompeted in Δcrl populations. Thus, these results indicate that the competitive advantage of the rpoS(Ty19) mutant is dependent on Crl and suggest that crl plays a role in the appearance of rpoS mutants in bacterial populations.

Facile biological synthetic strategy to morphologically aligned CeO2/ZrO2 core nanoparticles using Justicia adhatoda extract and ionic liquid: Enhancement of its bio-medical properties.

PubMed

Pandiyan, Nithya; Murugesan, Balaji; Sonamuthu, Jegatheeswaran; Samayanan, Selvam; Mahalingam, Sundrarajan

2018-01-01

In this study, a typical green synthesis route has approached for CeO 2 /ZrO 2 core metal oxide nanoparticles using ionic liquid mediated Justicia adhatoda extract. This synthesis method is carried out at simple room temperature condition to obtain the core metal oxide nanoparticles. XRD, SEM and TEM studies employed to study the crystalline and surface morphological properties under nucleation, growth, and aggregation processes. CeO 2 /ZrO 2 core metal oxides display agglomerated nano stick-like structure with 20-45nm size. GC-MS spectroscopy confirms the presence of vasicinone and N,N-Dimethylglycine present in the plant extract, which are capable of converting the corresponding metal ion precursor to CeO 2 /ZrO 2 core metal oxide nanoparticles. In FTIR, the corresponding stretching for Ce-O and Zr-O bands indicated at 498 and 416cm -1 and Raman spectroscopy also supports typical stretching frequencies at 463 and 160cm -1 . Band gap energy of the CeO 2 /ZrO 2 core metal oxide is 3.37eV calculated from UV- DRS spectroscopy. The anti-bacterial studies performed against a set of bacterial strains the result showed that core metal oxide nanoparticles more susceptible to gram-positive (G+) bacteria than gram-negative (G-) bacteria. A unique feature of the antioxidant behaviors core metal oxides reduces the concentration of DPPH radical up to 89%. The CeO 2 /ZrO 2 core metal oxide nanoparticles control the S. marcescent bio-film formation and restrict the quorum sensing. The toxicology behavior of CeO 2 /ZrO 2 core metal oxide NPs is found due to the high oxygen site vacancies, ROS formation, smallest particle size and higher surface area. This type of green synthesis route may efficient and the core metal oxide nanoparticles will possess a good bio-medical agent in future. Copyright © 2017 Elsevier B.V. All rights reserved.

Cytotoxicity of Ultrasmall Gold Nanoparticles on Planktonic and Biofilm Encapsulated Gram-Positive Staphylococci.

PubMed

Boda, Sunil Kumar; Broda, Janine; Schiefer, Frank; Weber-Heynemann, Josefine; Hoss, Mareike; Simon, Ulrich; Basu, Bikramjit; Jahnen-Dechent, Willi

2015-07-01

The emergence of multidrug resistant bacteria, especially biofilm-associated Staphylococci, urgently requires novel antimicrobial agents. The antibacterial activity of ultrasmall gold nanoparticles (AuNPs) is tested against two gram positive: S. aureus and S. epidermidis and two gram negative: Escherichia coli and Pseudomonas aeruginosa strains. Ultrasmall AuNPs with core diameters of 0.8 and 1.4 nm and a triphenylphosphine-monosulfonate shell (Au0.8MS and Au1.4MS) both have minimum inhibitory concentration (MIC) and minimum bactericidal concentration of 25 × 10(-6) m [Au]. Disc agar diffusion test demonstrates greater bactericidal activity of the Au0.8MS nanoparticles over Au1.4MS. In contrast, thiol-stabilized AuNPs with a diameter of 1.9 nm (AuroVist) cause no significant toxicity in any of the bacterial strains. Ultrasmall AuNPs cause a near 5 log bacterial growth reduction in the first 5 h of exposure, and incomplete recovery after 21 h. Bacteria show marked membrane blebbing and lysis in biofilm-associated bacteria treated with ultrasmall AuNP. Importantly, a twofold MIC dosage of Au0.8MS and Au1.4MS each cause around 80%-90% reduction in the viability of Staphylococci enveloped in biofilms. Altogether, this study demonstrates potential therapeutic activity of ultrasmall AuNPs as an effective treatment option against staphylococcal infections. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An environmentally benign antimicrobial nanoparticle based on a silver-infused lignin core.

PubMed

Richter, Alexander P; Brown, Joseph S; Bharti, Bhuvnesh; Wang, Amy; Gangwal, Sumit; Houck, Keith; Cohen Hubal, Elaine A; Paunov, Vesselin N; Stoyanov, Simeon D; Velev, Orlin D

2015-09-01

Silver nanoparticles have antibacterial properties, but their use has been a cause for concern because they persist in the environment. Here, we show that lignin nanoparticles infused with silver ions and coated with a cationic polyelectrolyte layer form a biodegradable and green alternative to silver nanoparticles. The polyelectrolyte layer promotes the adhesion of the particles to bacterial cell membranes and, together with silver ions, can kill a broad spectrum of bacteria, including Escherichia coli, Pseudomonas aeruginosa and quaternary-amine-resistant Ralstonia sp. Ion depletion studies have shown that the bioactivity of these nanoparticles is time-limited because of the desorption of silver ions. High-throughput bioactivity screening did not reveal increased toxicity of the particles when compared to an equivalent mass of metallic silver nanoparticles or silver nitrate solution. Our results demonstrate that the application of green chemistry principles may allow the synthesis of nanoparticles with biodegradable cores that have higher antimicrobial activity and smaller environmental impact than metallic silver nanoparticles.

Interaction of sigma 70 with Escherichia coli RNA polymerase core enzyme studied by surface plasmon resonance.

PubMed

Ferguson, A L; Hughes, A D; Tufail, U; Baumann, C G; Scott, D J; Hoggett, J G

2000-09-22

The interaction between the core form of bacterial RNA polymerases and sigma factors is essential for specific promoter recognition, and for coordinating the expression of different sets of genes in response to varying cellular needs. The interaction between Escherichia coli core RNA polymerase and sigma 70 has been investigated by surface plasmon resonance. The His-tagged form of sigma 70 factor was immobilised on a Ni2+-NTA chip for monitoring its interaction with core polymerase. The binding constant for the interaction was found to be 1.9x10(-7) M, and the dissociation rate constant for release of sigma from core, in the absence of DNA or transcription, was 4x10(-3) s(-1), corresponding to a half-life of about 200 s.

Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

PubMed Central

2013-01-01

Background Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples. Results First, as compared with normal individuals, in gallstone patients there were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs) from gallstone patients were detectable in the biliary tract and bacteria diversity of biliary tract was significantly (P < 0.001) higher than that of gut. Third, analysis of the biliary tract core microbiome (represented by 106 bacteria OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be matched to known bacterial species (15 of which have publicly available genomes). A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with the formation of cholesterol gallstones showed that all 15 species with known genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas putida) contained at least contained one of the four genes. This finding could potentially provide underlying information needed to explain the association between biliary tract microbiota and the formation of cholesterol gallstones. Conclusions To the best of our knowledge, this is the first study to discover gut microbiota dysbiosis among gallstone patients, the presence of which may be a key contributor to the complex bacteria community assembly linked with the presence of cholesterol gallstones. Likewise, this study also provides the first large-scale glimpse of biliary tract microbiota potentially associated with cholesterol gallstones. Such a characterization of the biliary tract core microbiome has potentially important biological and medical implications regarding the role of bacteria in the formation cholesterol gallstones. PMID:24083370

Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

PubMed

Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

2017-06-01

While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Regulation of Chemokine Expression by Lipopolysaccharide In Vitro and In Vivo

DTIC Science & Technology

2002-06-10

chain, the core polysaccharide , and the lipid A domain (Figure 1A). The hydrophilic O-specific chain is a polymer of repeating oligosaccharide units...necessary for protection from phagocytosis and complement-mediated lysis in vivo (9, 10). Linking the O-specific chain to lipid A is a core polysaccharide ...region that is relatively conserved among bacterial families on the basis of its monosaccharide composition. Among the common elements in the

Uranium and plutonium in anoxic marine sediments of the Santiago River mouth (Eastern Pacific, Mexico).

PubMed

Almazán-Torres, María Guadalupe; Ordóñez-Regil, Eduardo; Ruiz-Fernández, Ana Carolina

2016-11-01

The uranium (U) and plutonium (Pu) content with depth in a sediment core collected in the continental shelf off the mouth of the Santiago River in the Mexican Pacific was studied to evaluate the contamination effects of the effluent of the Santiago-Lerma River as it moves into the sea. The large mass of terrestrial detritus delivered by the river influences the physicochemical and geochemical processes in the seafloor. Abnormal concentrations of U and Pu in sediments were examined as indicative of the effects of anoxic conditions. One of the indicators of pollution of seawater is the bacterial activity of the shallow seabed layer; and among the prevailing bacteria, the magnetotactic ones induce the formation of euhedral and framboidal shapes (pyrite). These pyrite entities are by-products of anoxic environments loaded with decomposing detrital material and are very abundant in the surface layers of the sediment core analyzed. The pyrite formation is the result of a biochemical reaction between iron and organic sulphur reduced by bacteria, and the pyrite entities precipitate to the seafloor. In the same upper zone of the profile, 238 U is readily immobilized, while 234 U is oxidized and dissolved in seawater by the effect of hot atom chemistry. This may cause the activity ratio (AR) 234 U/ 238 U disequilibrium (near 0.41). Furthermore, in the shallow layer of the sediment core, an abnormally high concentration of 239+240 Pu was detected. In this upper layer, the activity concentrations found were 3.19 Bq kg -1 for 238 U, 1.32 kg -1 for 234 U and 2.78 Bq kg -1 for 239+240 Pu. In the lower fractions of the sediment core, normal values of AR 234 U/ 238 U (≈1) were found, with traces of 239+240 Pu. Copyright © 2016 Elsevier Ltd. All rights reserved.

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture.

PubMed

Pitta, D W; Pinchak, W E; Dowd, S; Dorton, K; Yoon, I; Min, B R; Fulford, J D; Wickersham, T A; Malinowski, D P

2014-12-01

Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59-77%) and Firmicutes (20-33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (P<0.05) in the fiber fraction. Such changes were diminished as the CP concentration declined over the course of the study. The abundance of Firmicutes was noticeable by 76 d in both fractions which signifies the development of a core microbiome associated with digestion of a more recalcitrant fiber in the mature wheat. This study demonstrates dynamics in the rumen microbiome and their association with fermentation activity in the rumen of steers during the vegetative (bloat-prone) and reproductive stages of wheat forage. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats.

PubMed

Attermeyer, Katrin; Premke, Katrin; Hornick, Thomas; Hilt, Sabine; Grossart, Hans-Peter

2013-12-01

In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using 13C-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POM(L) and via benthic macroinvertebrates by shredding of t-POM(L). The latter pathway represents a "benthic shortcut" which efficiently transfers t-POM(L) to higher trophic levels.

A novel nanoparticle approach for imaging nutrient uptake by soil bacteria

NASA Astrophysics Data System (ADS)

O'Brien, S. L.; Whiteside, M. D.; Sholto-Douglas, D.; Antonopoulos, D. A.; Boyanov, M.; Durall, D. M.; Jones, M. D.; Lai, B.; O'Loughlin, E. J.; Kemner, K. M.

2014-12-01

The metabolic activities of soil microbes are the primary drivers of biogeochemical processes controlling the terrestrial carbon cycle, nutrient availability to plants, contaminant remediation, water quality, and other ecosystem services. However, we have a limited understanding of microbial metabolic processes such as nutrient uptake rates, substrate preferences, or how microbes and microbial metabolism are distributed throughout their habitat. Here we use a novel imaging technique with quantum dots (QDs, engineered semiconductor nanoparticles that produce size or composition-dependent fluorescence) to measure bacterial uptake of substrates of varying complexity. Cultures of two organisms differing in cell wall structure — Bacillus subtilis and Pseudomonas fluorescens — were grown in one of four ecologically relevant experimental conditions: nitrogen (N) limitation, phosphorus (P) limitation, N and P limitation, or no nutrient limitation. The cultures were then exposed to QDs with and without organic nutrients attached. X-ray fluorescence imaging was performed at 2ID-D at the Advanced Photon Source (APS) to determine the elemental distributions within both planktonic and surface-adhered (i.e, biofilms) cells. Uptake of unconjugated QDs was neglibible, and QDs conjugated to organic substrates varied depending on growth conditions and substrate, suggesting that they are a useful indicator of bacterial ecology. Cellular uptake was similar for the two bacterial species (2212 ± 273 nanoparticles per cm3 of cell volume for B. subtilis and 1682 ± 264 for P. fluorescens). On average, QD assimilation was six times greater when N or P was limiting, and cells took up about twice as much phosphoserine compared to other substrates, likely because it was the only compound providing both N and P. These results showed that regardless of their cell wall structure, bacteria can selectively take up quantifiable levels of QDs based on substrate and environmental conditions. APS images are consistent with those produced with confocal and optical microscopes, indicating that the XRF approach can detect bacterial uptake of CdSe-core QDs. These findings offer a new way to experimentally investigate basic bacterial ecology such as metabolic activity and biofilm development and function.

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope.

PubMed

Helmann, John D

2016-04-01

Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Direct quantification of bacterial biomass in influent, effluent and activated sludge of wastewater treatment plants by using flow cytometry.

PubMed

Foladori, P; Bruni, L; Tamburini, S; Ziglio, G

2010-07-01

A rapid multi-step procedure, potentially amenable to automation, was proposed for quantifying viable and active bacterial cells, estimating their biovolume using flow cytometry (FCM) and to calculate their biomass within the main stages of a wastewater treatment plant: raw wastewater, settled wastewater, activated sludge and effluent. Fluorescent staining of bacteria using SYBR-Green I + Propidium Iodide (to discriminate cell integrity or permeabilisation) and BCECF-AM (to identify enzymatic activity) was applied to count bacterial cells by FCM. A recently developed specific procedure was applied to convert Forward Angle Light Scatter measured by FCM into the corresponding bacterial biovolume. This conversion permits the calculation of the viable and active bacterial biomass in wastewater, activated sludge and effluent, expressed as Volatile Suspended Solids (VSS) or particulate Chemical Oxygen Demand (COD). Viable bacterial biomass represented only a small part of particulate COD in raw wastewater (4.8 +/- 2.4%), settled wastewater (10.7 +/- 3.1%), activated sludge (11.1 +/- 2.1%) and effluent (3.2 +/- 2.2%). Active bacterial biomass counted for a percentage of 30-47% of the viable bacterial biomass within the stages of the wastewater treatment plant. Copyright 2010 Elsevier Ltd. All rights reserved.

Evidence for a core gut microbiota in the zebrafish

PubMed Central

Roeselers, Guus; Mittge, Erika K; Stephens, W Zac; Parichy, David M; Cavanaugh, Colleen M; Guillemin, Karen; Rawls, John F

2011-01-01

Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status. PMID:21472014

Magnetic susceptibility as an indicator to paleo-environmental pollution in an urban lagoon near Istanbul city

NASA Astrophysics Data System (ADS)

Alpar, Bedri; Unlu, Selma; Altinok, Yildiz; Ongen, Sinan

2014-05-01

For assessing anthropogenic pollution, magnetic susceptibility profiles and accompanying data were measured along three short cores recovered at the southern part of an urban lagoon; Kucukcekmece, Istanbul, Turkey. This marine inlet, connected to the Sea of Marmara by a very narrow channel, was used as a drinking water reservoir 40-50 years ago before it was contaminated by municipal, agricultural and industrial activities, mainly carried by three streams feeding the lagoon. The magnetic signals decrease gradually from the lake bottom towards the core base showing some characteristic anomalies. These signatures were tested as an environmental magnetic parameter against the lithological diversity (silici-clastic, total organic matter and carbonate), metal enrichments with larger variations (Pb, Mn, Zn, Ni, Co, Cr, U and Al) and probable hydrocarbon contamination. Mineral assemblage was determined by a computer driven X-ray diffractometer. The heavy metal concentrations and total petroleum hydrocarbons (TPH) were measured by ICP-MS and UVF spectrometry, respectively. Magnetic susceptibility shows slightly higher values in interlayers containing higher silici-clastic material and organic content which may suggest first-order changes in the relative supplies of terrigenous and biogenic materials. On the basis of cluster analyses, enhanced magnetic signals could be correlated with the elevated concentrations of Co, Zn, U, Pb and TPH along the cores. The Pb concentrations at the upper parts of the cores were higher than the "Severe Effect Level" and could pose a potential risk for living organisms. Greater amounts of organic carbon tend to accumulate in muddy sediments. In fact, there are a few studies reporting some relationship between enhanced magnetic signals and organic contamination mainly due to petroleum aromatic hydrocarbons. In conclusion, the magnetic susceptibility changes in sedimentary depositional environments could be used as a rapid and cost-effective tool in identification of silici-clastic content, enrichment of some metals (iron cycling and bacterial activity) and increased TPH concentrations in hydrocarbon contaminated sediments along the cores.

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

PubMed

Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

PubMed Central

Zhang, Yao; Zhao, Zihao; Dai, Minhan; Jiao, Nianzhi; Herndl, Gerhard J

2014-01-01

To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. PMID:24684298

Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.

PubMed

Williamson, Adele; Rothweiler, Ulli; Leiros, Hanna Kirsti Schrøder

2014-11-01

DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.

Effects of invasion history on physiological responses to immune system activation in invasive Australian cane toads

PubMed Central

West, Andrea J.; Brown, Gregory P.; Fanson, Kerry V.; Addison, BriAnne; Rollins, Lee A.; Shine, Richard

2017-01-01

The cane toad (Rhinella marina) has undergone rapid evolution during its invasion of tropical Australia. Toads from invasion front populations (in Western Australia) have been reported to exhibit a stronger baseline phagocytic immune response than do conspecifics from range core populations (in Queensland). To explore this difference, we injected wild-caught toads from both areas with the experimental antigen lipopolysaccharide (LPS, to mimic bacterial infection) and measured whole-blood phagocytosis. Because the hypothalamic-pituitary-adrenal axis is stimulated by infection (and may influence immune responses), we measured glucocorticoid response through urinary corticosterone levels. Relative to injection of a control (phosphate-buffered saline), LPS injection increased both phagocytosis and the proportion of neutrophils in the blood. However, responses were similar in toads from both populations. This null result may reflect the ubiquity of bacterial risks across the toad’s invaded range; utilization of this immune pathway may not have altered during the process of invasion. LPS injection also induced a reduction in urinary corticosterone levels, perhaps as a result of chronic stress. PMID:29018604

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions

PubMed Central

Theisen, Stefan; Abdul-Aziz, Muslihudeen A.; Mrotzek, Grit; Palm, Harry W.; Saluz, Hans Peter

2016-01-01

In this study we analysed fecal bacterial communities and parasites of three important Indonesian fish species, Epinephelus fuscoguttatus, Epinephelus sexfasciatus and Atule mate. We then compared the biodiversity of bacterial communities and parasites of these three fish species collected in highly polluted Jakarta Bay with those collected in less polluted Indonesian areas of Cilacap (E. sexfasciatus, A. mate) and Thousand Islands (E. fuscoguttatus). In addition, E. fuscoguttatus from net cages in an open water mariculture facility was compared with free living E. fuscoguttatus from its surroundings. Both core and shared microbiomes were investigated. Our results reveal that, while the core microbiomes of all three fish species were composed of fairly the same classes of bacteria, the proportions of these bacterial classes strongly varied. The microbial composition of phylogenetically distant fish species, i.e. A. mate and E. sexfasciatus from Jakarta Bay and Cilacap were more closely related than the microbial composition of more phylogentically closer species, i.e. E. fuscoguttatus, E. sexfasciatus from Jakarta Bay, Cilacap and Thousand Islands. In addition, we detected a weak negative correlation between the load of selected bacterial pathogens, i.e. Vibrio sp. and Photobacterium sp. and the number of endoparasites. In the case of Flavobacterium sp. the opposite was observed, i.e. a weak positive correlation. Of the three recorded pathogenic bacterial genera, Vibrio sp. was commonly found in E. fuscoguttatus from mariculture, and lessly in the vicinity of the net cages and rarely in the fishes from the heavily polluted waters from Jakarta Bay. Flavobacterium sp. showed higher counts in mariculture fish and Photobacteria sp. was the most prominent in fish inside and close to the net cages. PMID:27018789

Bacterial community dynamics in a cooling tower with emphasis on pathogenic bacteria and Legionella species using universal and genus-specific deep sequencing.

PubMed

Pereira, Rui P A; Peplies, Jörg; Höfle, Manfred G; Brettar, Ingrid

2017-10-01

Cooling towers are the major source of outbreaks of legionellosis in Europe and worldwide. These outbreaks are mostly associated with Legionella species, primarily L. pneumophila, and its surveillance in cooling tower environments is of high relevance to public health. In this study, a combined NGS-based approach was used to study the whole bacterial community, specific waterborne and water-based bacterial pathogens, especially Legionella species, targeting the 16S rRNA gene. This approach was applied to water from a cooling tower obtained by monthly sampling during two years. The studied cooling tower was an open circuit cooling tower with lamellar cooling situated in Braunschweig, Germany. A highly diverse bacterial community was observed with 808 genera including 25 potentially pathogenic taxa using universal 16S rRNA primers. Sphingomonas and Legionella were the most abundant pathogenic genera. By applying genus-specific primers for Legionella, a diverse community with 85 phylotypes, and a representative core community with substantial temporal heterogeneity was observed. A high percentage of sequences (65%) could not be affiliated to an acknowledged species. L. pneumophila was part of the core community and the most abundant Legionella species reinforcing the importance of cooling towers as its environmental reservoir. Major temperature shifts (>10 °C) were the key environmental factor triggering the reduction or dominance of the Legionella species in the Legionella community dynamics. In addition, interventions by chlorine dioxide had a strong impact on the Legionella community composition but not on the whole bacterial community. Overall, the presented results demonstrated the value of a combined NGS approach for the molecular monitoring and surveillance of health related pathogens in man-made freshwater systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis

PubMed Central

Liu, Xiaokun; Grabherr, Heini M; Willmann, Roland; Kolb, Dagmar; Brunner, Frédéric; Bertsche, Ute; Kühner, Daniel; Franz-Wachtel, Mirita; Amin, Bushra; Felix, Georg; Ongena, Marc; Nürnberger, Thorsten; Gust, Andrea A

2014-01-01

Peptidoglycans (PGNs) are immunogenic bacterial surface patterns that trigger immune activation in metazoans and plants. It is generally unknown how complex bacterial structures such as PGNs are perceived by plant pattern recognition receptors (PRRs) and whether host hydrolytic activities facilitate decomposition of bacterial matrices and generation of soluble PRR ligands. Here we show that Arabidopsis thaliana, upon bacterial infection or exposure to microbial patterns, produces a metazoan lysozyme-like hydrolase (lysozyme 1, LYS1). LYS1 activity releases soluble PGN fragments from insoluble bacterial cell walls and cleavage products are able to trigger responses typically associated with plant immunity. Importantly, LYS1 mutant genotypes exhibit super-susceptibility to bacterial infections similar to that observed on PGN receptor mutants. We propose that plants employ hydrolytic activities for the decomposition of complex bacterial structures, and that soluble pattern generation might aid PRR-mediated immune activation in cell layers adjacent to infection sites. DOI: http://dx.doi.org/10.7554/eLife.01990.001 PMID:24957336

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

PubMed Central

Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Hélène Desmonts, Marie; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

2015-01-01

The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota. PMID:25333463

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap.

PubMed

Gokul, Jarishma K; Hodson, Andrew J; Saetnan, Eli R; Irvine-Fynn, Tristram D L; Westall, Philippa J; Detheridge, Andrew P; Takeuchi, Nozomu; Bussell, Jennifer; Mur, Luis A J; Edwards, Arwyn

2016-08-01

Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps. © 2016 John Wiley & Sons Ltd.

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.

PubMed

Batty, Elizabeth M; Chaemchuen, Suwittra; Blacksell, Stuart; Richards, Allen L; Paris, Daniel; Bowden, Rory; Chan, Caroline; Lachumanan, Ramkumar; Day, Nicholas; Donnelly, Peter; Chen, Swaine; Salje, Jeanne

2018-06-01

Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species. We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia. Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.

PubMed

Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Desmonts, Marie Hélène; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

2015-05-01

The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

Bacteria survival probability in bactericidal filter paper.

PubMed

Mansur-Azzam, Nura; Hosseinidoust, Zeinab; Woo, Su Gyeong; Vyhnalkova, Renata; Eisenberg, Adi; van de Ven, Theo G M

2014-05-01

Bactericidal filter papers offer the simplicity of gravity filtration to simultaneously eradicate microbial contaminants and particulates. We previously detailed the development of biocidal block copolymer micelles that could be immobilized on a filter paper to actively eradicate bacteria. Despite the many advantages offered by this system, its widespread use is hindered by its unknown mechanism of action which can result in non-reproducible outcomes. In this work, we sought to investigate the mechanism by which a certain percentage of Escherichia coli cells survived when passing through the bactericidal filter paper. Through the process of elimination, the possibility that the bacterial survival probability was controlled by the initial bacterial load or the existence of resistant sub-populations of E. coli was dismissed. It was observed that increasing the thickness or the number of layers of the filter significantly decreased bacterial survival probability for the biocidal filter paper but did not affect the efficiency of the blank filter paper (no biocide). The survival probability of bacteria passing through the antibacterial filter paper appeared to depend strongly on the number of collision between each bacterium and the biocide-loaded micelles. It was thus hypothesized that during each collision a certain number of biocide molecules were directly transferred from the hydrophobic core of the micelle to the bacterial lipid bilayer membrane. Therefore, each bacterium must encounter a certain number of collisions to take up enough biocide to kill the cell and cells that do not undergo the threshold number of collisions are expected to survive. Copyright © 2014 Elsevier B.V. All rights reserved.

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece)

NASA Astrophysics Data System (ADS)

Genitsaris, Savvas; Stefanidou, Natassa; Katsiapi, Matina; Kormas, Konstantinos A.; Sommer, Ulrich; Moustaka-Gouni, Maria

2017-05-01

The abundance, biomass and the taxonomic composition of the total airborne bacterial communities in a coastal urban area of Northeastern Mediterranean Sea were examined. In total, 27 air samples were collected across three seasons from a sampling point of approximately 30 m altitude in the center of the city. The abundance and biomass were determined with the use of epifluorescent microscopy, while the taxonomic composition was characterized by next-generation sequencing methods. Overall, the highest values of bacterial abundance were recorded during summer, with values exceeding abundances recorded in other urban sites across Europe, reaching 41 × 104 cells m-3. Out of 6 core meteorological parameters, only air temperature was found to significantly affect the abundance and biomass of airborne bacteria. Concerning the taxonomic composition of the airborne bacterial community, the group of Proteobacteria was the most diverse, with 47% of the total number of OTUs belonging to them, followed by Firmicutes, Actinobacteria and Bacteroidetes. The most dominant OTU belonged to γ-Proteobacteria, and was closely affiliated to Pseudomonas sp., a taxon commonly found to actively participate in the formation of ice-nuclei in the atmosphere. Finally, 19 OTUs were shared between all seasons and were found to be among the most dominant overall. The majority of these OTUs were affiliated to genera from soil and wastewater origin, while several were affiliated to genera that include known or opportunistic pathogens. Yet, only rare OTUs were affiliated to taxa with possible marine origin (e.g. Synechococcus sp.). The results showed that the atmosphere of the study area harbors a diverse and abundant bacterial community.

Copper effects on bacterial activity of estuarine silty sediments

NASA Astrophysics Data System (ADS)

Almeida, Adelaide; Cunha, Ângela; Fernandes, Sandra; Sobral, Paula; Alcântara, Fernanda

2007-07-01

Bacteria of silty estuarine sediments were spiked with copper to 200 μg Cu g -1 dry weight sediment in order to assess the impact of copper on bacterial degradation of organic matter and on bacterial biomass production. Bacterial density was determined by direct counting under epifluorescence microscopy and bacterial production by the incorporation of 3H-Leucine. Leucine turnover rate was evaluated by 14C-leucine incorporation and ectoenzymatic activities were estimated as the hydrolysis rate of model substrates for β-glucosidase and leucine-aminopeptidase. The presence of added copper in the microcosms elicited, after 21 days of incubation, generalised anoxia and a decrease in organic matter content. The non-eroded surface of the copper-spiked sediment showed, when compared to the control, a decrease in bacterial abundance and significant lower levels of bacterial production and of leucine turnover rate. Bacterial production and leucine turnover rate decreased to 1.4% and 13% of the control values, respectively. Ectoenzymatic activities were also negatively affected but by smaller factors. After erosion by the water current in laboratory flume conditions, the eroded surface of the control sediment showed a generalised decline in all bacterial activities. The erosion of the copper-spiked sediment showed, however, two types of responses with respect to bacterial activities at the exposed surface: positive responses of bacterial production and leucine turnover rate contrasting with slight negative responses of ectoenzymatic activities. The effects of experimental erosion in the suspended cells were also different in the control and in the copper-spiked sediment. Bacterial cells in the control microcosm exhibited, when compared to the non-eroded sediment cells, decreases in all activities after the 6-h suspension. The response of the average suspended copper-spiked sediment cell differed from the control by a less sharp decrease in ectoenzymatic activities and, mainly, by the great intensification of bacterial biomass production and leucine turnover rate. We conclude that the bacterial community of silty estuarine sediments seems to withstand considerable concentrations of copper at the cost of reduced bacterial organic matter degradation and of the almost halting of bacterial production. The toxic effects elicited by copper on protein and carbohydrate degradation were not rapidly repaired by erosion and oxygenation of the sediment cells but, in contrast, bacterial biomass production and leucine turnover were rapidly and efficiently reactivated.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus.

PubMed

Kellogg, Christina A; Ross, Steve W; Brooke, Sandra D

2016-01-01

Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus . Samples from five colonies of P. placomus were collected from Baltimore Canyon (379-382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68-90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas , which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

USGS Publications Warehouse

Kellogg, Christina A.; Ross, Steve W.; Brooke, Sandra D.

2016-01-01

Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomuscolonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomusdoes not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Fungal Innate Immunity Induced by Bacterial Microbe-Associated Molecular Patterns (MAMPs)

PubMed Central

Ipcho, Simon; Sundelin, Thomas; Erbs, Gitte; Kistler, H. Corby; Newman, Mari-Anne; Olsson, Stefan

2016-01-01

Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal–bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposing Fusarium graminearum to bacterial MAMPs led to increased fungal membrane hyperpolarization, a putative defense response, and a range of transcriptional responses. The fungus reacted with a different transcript profile to each of the three tested MAMPs, although a core set of genes related to energy generation, transport, amino acid production, secondary metabolism, and especially iron uptake were detected for all three. Half of the genes related to iron uptake were predicted MirA type transporters that potentially take up bacterial siderophores. These quick responses can be viewed as a preparation for further interactions with beneficial or pathogenic bacteria, and constitute a fungal innate immune response with similarities to those of plants and animals. PMID:27172188

Perturbing Tandem Energy Transfer in Luminescent Heterobinuclear Lanthanide Coordination Polymer Nanoparticles Enables Real-Time Monitoring of Release of the Anthrax Biomarker from Bacterial Spores.

PubMed

Gao, Nan; Zhang, Yunfang; Huang, Pengcheng; Xiang, Zhehao; Wu, Fang-Ying; Mao, Lanqun

2018-06-05

Lanthanide-based luminescent sensors have been widely used for the detection of the anthrax biomarker dipicolinic acid (DPA). However, mainly based on DPA sensitization to the lanthanide core, most of them failed to realize robust detection of DPA in bacterial spores. We proposed a new strategy for reliable detection of DPA by perturbing a tandem energy transfer in heterobinuclear lanthanide coordination polymer nanoparticles simply constructed by two kinds of lanthanide ions, Tb 3+ and Eu 3+ , and guanosine 5'-monophosphate. This smart luminescent probe was demonstrated to exhibit highly sensitive and selective visual luminescence color change upon exposure to DPA, enabling accurate detection of DPA in complex biosystems such as bacterial spores. DPA release from bacterial spores on physiological germination was also successfully monitored in real time by confocal imaging. This probe is thus expected to be a powerful tool for efficient detection of bacterial spores in responding to anthrax threats.

Antigenic potential of a highly conserved Neisseria meningitidis lipopolysaccharide inner core structure defined by chemical synthesis.

PubMed

Reinhardt, Anika; Yang, You; Claus, Heike; Pereira, Claney L; Cox, Andrew D; Vogel, Ulrich; Anish, Chakkumkal; Seeberger, Peter H

2015-01-22

Neisseria meningitidis is a leading cause of bacterial meningitis worldwide. We studied the potential of synthetic lipopolysaccharide (LPS) inner core structures as broadly protective antigens against N. meningitidis. Based on the specific reactivity of human serum antibodies to synthetic LPS cores, we selected a highly conserved LPS core tetrasaccharide as a promising antigen. This LPS inner core tetrasaccharide induced a robust IgG response in mice when formulated as an immunogenic glycoconjugate. Binding of raised mouse serum to a broad collection of N. meningitidis strains demonstrated the accessibility of the LPS core on viable bacteria. The distal trisaccharide was identified as the crucial epitope, whereas the proximal Kdo moiety was immunodominant and induced mainly nonprotective antibodies that are responsible for lack of functional protection in polyclonal serum. Our results identified key antigenic determinants of LPS core glycan and, hence, may aid the design of a broadly protective immunization against N. meningitidis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solution Structure of Homology Region (HR) Domain of Type II Secretion System*

PubMed Central

Gu, Shuang; Kelly, Geoff; Wang, Xiaohui; Frenkiel, Tom; Shevchik, Vladimir E.; Pickersgill, Richard W.

2012-01-01

The type II secretion system of Gram-negative bacteria is important for bacterial pathogenesis and survival; it is composed of 12 mostly multimeric core proteins, which build a sophisticated secretion machine spanning both bacterial membranes. OutC is the core component of the inner membrane subcomplex thought to be involved in both recognition of substrate and interaction with the outer membrane secretin OutD. Here, we report the solution structure of the HR domain of OutC and explore its interaction with the secretin. The HR domain adopts a β-sandwich-like fold consisting of two β-sheets each composed of three anti-parallel β-strands. This structure is strikingly similar to the periplasmic region of PilP, an inner membrane lipoprotein from the type IV pilus system highlighting the common evolutionary origin of these two systems and showing that all the core components of the type II secretion system have a structural or sequence ortholog within the type IV pili system. The HR domain is shown to interact with the N0 domain of the secretin. The importance of this interaction is explored in the context of the functional secretion system. PMID:22253442

Biodegradation of 2,4,6-tribromophenol during transport in fractured chalk.

PubMed

Arnon, Shai; Adar, Eilon; Ronen, Zeev; Nejidat, Ali; Yakirevich, Alexander; Nativ, Ronit

2005-02-01

The effect of physicochemical conditions (residence time, oxygen concentrations, and chalk characteristics) on the biodegradation of 2,4,6-tribromophenol (TBP) during transport was investigated in low-permeability fractured-chalk cores. Long-term (approximately 600 d) biodegradation experiments were conducted in two cores (approximately 21 cm diameter, 31 and 44 cm long, respectively), intersected by a natural fracture. TBP was used as a model contaminant and as the sole carbon source for aerobic microbial activity. Bacterial isolates were recovered and identified by both Biolog identification kit and 16S rDNA sequences from batch enrichment cultures. One of the strains, with 98% similarity (based on the 16S rDNA data) to Achromobacter xylosoxidans, was shown to have the ability to degrade TBP in the presence of chalk. The decrease in TBP concentration along the fracture due to biodegradation was not affected by reducing the residence time from 49 to 8 min. In contrast, adding oxygen to the water at the inlet and increasing the flow rates improved TBP removal. Although the matrix pore-size distribution limits microbial activity to the fracture void, the chalk appears to provide an excellent environment for biodegradation activity. Approximately 90% of TBP removal occurred within 10 cm of the TBP source, indicating that in-situ bioremediation can be used to remove organic contaminants in low-permeability fractured rocks if nutrient-delivery pathways within the aquifer are secured.

Diversity and physiology of culturable bacteria associated with a coastal Antarctic ice core.

PubMed

Antony, Runa; Krishnan, K P; Laluraj, C M; Thamban, Meloth; Dhakephalkar, P K; Engineer, Anupama S; Shivaji, S

2012-06-20

Microbiological studies of polar ice at different depths may provide important comparisons, as they preserve records of microbial cells and past climate. In this study, we examined bacterial abundance, diversity and glaciochemical composition from three depths of an ice core from coastal Dronning Maud Land, East Antarctica. Higher bacterial abundance corresponded with high in situ sea-salt Na(+) and dust concentration, suggesting that bacteria might have been transported and deposited into ice along with dust particles and marine aerosols. Fourteen bacterial isolates belonging to the genera Methylobacterium, Brevundimonas, Paenibacillus, Bacillus and Micrococcus were retrieved. Frequent isolation of similar bacterial genera from different cold environments suggests that they possess features that enable survival and metabolism for extended periods of time at sub-zero temperatures. The highest number and diversity of recoverable bacteria was obtained from 49 m depth corresponding to 1926 AD and consisted of bacteria from 4 different genera whereas at 11 m (1989 AD) and 33 m (1953 AD) samples only species belonging to the genera Bacillus was recovered. Among the Bacillus species, Bacillus aryabhattai which has been reported only from the upper stratosphere, was isolated and is the first record from the Earth's surface. Methylobacterium was the most dominant genera at 49 m depth and its prevalence is attributable to a combination of high in situ methanesulfonate concentration, specialized metabolism and environmental hardiness of Methylobacterium. Some of the isolated bacteria were found to respire and grow using methanesulfonate, suggesting that they may utilize this substrate to sustain growth in ice. In addition, NO(3)(-) (2.93-3.69 μM), NH(4)(+) (1.45-3.90 μM) and PO(4)(3-) (0.01-0.75 μM) present in the ice could be potential sources fueling bacterial metabolism in this environment. It could be deduced from the study that variation in bacterial abundance and diversity was probably associated with the prevailing in situ conditions in ice. Copyright © 2012 Elsevier GmbH. All rights reserved.

Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge.

PubMed

Petri, Renee M; Schwaiger, Tyler; Penner, Greg B; Beauchemin, Karen A; Forster, Robert J; McKinnon, John J; McAllister, Tim A

2013-01-01

This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated.

Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge

PubMed Central

Petri, Renee M.; Schwaiger, Tyler; Penner, Greg B.; Beauchemin, Karen A.; Forster, Robert J.; McKinnon, John J.; McAllister, Tim A.

2013-01-01

This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated. PMID:24391765

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Diversity, specificity, co-occurrence and hub taxa of the bacterial-fungal pollen microbiome.

PubMed

Manirajan, Binoy Ambika; Maisinger, Corinna; Ratering, Stefan; Rusch, Volker; Schwiertz, Andreas; Cardinale, Massimiliano; Schnell, Sylvia

2018-06-06

Flower pollen represents a unique microbial habitat, however the factors driving microbial assemblages and microbe-microbe interactions remain largely unexplored. Here we compared the structure and diversity of the bacterial-fungal microbiome between eight different pollen species (four wind-pollinated and four insect-pollinated) from close geographical locations, using high-throughput sequencing of a 16S the rRNA gene fragment (bacteria) and the internal transcribed spacer 2 (ITS2, fungi). Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla, respectively. Pseudomonas (bacterial) and Cladosporium (fungal) were the most abundant genera. Both bacterial and fungal microbiota were significantly influenced by plant species and pollination type, but showed a core microbiome consisting of 12 bacterial and 33 fungal genera. Co-occurrence analysis highlighted significant inter- and intra-kingdom interactions, and the interaction network was shaped by four bacterial hub taxa: Methylobacterium (two OTUs), Friedmanniella and Rosenbergiella. Rosenbergiella prevailed in insect-pollinated pollen and was negatively correlated with the other hubs, indicating habitat complementarity. Inter-kingdom co-occurrence showed a predominant effect of fungal on bacterial taxa. This study enhances our basic knowledge of pollen microbiota, and poses the basis for further inter- and intra-kingdom interaction studies in the plant reproductive organs.

Different Types of Dietary Fibers Trigger Specific Alterations in Composition and Predicted Functions of Colonic Bacterial Communities in BALB/c Mice.

PubMed

Luo, Yuheng; Zhang, Ling; Li, Hua; Smidt, Hauke; Wright, André-Denis G; Zhang, Keying; Ding, Xuemei; Zeng, Qiufeng; Bai, Shiping; Wang, Jianping; Li, Jian; Zheng, Ping; Tian, Gang; Cai, Jingyi; Chen, Daiwen

2017-01-01

Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice ( n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake ( p < 0.05) but no change on the average body weight gain ( p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate ( p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups ( p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased ( p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides , Dehalobacterium , and Prevotella , including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia , Odoribacter , and Coprococcus were significantly more abundant in group M, whereas Oscillospira , Desulfovibrio , and Ruminoccaceae , typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM ( p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria , Betaproteobacteria , Gammaproteobacteria (including Enterobacteriaceae ) and Deltaproteobacteria , were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of "Energy metabolism" and "Carbohydrate metabolism" pathways in mice from group G and M, suggesting that the altered bacterial community in the colon of mice with the two dietary fibers probably resulted in a more efficient degradation of dietary polysaccharides. Our result suggests that the influence of dietary β-glucan (SDF) on colonic bacterial community of mice was more extensively than MCC (IDF). Co-supplementation of the two fibers may help to increase the bacterial diversity and reduce the conditional pathogens in the colon of mice.

Noble metal-modified titania with visible-light activity for the decomposition of microorganisms

PubMed Central

Endo, Maya; Wei, Zhishun; Wang, Kunlei; Karabiyik, Baris; Yoshiiri, Kenta; Rokicka, Paulina; Ohtani, Bunsho

2018-01-01

Commercial titania photocatalysts were modified with silver and gold by photodeposition, and characterized by diffuse reflectance spectroscopy (DRS), X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and scanning transmission electron microscopy (STEM). It was found that silver co-existed in zero valent (core) and oxidized (shell) forms, whereas gold was mainly zero valent. The obtained noble metal-modified samples were examined with regard to antibacterial (Escherichia coli (E. coli)) and antifungal (Aspergillus niger (A. niger), Aspergillus melleus (A. melleus), Penicillium chrysogenum (P. chrysogenum), Candida albicans (C. albicans)) activity under visible-light irradiation and in the dark using disk diffusion, suspension, colony growth (“poisoned food”) and sporulation methods. It was found that silver-modified titania, besides remarkably high antibacterial activity (inhibition of bacterial proliferation), could also decompose bacterial cells under visible-light irradiation, possibly due to an enhanced generation of reactive oxygen species and the intrinsic properties of silver. Gold-modified samples were almost inactive against bacteria in the dark, whereas significant bactericidal effect under visible-light irradiation suggested that the mechanism of bacteria inactivation was initiated by plasmonic excitation of titania by localized surface plasmon resonance of gold. The antifungal activity tests showed efficient suppression of mycelium growth by bare titania, and suppression of mycotoxin generation and sporulation by gold-modified titania. Although, the growth of fungi was hardly inhibited through disc diffusion (inhibition zones around discs), it indicates that gold does not penetrate into the media, and thus, a good stability of plasmonic photocatalysts has been confirmed. In summary, it was found that silver-modified titania showed superior antibacterial activity, whereas gold-modified samples were very active against fungi, suggesting that bimetallic photocatalysts containing both gold and silver should exhibit excellent antimicrobial properties. PMID:29600144

Neo-Archaean Palaeo-Environmental Changes Determined by Microbial Activities Using Stable Isotopic Compositions.

NASA Astrophysics Data System (ADS)

Grassineau, N.; Yang, J.; Zerkle, A.; Nisbet, E. G.

2017-12-01

Reconstitution of Archaean environments can be challenging due to the lack of complete rock records and thermal overprinting, and information is then lost. Many past studies have been based on scattered results because of limited material available. They relate to very specific time "capsules" and it is not always appropriate to generalize the findings at a global scale. As now in the Phanerozoic, environmental variations existed in the Archaean and one model-fits-all can be misleading. Recent studies have uncovered how remarkably similar some of the conditions in the Archaean are to more recent periods. Each new Archaean locality adds to the general database to help to create a more complete picture, however a continuous record for one locality can bring more information because of its temporal and spatial context. Studying metabolisms of early life in Archaean is a very good approach to determine environmental conditions, and Greenstone Belts are the preferred formations to look for traces of life. Carbon and sulphur isotopes are important tools to study them, as metabolic processes leave isotopic fingerprints, which are often the only remaining evidence of biological activity. Study of carbon- and sulphur-rich cherts and dark shales of 2.7 to 2.65 Ga deposited in a sedimentary basin, from three well-preserved cores and coexisting stromatolites in the Belingwe Greenstone Belt (Zimbabwe), allows reconstitution of contemporary Archaean environments by determining how life responded to changes in its ecosystem. Overall ranges of 39‰ for delta13Cred and 40‰ for delta34S suggest a wide spectrum of bacterial activities. There is evidence of a change from aerobic to more anaerobic activity, most likely due to modification of the environmental conditions. New major and trace element data also confirm changes in the basin deposition with decrease in Al, K, Ba and Rb concentrations towards the upper sediments. These parameters indicate a deepening of the basin. The reducing environment corresponds to a lower sedimentation rate. Stable isotopic study of microbial activities in 3 cores determines spatial and temporal variation within the basin at different depths. Even in the Neo-Archaean, well established sulphur and carbon biological cycles allowed interactive bacterial communities to adapt to the changing environment.

Silencing of ecdysone receptor, insect intestinal mucin and sericotropin genes by bacterially produced double-stranded RNA affects larval growth and development in Plutella xylostella and Helicoverpa armigera.

PubMed

Israni, B; Rajam, M V

2017-04-01

RNA interference mediated gene silencing, which is triggered by double-stranded RNA (dsRNA), has become a important tool for functional genomics studies in various systems, including insects. Bacterially produced dsRNA employs the use of a bacterial strain lacking in RNaseIII activity and harbouring a vector with dual T7 promoter sites, which allow the production of intact dsRNA molecules. Here, we report an assessment of the functional relevance of the ecdysone receptor, insect intestinal mucin and sericotropin genes through silencing by dsRNA in two lepidopteran insect pests, Helicoverpa armigera and Plutella xylostella, both of which cause serious crop losses. Oral feeding of dsRNA led to significant reduction in transcripts of the target insect genes, which caused significant larval mortality with various moulting anomalies and an overall developmental delay. We also found a significant decrease in reproductive potential in female moths, with a drop in egg laying and compromised egg hatching from treated larvae as compared to controls. dsRNA was stable in the insect gut and was efficiently processed into small interfering RNAs (siRNAs), thus accounting for the phenotypes observed in the present work. The study revealed the importance of these genes in core insect processes, which are essential for insect development and survival. © 2016 The Royal Entomological Society.

Hepatitis C virus core protein subverts the antiviral activities of human Kupffer cells.

PubMed

Tu, Zhengkun; Pierce, Robert H; Kurtis, Jonathan; Kuroki, Yoshio; Crispe, I Nicholas; Orloff, Mark S

2010-01-01

Kupffer cells (KC) are important innate immune cells of the liver, functioning as scavenging sinusoidal phagocytes and transducers of pattern recognition signals, including those of toll-like receptors (TLRs). The hepatitis C virus core protein (HCVc) engages TLR2 on peripheral blood monocytes and induces production of multiple inflammatory cytokines. We examined the effects of HCVc on human primary KC functions. KC were isolated from living donor allografts and stimulated with HCVc and/or ligands for TLRs. KC were examined for production of cytokines, expression of programmed death-ligand 1 (PD-L1), secretion of type 1 interferons (IFNs), and expression of the apoptosis-inducing protein tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL). HCVc acts as a ligand for TLR2 on human KC, inducing them to secrete interleukin (IL)-1beta, TNF-alpha, and IL-10 and up-regulate cell surface PD-L1. HCVc blocked TLR3-mediated secretion of IFN-alpha, IFN-beta, and cell surface expression of the cytotoxic molecule TRAIL. Inhibition of phosphoinositide 3 kinase with LY294002 blocked the up-regulation of PD-L1 by TLR ligands and the TLR3-specific induction of TRAIL and type 1 IFNs. KC are intravascular macrophages that are continuously exposed to, and tolerant of, bacterial TLR ligands, which are delivered via the portal circulation. By mimicking a bacterial TLR2 ligand and effectively blocking the TLR3-mediated, double-stranded RNA-induced antiviral response, HCVc might appear to exploit this unique aspect of immunity in the liver. Copyright 2010 AGA Institute. Published by Elsevier Inc. All rights reserved.

Manure fertilization alters the population of ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea in a paddy soil.

PubMed

Wang, Yu; Zhu, Guibing; Song, Liyan; Wang, Shanyun; Yin, Chengqing

2014-03-01

Manure fertilizers are widely used in agriculture and highly impacted the soil microbial communities such as ammonia oxidizers. However, the knowledge on the communities of archaeal versus bacterial ammonia oxidizers in paddy soil affected by manure fertilization remains largely unknown, especially for a long-term influence. In present work, the impact of manure fertilization on the population of ammonia oxidizers, related potential nitrification rates (PNRs) and the key factors manipulating the impact were investigated through studying two composite soil cores (long-term fed with manure fertilization versus undisturbed). Moreover, soil incubated with NH(4)(+) for 5 weeks was designed to verify the field research. The results showed that the copy numbers of bacterial amoA gene in the manure fed soil were significant higher than those in the unfed soil (p < 0.05), suggesting a clear stimulating effect of long-term manure fertilization on the population of ammonia-oxidizing bacteria (AOB). The detected PNRs in the manure fed soil core (14-218 nmol L(-1)  N g(-1)  h(-1)) were significant higher than those in the unfed soil core (5-72 nmol L(-1)  N g(-1)  h(-1) ; p < 0.05). Highly correlations between the PNRs and the bacterial amoA gene copies rather than archaeal amoA gene were observed, indicating strong nitrification capacity related to bacterial ammonia oxidizers. The NH(4)(+) -N significantly correlated to the abundance of AOB (p < 0.01) and explained 96.1% of the environmental variation, showing the NH(4)(+) -N was the main factor impacting the population of AOB. The incubation experiment demonstrated a clear increase of the bacterial amoA gene abundance (2.0 × 10(6) to 8.4 × 10(6)  g(-1) d.w.s. and 1.6 × 10(4) to 4.8 × 10(5)  g(-1) d.w.s.) in both soil but not for the archaeal amoA gene, in agreement with the field observation. Overall, our results suggested that manure fertilization promoted the population size of bacterial ammonia oxidizers rather than their archaeal counterparts whether in long-term or short-term usage and the NH(4)(+) -N was the key impact factor. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In situ experimentation at the water/sediment interface in the deep sea: 2. Biotransformation of dissolved organic substrates by microbial communities at 2000m depth in the Bay of Biscay

NASA Astrophysics Data System (ADS)

Cahet, Guy; Daumas, Raoul; Sibuet, Myriam

Few attempts have been made to quantify the utilization of organic matter by the bacteria of the superficial layers of deep sea sediment. During two BIOCYAN cruises (August 1986 and June 1987) we used the submersible Cyana, to incubate sediment samples in situ in a specially designed box core in presence of 14C-glutamic acid and 3H leucine. These experiments were conducted at 2000m depth in the Bay of Biscay. Bacterial activity was stopped by the injection of formaldehyde. Samples were retrieved with the research submersible Cyana and its accompanying free vehicle shuttle. Sediment organic matter was fractioned into four components: 1) 14CO 2; 2) nucleic components and polysacharids; 3) labile proteins; and 4) condensed hydrolysable polymers. To evaluate the barotolerance of deep-sea bacteria, undisturbed superficial layer samples were also incubated with the same labelled substrates at 4°C at the atmospheric pressure. In both cases, and except for glucose, our results show that distributions of radioactivity in the different components of the organic material were almost similar. However, the rate of incorporation was usually higher for in situ experiments than for decompressed samples. Bacterial utilization of both 14C glutamic acid and 14C glucose were higher in June than in August. Such differences may result from changes in the food supply arriving as sinking particles and deriving from the photosynthetically productive surface waters. Food input was probably more important in June than in August leading to corresponding increases in: 1) the abundance of derived bacteria, and 2) deep-sea bacterial activities.

The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair.

PubMed

Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

2012-11-01

Base excision repair (BER) is one of the most commonly used DNA repair pathways involved in genome stability. X-family DNA polymerases (PolXs) play critical roles in BER, especially in filling single-nucleotide gaps. In addition to a polymerase core domain, bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain with phosphoesterase activity which is also required for BER. However, the role of the PHP domain of PolX in bacterial BER remains unresolved. We found that the PHP domain of Thermus thermophilus HB8 PolX (ttPolX) functions as two types of phosphoesterase in BER, including a 3'-phosphatase and an apurinic/apyrimidinic (AP) endonuclease. Experiments using T. thermophilus HB8 cell lysates revealed that the majority of the 3'-phosphatase and AP endonuclease activities are attributable to the another phosphoesterase in T. thermophilus HB8, endonuclease IV (ttEndoIV). However, ttPolX possesses significant 3'-phosphatase activity in ΔttendoIV cell lysate, indicating possible complementation. Our experiments also reveal that there are only two enzymes that display the 3'-phosphatase activity in the T. thermophilus HB8 cell, ttPolX and ttEndoIV. Furthermore, phenotypic analysis of ΔttpolX, ΔttendoIV, and ΔttpolX/ΔttendoIV using hydrogen peroxide and sodium nitrite supports the hypothesis that ttPolX functions as a backup for ttEndoIV in BER. Copyright © 2012 Elsevier B.V. All rights reserved.

Greenlandic Microbiomes and Greenhouse Gas Emissions

NASA Astrophysics Data System (ADS)

Jacobsen, C. S.; Nielsen, M. S.; Priemé, A.; Holben, W. E.; Stibal, M.; Morales, S.; Bælum, J.; Elberling, B.; Kuhry, P.; Hugelius, G.

2014-12-01

Thawing permafrost and the resulting mineralization of previously frozen organic carbon (C) and nitrogen (N) are considered important future feedbacks from terrestrial ecosystems to the atmosphere. We characterized two contrasting permafrost cores as well as 21 top permafrost cores from Zackenberg in High-Arctic Greenland which is a site characterized by progressive permafrost thawing of more than 1 cm y-1 since 1996. Samples have been analyzed for total C and N content, dissolved C and N as well as the potential production of carbon dioxide, methane and nitrous oxide in an incubation experiment. 10 days after the thawing was initiated, rRNA from selected samples were extracted, transformed into cDNA and cloned to obtain an overview of the most abundant active bacterial populations in the incubation experiment. A total of 697 clones were successfully sequenced, yielding 21 unique OTUs. Despite the relatively high coverage values the diversity of bacteria in the samples was low (with a maximum Shannon-Wiener diversity index of 2.1). Firmicutes (6 OTUs, 45-77% of clones) and Gammaproteobacteria (5 OTUs, 19-47% of clones) were the dominant groups in the samples, with Betaproteobacteria (4 OTUs), Actinobacteria (4 OTUs), Alphaproteobacteria (1 OTU) and Bacteroidetes (1 OTU) being less dominant. These characterizations revealed that those bacteria that are able to quickly colonize the thawing permafrost are mainly related to three groups of bacterial clones: Lysinibacillus; Pseudomonas and Clostridium. Quantification of functional genes related to soil nitrogen transformation were performed both on the DNA and on the mRNA level using primers specific for genes involved in production of nitrous oxide (nirS, nirK) and consumption of nitrous oxide (nosZ). This showed that the genes were found in most soils, but that they only were expressed at a low level. We further measured the rates of nitrous oxide release from the soils and found that these were not clearly related to the potential (DNA) and activity (mRNA) found in the soils. However, distinct differences were found in the active microbiomes of the thawed soils, and this is discussed in relation to the emission of N2O, CH4 and CO2.

Identification of an unusual type II thioesterase in the dithiolopyrrolone antibiotics biosynthetic pathway.

PubMed

Zhai, Ying; Bai, Silei; Liu, Jingjing; Yang, Liyuan; Han, Li; Huang, Xueshi; He, Jing

2016-04-22

Dithiolopyrrolone group antibiotics characterized by an electronically unique dithiolopyrrolone heterobicyclic core are known for their antibacterial, antifungal, insecticidal and antitumor activities. Recently the biosynthetic gene clusters for two dithiolopyrrolone compounds, holomycin and thiomarinol, have been identified respectively in different bacterial species. Here, we report a novel dithiolopyrrolone biosynthetic gene cluster (aut) isolated from Streptomyces thioluteus DSM 40027 which produces two pyrrothine derivatives, aureothricin and thiolutin. By comparison with other characterized dithiolopyrrolone clusters, eight genes in the aut cluster were verified to be responsible for the assembly of dithiolopyrrolone core. The aut cluster was further confirmed by heterologous expression and in-frame gene deletion experiments. Intriguingly, we found that the heterogenetic thioesterase HlmK derived from the holomycin (hlm) gene cluster in Streptomyces clavuligerus significantly improved heterologous biosynthesis of dithiolopyrrolones in Streptomyces albus through coexpression with the aut cluster. In the previous studies, HlmK was considered invalid because it has a Ser to Gly point mutation within the canonical Ser-His-Asp catalytic triad of thioesterases. However, gene inactivation and complementation experiments in our study unequivocally demonstrated that HlmK is an active distinctive type II thioesterase that plays a beneficial role in dithiolopyrrolone biosynthesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Antibiotic-loaded, silver core-embedded mesoporous silica nanovehicles as a synergistic antibacterial agent for the treatment of drug-resistant infections.

PubMed

Wang, Yao; Ding, Xiali; Chen, Yuan; Guo, Mingquan; Zhang, Yan; Guo, Xiaokui; Gu, Hongchen

2016-09-01

Drug-resistant bacterial infections have become one of the most serious risks in public health as they make the conventional antibiotics less efficient. There is an urgent need for developing new generations of antibacterial agents in this field. In this work, a nanoplatform of LEVO-loaded and silver core-embedded mesoporous silica nanovehicles (Ag@MSNs@LEVO) is demonstrated as a synergistic antibacterial agent for the treatment of drug-resistant infections both in vitro and in vivo. The combination of the inner Ag core and the loaded antibiotic drug in mesopores endows the single-particle nanoplatform with a synergistic effect on killing the drug-resistant bacteria. The nanoplatform of Ag@MSNs@LEVO exhibits superior antibacterial activity to LEVO-loaded MSNs (MSNs@LEVO) and silver core-embedded MSNs (Ag@MSNs) in vitro. In the in vivo acute peritonitis model, the infected drug-resistant Escherichia coli GN102 in peritoneal cavity of the mice is reduced by nearly three orders of magnitude and the aberrant pathological feature of spleen and peritoneum disappears after treatment with Ag@MSNs@LEVO. Importantly, this nanopaltform renders no obvious toxic side effect to the mice during the tested time. There is no doubt that this study strongly indicates a promising potential of Ag@MSNs@LEVO as a synergistic and safety therapy tool for the clinical drug-resistant infections. Copyright © 2016 Elsevier Ltd. All rights reserved.

In Silico Characterization of the Binding Affinity of Dendrimers to Penicillin-Binding Proteins (PBPs): Can PBPs be Potential Targets for Antibacterial Dendrimers?

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Ramesh, Muthusamy; Kalhapure, Rahul; Suleman, Nadia; Govender, Thirumala

2016-04-01

We have shown that novel silver salts of poly (propyl ether) imine (PETIM) dendron and dendrimers developed in our group exhibit preferential antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus. This led us to examine whether molecular modeling methods could be used to identify the key structural design principles for a bioactive lead molecule, explore the mechanism of binding with biological targets, and explain their preferential antibacterial activity. The current article reports the conformational landscape as well as mechanism of binding of generation 1 PETIM dendron and dendrimers to penicillin-binding proteins (PBPs) in order to understand the antibacterial activity profiles of their silver salts. Molecular dynamics at different simulation protocols and conformational analysis were performed to elaborate on the conformational features of the studied dendrimers, as well as to create the initial structure for further binding studies. The results showed that for all compounds, there were no significant conformational changes due to variation in simulation conditions. Molecular docking calculations were performed to investigate the binding theme between the studied dendrimers and PBPs. Interestingly, in significant accordance with the experimental data, dendron and dendrimer with aliphatic cores were found to show higher activity against S. aureus than the dendrimer with an aromatic core. The latter showed higher activity against MRSA. The findings from this computational and molecular modeling report together with the experimental results serve as a road map toward designing more potent antibacterial dendrimers against resistant bacterial strains.

THE RELATIONSHIP OF THE CHEMOTACTIC BEHAVIOR OF THE COMPLEMENT-DERIVED FACTORS, C3a, C5a, AND C567, AND A BACTERIAL CHEMOTACTIC FACTOR TO THEIR ABILITY TO ACTIVATE THE PROESTERASE 1 OF RABBIT POLYMORPHONUCLEAR LEUKOCYTES

PubMed Central

Becker, Elmer L.

1972-01-01

The inhibition profiles obtained when a series of p-nitrophenyl ethyl alkylphosphonates and of p-nitrophenyl ethyl chloroalkylphosphonates were used to interfere with the chemotactic activity of polymorphonuclear leukocytes stimulated by C3a, C5a, and bacterial factor were the same as found previously when C567 was the chemotactic agent. This indicates that as in the chemotactic activity induced by C567, an obligatory step in the chemotaxis caused by C3a, C5a, and bacterial factor is the activation of proesterase 1 of the rabbit polymorphonuclear leukocyte. C5a and C3a activate proesterase 1 of peripheral blood polymophonuclear leukocytes as measured by the increase of acetyl DL-phenylalanine β-naphthyl esterase activity. Attempts to detect in a like manner the proesterase 1 of the same leukocytes using bacterial factor under varying circumstances have consistently failed. It is concluded that bacterial factor, for unknown reasons, is unable to activate proesterase 1 to the same extent as the complement-derived chemotactic factors. The hypothesis of there being a quantitative difference in the ability of bacterial factor to activate proesterase 1 compared with the complement-derived factors explains the previous observations that bacterial factor can not deactivate to itself or to the complement-derived factors, although these latter factors can deactivate to themselves, to each other, and to the bacterial factor. The quantitative difference in the ability of bacterial factor to activate proesterase 1 compared to the complement-derived factors is also associated with and explains the finding that the maximal chemotactic activity attainable when bacterial factor is the chemotactic agent is distinctly less than that obtained using either C3a, C5a, or C567. These results indicate that the activation of proesterase 1 is a general requirement for the chemotactic activity of rabbit polymorphonuclear leukocytes with known macromolecular chemotactic agents and suggest that under several different circumstances the level of chemotactic activity attained is related to the degree of such activation. PMID:4551218

Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

PubMed

Bressuire-Isoard, Christelle; Broussolle, Véronique; Carlin, Frédéric

2018-05-17

Bacterial spores are resistant to physical and chemical insults, which make them a major concern for public health and for industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection, and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination, and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.

Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa.

PubMed

Villegas, Luis Martínez; Pimenta, Paulo Filemon Paolucci

2014-08-01

Anophelines harbour a diverse microbial consortium that may represent an extended gene pool for the host. The proposed effects of the insect microbiota span physiological, metabolic and immune processes. Here we synthesise how current metagenomic tools combined with classical culture-dependent techniques provide new insights in the elucidation of the role of the Anopheles-associated microbiota. Many proposed malaria control strategies have been based upon the immunomodulating effects that the bacterial components of the microbiota appear to exert and their ability to express anti-Plasmodium peptides. The number of identified bacterial taxa has increased in the current "omics" era and the available data are mostly scattered or in "tables" that are difficult to exploit. Published microbiota reports for multiple anopheline species were compiled in an Excel® spreadsheet. We then filtered the microbiota data using a continent-oriented criterion and generated a visual correlation showing the exclusive and shared bacterial genera among four continents. The data suggested the existence of a core group of bacteria associated in a stable manner with their anopheline hosts. However, the lack of data from Neotropical vectors may reduce the possibility of defining the core microbiota and understanding the mosquito-bacteria interactive consortium.

Effect of organic contamination upon microbial distributions and heterotrophic uptake in a cape cod, mass., aquifer

USGS Publications Warehouse

Harvey, R.W.; Smith, R.L.; George, L.

1984-01-01

Bacterial abundance, distribution, and heterotrophic uptake in a freshwater aquifer contaminated by treated sewage were determined from analyses of groundwater and sediment-core samples. The number of free-living (unattached) bacteria in contaminated groundwater declined steadily with increasing distance from the source of sewage infiltration, from 1.94 ?? (?? 0.20) x 106 ml-1 at 0.21 km to 0.25 (?? 0.02) x 106 ml-1 at 0.97 km. Bacterial abundance in groundwater sampled at 0.31 km correlated strongly with specific conductance and increased sharply from 4.0 (?? 0.3) x 104 ml-1 at a depth of 6 m to 1.58 (?? 0.12) x 106 ml-1 at 14 m, then declined at 20 and 31 m to 1.29 (?? 0.12) x 106 and 0.96 (?? 0.12) x 106 ml-1, respectively. A majority of the bacteria in contaminated and uncontaminated zones of the aquifer were bound to the surfaces of particulates, <60 ??m in diameter. The glucose uptake rate, assayed at in situ and 5 ??M concentrations, declined steadily in contaminated groundwater sampled along a transect. A preparative wet-sieving technique for use in processing core samples for bacterial enumeration is described and evaluated.

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

PubMed Central

Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

2014-01-01

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber

PubMed Central

Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

2017-01-01

Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level. PMID:28966849

Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber.

PubMed

Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

2017-09-01

Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level.

A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations

PubMed Central

Huang, Yvonne J.; Kim, Eugenia; Cox, Michael J.; Brodie, Eoin L.; Brown, Ron; Wiener-Kronish, Jeanine P.

2010-01-01

Abstract Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases. PMID:20141328

Characteristics of aquatic bacterial community and the influencing factors in an urban river.

PubMed

Wang, Peng; Chen, Bo; Yuan, Ruiqiang; Li, Chuangqiong; Li, Yan

2016-11-01

Bacteria play a critical role in environmental and ecological processes in river ecosystems. We studied the bacterial community in the Ganjiang River, a major tributary of the Yangtze River, as it flowed through Nanchang, the largest city in the Ganjiang River basin. Water was sampled at five sites monthly during the wet season, and the bacterial community was characterized using Illumina high-throughput sequencing. A total of 811 operational taxonomic units (OTUs) were observed for all samples, ranging from 321 to 519 for each sample. The bacterial communities were maintained by a core of OTUs that persisted longitudinally and monthly. Actinobacteria (41.17% of total sequences) and Proteobacteria (31.80%) were the dominant phyla, while Firmicutes (mostly genus Lactococcus) became most abundant during flooding. Temperature and flow rate, rather than water chemistry, were the main factors influencing the bacterial community in river water. Temperature was the best individual parameter explaining the variations in OTU abundance, while flow rate was the best individual parameter explaining the variations in phylum abundance. Except for Proteobacteria, the relative abundance of bacterial phyla did not differ significantly between sites, and the degrees of influence of urban landscape on the bacterial community were estimated to be 17%-34%. Copyright © 2016 Elsevier B.V. All rights reserved.

Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core

NASA Technical Reports Server (NTRS)

Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

2003-01-01

The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.

Phylogenetic Analysis of Anaerobic Psychrophilic Enrichment Cultures Obtained from a Greenland Glacier Ice Core

PubMed Central

Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

2003-01-01

The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at −9°C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 × 107 cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at −2°C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years. PMID:12676695

Bacterial Transport in Heterogeneous Porous Media: Laboratory and Field Experiments

NASA Astrophysics Data System (ADS)

Fuller, M. E.

2001-12-01

A fully instrumented research site for examining field-scale bacterial transport has been established on the eastern shore of Virginia. Studies employing intact sediment cores from the South Oyster site have been performed to examine the effects of physical and chemical heterogeneity, to derive transport parameters, and to aid in the selection of bacterial strains for use in field experiments. A variety of innovative methods for tracking bacteria were developed and evaluated under both laboratory and field conditions, providing the tools to detect target cell concentrations in groundwater down to <20 cells/ml, and to perform real-time monitoring in the field. Comprehensive modeling efforts have provided a framework for the layout and instrumentation of the field site, and have aided in the design and interpretation of field-scale bacterial transport experiments. Field transport experiments were conducted in both aerobic and an anoxic flow cells to determine the effects of physical and chemical heterogeneity on field-scale bacterial transport. The results of this research not only contribute to the development of more effective bioremediation strategies, but also have implications for a better understanding of bacterial movement in the subsurface as it relates to public health microbiology and general microbial ecology.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

PubMed

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures

PubMed Central

Wilkins, Laetitia G. E.; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-01-01

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area. PMID:26611640

Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by illumina high-throughput sequencing.

PubMed

Xie, Wan-Ying; Su, Jian-Qiang; Zhu, Yong-Guan

2015-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

PubMed Central

Xie, Wan-Ying

2014-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. PMID:25362067

Bacterial selection by mycospheres of Atlantic Rainforest mushrooms.

PubMed

Halsey, Joshua Andrew; de Cássia Pereira E Silva, Michele; Andreote, Fernando Dini

2016-10-01

This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives.

PubMed

Rokop, Z P; Horton, M A; Newton, I L G

2015-10-01

In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific "core" members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of "noncore" and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Near-bottom pelagic bacteria at a deep-water sewage sludge disposal site.

PubMed

Takizawa, M; Straube, W L; Hill, R T; Colwell, R R

1993-10-01

The epibenthic bacterial community at deep-ocean sewage sludge disposal site DWD-106, located approximately 106 miles (ca. 196 km) off the coast of New Jersey, was assessed for changes associated with the introduction of large amounts of sewage sludge. Mixed cultures and bacterial isolates obtained from water overlying sediment core samples collected at the deep-water (2,500 m) municipal sewage disposal site were tested for the ability to grow under in situ conditions of temperature and pressure. The responses of cultures collected at a DWD-106 station heavily impacted by sewage sludge were compared with those of samples collected from a station at the same depth which was not contaminated by sewage sludge. Significant differences were observed in the ability of mixed bacterial cultures and isolates from the two sites to grow under deep-sea pressure and temperature conditions. The levels of sludge contamination were established by enumerating Clostridium perfringens, a sewage indicator bacterium, in sediment samples from the two sites. The results of hybridization experiments in which DNAs extracted directly from the water overlying sediment core samples were used indicate that the reference site epibenthic community, the disposal site epibenthic community, and the community in a surface sludge plume share many members. Decreased culturability of reference site mixed cultures in the presence of sewage sludge was observed. Thus, the culturable portions of both the autochthonous and allochthonous bacterial communities at the disposal site may be inhibited in situ, the former by sewage sludge and the latter by high pressure and low temperature.

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

PubMed

Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

2017-02-01

Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems.

PubMed

Frouin, Eléonore; Bes, Méline; Ollivier, Bernard; Quéméneur, Marianne; Postec, Anne; Debroas, Didier; Armougom, Fabrice; Erauso, Gaël

2018-01-01

The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing. We show that the bacterial community of the intertidal site is clearly distinct from that of the submarine sites with species distribution patterns driven by only a few abundant populations, affiliated to the Chloroflexi and Proteobacteria phyla. In contrast, the distribution of archaeal taxa seems less site-dependent, as exemplified by the co-occurrence, in both submarine and intertidal sites, of two dominant phylotypes of Methanosarcinales previously thought to be restricted to serpentinizing systems, either marine (Lost City Hydrothermal Field) or terrestrial (The Cedars ultrabasic springs). Over 70% of the phylotypes were rare and included, among others, all those affiliated to candidate divisions. We finally compared the distribution of bacterial and archaeal phylotypes of Prony Hydrothermal Field with those of five previously studied serpentinizing systems of geographically distant sites. Although sensu stricto no core microbial community was identified, a few uncultivated lineages, notably within the archaeal order Methanosarcinales and the bacterial class Dehalococcoidia (the candidate division MSBL5) were exclusively found in a few serpentinizing systems while other operational taxonomic units belonging to the orders Clostridiales, Thermoanaerobacterales , or the genus Hydrogenophaga , were abundantly distributed in several sites. These lineages may represent taxonomic signatures of serpentinizing ecosystems. These findings extend our current knowledge of the microbial diversity inhabiting serpentinizing systems and their biogeography.

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia.

PubMed

Bashenkhaeva, Maria V; Zakharova, Yulia R; Petrova, Darya P; Khanaev, Igor V; Galachyants, Yuri P; Likhoshway, Yelena V

2015-10-01

The sub-ice environment of Lake Baikal represents a special ecotope where strongly increasing microbial biomass causes an "ice-bloom" contributing therefore to the ecosystem functioning and global element turnover under low temperature in the world's largest freshwater lake. In this work, we analyzed bacterial and microalgal communities and their succession in the sub-ice environment in March-April 2010-2012. It was found out that two dinoflagellate species (Gymnodinium baicalense var. minor and Peridinium baicalense Kisselew et Zwetkow) and four diatom species (Aulacoseira islandica, A. baicalensis, Synedra acus subsp. radians, and Synedra ulna) predominated in the microalgal communities. Interestingly, among all microalgae, the diatom A. islandica showed the highest number of physically attached bacterial cells (up to 67 ± 16 bacteria per alga). Bacterial communities analyzed with pyrosequencing of 16S rRNA gene fragments were diverse and represented by 161 genera. Phyla Proteobacteria, Verrucomicrobia, Actinobacteria, Acidobacteria, Bacteroidetes, and Cyanobacteria represented a core community independently on microalgal composition, although the relative abundance of these bacterial phyla strongly varied across sampling sites and time points; unique OTUs from other groups were rare.

Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.

PubMed

Fujii, Takashi; Kato, Takayuki; Namba, Keiichi

2009-11-11

The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.

Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA.

PubMed

Liu, Guo-Hua; Nakamura, Tatsuo; Amemiya, Takashi; Rajendran, Narasimmalu; Itoh, Kiminori

2011-01-01

Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.

Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA.

PubMed

Queck, Shu Y; Khan, Burhan A; Wang, Rong; Bach, Thanh-Huy L; Kretschmer, Dorothee; Chen, Liang; Kreiswirth, Barry N; Peschel, Andreas; Deleo, Frank R; Otto, Michael

2009-07-01

Bacterial virulence and antibiotic resistance have a significant influence on disease severity and treatment options during bacterial infections. Frequently, the underlying genetic determinants are encoded on mobile genetic elements (MGEs). In the leading human pathogen Staphylococcus aureus, MGEs that contain antibiotic resistance genes commonly do not contain genes for virulence determinants. The phenol-soluble modulins (PSMs) are staphylococcal cytolytic toxins with a crucial role in immune evasion. While all known PSMs are core genome-encoded, we here describe a previously unidentified psm gene, psm-mec, within the staphylococcal methicillin resistance-encoding MGE SCCmec. PSM-mec was strongly expressed in many strains and showed the physico-chemical, pro-inflammatory, and cytolytic characteristics typical of PSMs. Notably, in an S. aureus strain with low production of core genome-encoded PSMs, expression of PSM-mec had a significant impact on immune evasion and disease. In addition to providing high-level resistance to methicillin, acquisition of SCCmec elements encoding PSM-mec by horizontal gene transfer may therefore contribute to staphylococcal virulence by substituting for the lack of expression of core genome-encoded PSMs. Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs.

Molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at Vostok, East Antarctica.

PubMed

Alekhina, Irina A; Marie, Dominique; Petit, Jean Robert; Lukin, Valery V; Zubkov, Vladimir M; Bulat, Sergey A

2007-02-01

Decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. At the Vostok drill site, a total of 3650 m of ice core have now been obtained from the East Antarctic ice sheet. The ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. In the present study we used 16S rRNA gene sequencing to analyze the bacterial content of the Vostok drilling fluid sampled from four depths in the borehole. Six phylotypes were identified in three of four samples studied. The two dominant phylotypes recovered from the deepest (3400 and 3600 m) and comparatively warm (-10 degrees C and -6 degrees C, respectively) borehole horizons were from within the genus Sphingomonas, a well-known degrader of polyaromatic hydrocarbons. The remaining phylotypes encountered in all samples proved to be human- or soil-associated bacteria and were presumed to be drilling fluid contaminants of rare occurrence. The results obtained indicate the persistence of bacteria in extremely cold, hydrocarbon-rich environments. They show the potential for contamination of ice and subglacial water samples during lake exploration, and the need to develop a microbiological database of drilling fluid findings.

In vitro anti-biofilm and anti-bacterial activity of Junceella juncea for its biomedical application

PubMed Central

Kumar, P; Selvi, S Senthamil; Govindaraju, M

2012-01-01

Objective To investigate the anti-biofilm and anti-bacterial activity of Junceella juncea (J. juncea) against biofilm forming pathogenic strains. Methods Gorgonians were extracted with methanol and analysed with fourier transform infrared spectroscopy. Biofilm forming pathogens were identified by Congo red agar supplemented with sucrose. A quantitative spectrophotometric method was used to monitor in vitro biofilm reduction by microtitre plate assay. Anti-bacterial activity of methanolic gorgonian extract (MGE) was carried out by disc diffusion method followed by calculating the percentage of increase with crude methanol (CM). Results The presence of active functional group was exemplified by FT-IR spectroscopy. Dry, black, crystalline colonies confirm the production of extracellular polymeric substances responsible for biofilm formation in Congo red agar. MGE exhibited potential anti-biofilm activity against all tested bacterial strains. The anti-bacterial activity of methanolic extract was comparably higher in Salmonella typhii followed by Escherichia coli, Vibrio cholerae and Shigella flexneri. The overall percentage of increase was higher by 50.2% to CM. Conclusions To conclude, anti-biofilm and anti-bacterial efficacy of J. juncea is impressive over biofilm producing pathogens and are good source for novel anti-bacterial compounds. PMID:23593571

Potential antibacterial activity of some Saudi Arabia honey

PubMed Central

Hegazi, Ahmed G.; Guthami, Faiz M. Al; Gethami, Ahmed F. M. Al; Allah, Fyrouz M. Abd; Saleh, Ashraf A.; Fouad, Ehab A.

2017-01-01

Aim: The aim of this study was to investigate the potential antibacterial activity of some Saudi Arabia honey against selected bacterial strains of medical importance. Materials and Methods: A total of 10 Saudi Arabia honey used to evaluate their antimicrobial activity against some antibiotic-resistant pathogenic bacterial strains. The bacterial strains were Staphylococcus aureus, Streptococcus pyogenes, Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa. Results: The antibacterial activity of Saudi honey against five bacterial strains showed different levels of inhibition according to the type of honey. The overall results showed that the potential activity was differing according to the pathogen and honey type. Conclusion: It could be concluded that the Saudi honey inhibit the growth of bacterial strains and that honey can be used as complementary antimicrobial agent against selected pathogenic bacteria. PMID:28344408

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core

PubMed Central

Leite, Deborah C. A.; Leão, Pedro; Garrido, Amana G.; Lins, Ulysses; Santos, Henrique F.; Pires, Débora O.; Castro, Clovis B.; van Elsas, Jan D.; Zilberberg, Carla; Rosado, Alexandre S.; Peixoto, Raquel S.

2017-01-01

The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms. PMID:28223979

Relationship among Phosphorus Circulation Activity, Bacterial Biomass, pH, and Mineral Concentration in Agricultural Soil.

PubMed

Adhikari, Dinesh; Jiang, Tianyi; Kawagoe, Taiki; Kai, Takamitsu; Kubota, Kenzo; Araki, Kiwako S; Kubo, Motoki

2017-12-04

Improvement of phosphorus circulation in the soil is necessary to enhance phosphorus availability to plants. Phosphorus circulation activity is an index of soil's ability to supply soluble phosphorus from organic phosphorus in the soil solution. To understand the relationship among phosphorus circulation activity; bacterial biomass; pH; and Fe, Al, and Ca concentrations (described as mineral concentration in this paper) in agricultural soil, 232 soil samples from various agricultural fields were collected and analyzed. A weak relationship between phosphorus circulation activity and bacterial biomass was observed in all soil samples ( R ² = 0.25), and this relationship became significantly stronger at near-neutral pH (6.0-7.3; R ² = 0.67). No relationship between phosphorus circulation activity and bacterial biomass was observed at acidic (pH < 6.0) or alkaline (pH > 7.3) pH. A negative correlation between Fe and Al concentrations and phosphorus circulation activity was observed at acidic pH ( R ² = 0.72 and 0.73, respectively), as well as for Ca at alkaline pH ( R ² = 0.64). Therefore, bacterial biomass, pH, and mineral concentration should be considered together for activation of phosphorus circulation activity in the soil. A relationship model was proposed based on the effects of bacterial biomass and mineral concentration on phosphorus circulation activity. The suitable conditions of bacterial biomass, pH, and mineral concentration for phosphorus circulation activity could be estimated from the relationship model.

Sustained Ocular Delivery of Ciprofloxacin Using Nanospheres and Conventional Contact Lens Materials

PubMed Central

Garhwal, Rahul; Shady, Sally F.; Ellis, Edward J.; Ellis, Jeanne Y.; Leahy, Charles D.; McCarthy, Stephen P.; Crawford, Kathryn S.

2012-01-01

Purpose. To formulate conventional contact lenses that incorporate nanosphere-encapsulated antibiotic and demonstrate that the lenses provide for sustained antibacterial activity. Methods. A copolymer composed of pullulan and polycaprolactone (PCL) was used to synthesize core-shell nanospheres that encapsulated ciprofloxacin. Bactericidal activity of the nanosphere-encapsulated ciprofloxacin (nanosphere/cipro) was tested by using liquid cultures of either Staphylococcus aureus or Pseudomonas aeruginosa. Nanosphere/cipro was then incorporated into HEMA-based contact lenses that were tested for growth inhibition of S. aureus or P. aeruginosa in liquid cultures inoculated daily with fresh bacteria. Lens designs included thin or thick lenses incorporating nanosphere/cipro and ciprofloxacin-HCl-soaked Acuvue lenses (Acuvue; Johnson & Johnson Vision Care, Inc., Jacksonville, FL). Results. Less than 2 μg/mL of nanosphere/cipro effectively inhibited the proliferation of cultures inoculated with 107 or 108 bacteria/mL of S. aureus and P. aeruginosa, respectively. HEMA-based contact lenses polymerized with nanosphere/cipro were transparent, effectively inhibited the proliferation of greater than 107/mL of bacteria added daily over 3 days of culture, and killed up to 5 × 109 total microbes in a single inoculation. A thicker lens design provided additional inhibition of bacterial growth for up to 96 hours. Conclusions. Core-shell nanospheres loaded with an antibiotic can be incorporated into a conventional, transparent contact lens and provide for sustained and effective bactericidal activity and thereby provide a new drug delivery platform for widespread use in treating ocular disorders. PMID:22266514

Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.

PubMed

Young, Erica B; Sielicki, Jessica; Grothjan, Jacob J

2018-04-20

Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.

Impact of microbial activity on the hydraulic properties of fractured chalk.

PubMed

Arnon, Shai; Adar, Eilon; Ronen, Zeev; Yakirevich, Alexander; Nativ, Ronit

2005-02-01

The impact of microbial activity on fractured chalk transmissivity was investigated on a laboratory scale. Long-term experiments were conducted on six fractured chalk cores (20 cm diameter, 23-44 cm long) containing a single natural fracture embedded in a porous matrix. Biodegradation experiments were conducted under various conditions, including several substrate and oxygen concentrations and flow rates. 2,4,6-Tribromophenol (TBP) was used as a model contaminant (substrate). TBP biodegradation efficiency depended mainly on the amount of oxygen. However, under constant oxygen concentration at the core inlet, elevating the flow rates increased the removal rate of TBP. Transmissivity reduction was clearly related to TBP removal rate, following an initial slow decline and a further sharp decrease with time. The fracture's transmissivity was reduced by as much as 97% relative to the initial value, with no leveling off of the clogging process. For the most extreme cases, reductions of 262 and 157 microm in the equivalent hydraulic apertures were recorded for fractures with initial apertures of 495 and 207 microm, respectively. The reductions in fracture transmissivity occurred primarily because of clogging by bacterial cells and extracellular polymeric substances (EPS) produced by the bacteria. Most of the biodegradation activity was concentrated near the fracture inlet, where the most suitable biodegradation conditions (nutrients and oxygen) prevailed, suggesting that the clogging had occurred in that vicinity. The clogging must have changed the structure of the fracture void, thereby reducing the active volume participating in flow and transport processes. This phenomenon caused accelerated transport of non-reactive tracers and doubled the fracture's dispersivity under constant flow rates.

Microbial gut diversity of Africanized and European honey bee larval instars

USDA-ARS?s Scientific Manuscript database

The first step in understanding gut microbial ecology is determining the presence and potential niche breadth of associated microbes. While the core gut bacteria of adult honey bees is becoming increasingly apparent, there is very little and inconsistent information concerning symbiotic bacterial co...

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers

USDA-ARS?s Scientific Manuscript database

Microbial symbionts living within animal guts are largely composed of resident bacterial species, forming communities that often provide benefits to the host. Gut microbiomes of adult honey bees (Apis mel- lifera) include core residents such as the betaproteobacterium Snod- grassella alvi, alongside...

Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest.

PubMed

Cabugao, Kristine G; Timm, Collin M; Carrell, Alyssa A; Childs, Joanne; Lu, Tse-Yuan S; Pelletier, Dale A; Weston, David J; Norby, Richard J

2017-01-01

Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result in soils lacking orthophosphate, the form of P most easily metabolized by plants and microbes. In these soils, mineralization of organic P can be the major source for orthophosphate. Both plants and microbes encode for phosphatases capable of mineralizing a range of organic P compounds. However, the activity of these enzymes depends on several edaphic factors including P availability, tree species, and microbial communities. Thus, phosphatase activity in both roots and the root microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. To relate phosphatase activity of roots and bacteria in tropical forests, we measured phosphatase activity in roots and bacterial isolates as well as bacterial community composition from the rhizosphere. Three forests in the Luquillo Mountains of Puerto Rico were selected to represent a range of soil P availability as measured using the resin P method. Within each site, a minimum of three tree species were chosen to sample. Root and bacterial phosphatase activity were both measured using a colorimetric assay with para-nitrophenyl phosphate as a substrate for the phosphomonoesterase enzyme. Both root and bacterial phosphatase were chiefly influenced by tree species. Though tree species was the only significant factor in root phosphatase activity, there was a negative trend between soil P availability and phosphatase activity in linear regressions of average root phosphatase and resin P. Permutational multivariate analysis of variance of bacterial community composition based on 16S amplicon sequencing indicated that bacterial composition was strongly controlled by soil P availability ( p -value < 0.05). These results indicate that although root and bacterial phosphatase activity were influenced by tree species; bacterial community composition was chiefly influenced by P availability. Although the sample size is limited given the tremendous diversity of tropical forests, our study indicates the importance of roots and bacterial function to understanding phosphatase activity. Future work will broaden the diversity of tree species and microbial members sampled to provide insight into P mineralization and model representation of tropical forests.

A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome

PubMed Central

Gloux, Karine; Berteau, Olivier; El oumami, Hanane; Béguet, Fabienne; Leclerc, Marion; Doré, Joël

2011-01-01

In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some of the beneficial effects of dietary compounds. Despite their biological significance, investigations are hampered by the fact that only a few BGs have so far been studied. A functional metagenomic approach was therefore performed on intestinal metagenomic libraries using chromogenic glucuronides as probes. Using this strategy, 19 positive metagenomic clones were identified but only one exhibited strong β-D-glucuronidase activity when subcloned into an expression vector. The cloned gene encoded a β-D-glucuronidase (called H11G11-BG) that had distant amino acid sequence homologies and an additional C terminus domain compared with known β-D-glucuronidases. Fifteen homologs were identified in public bacterial genome databases (38–57% identity with H11G11-BG) in the Firmicutes phylum. The genomes identified derived from strains from Ruminococcaceae, Lachnospiraceae, and Clostridiaceae. The genetic context diversity, with closely related symporters and gene duplication, argued for functional diversity and contribution to adaptive mechanisms. In contrast to the previously known β-D-glucuronidases, this previously undescribed type was present in the published microbiome of each healthy adult/child investigated (n = 11) and was specific to the human gut ecosystem. In conclusion, our functional metagenomic approach revealed a class of BGs that may be part of a functional core specifically evolved to adapt to the human gut environment with major health implications. We propose consensus motifs for this unique Firmicutes β-D-glucuronidase subfamily and for the glycosyl hydrolase family 2. PMID:20615998

Relative Contribution of nirK- and nirS- Bacterial Denitrifiers as Well as Fungal Denitrifiers to Nitrous Oxide Production from Dairy Manure Compost.

PubMed

Maeda, Koki; Toyoda, Sakae; Philippot, Laurent; Hattori, Shohei; Nakajima, Keiichi; Ito, Yumi; Yoshida, Naohiro

2017-12-19

The relative contribution of fungi, bacteria, and nirS and nirK denirifiers to nitrous oxide (N 2 O) emission with unknown isotopic signature from dairy manure compost was examined by selective inhibition techniques. Chloramphenicol (CHP), cycloheximide (CYH), and diethyl dithiocarbamate (DDTC) were used to suppress the activity of bacteria, fungi, and nirK-possessing denitrifiers, respectively. Produced N 2 O were surveyed to isotopocule analysis, and its 15 N site preference (SP) and δ 18 O values were compared. Bacteria, fungi, nirS, and nirK gene abundances were compared by qPCR. The results showed that N 2 O production was strongly inhibited by CHP addition in surface pile samples (82.2%) as well as in nitrite-amended core samples (98.4%), while CYH addition did not inhibit the N 2 O production. N 2 O with unknown isotopic signature (SP = 15.3-16.2‰), accompanied by δ 18 O (19.0-26.8‰) values which were close to bacterial denitrification, was also suppressed by CHP and DDTC addition (95.3%) indicating that nirK denitrifiers were responsible for this N 2 O production despite being less abundant than nirS denitrifiers. Altogether, our results suggest that bacteria are important for N 2 O production with different SP values both from compost surface and pile core. However, further work is required to decipher whether N 2 O with unknown isotopic signature is mostly due to nirK denitrifiers that are taxonomically different from the SP-characterized strains and therefore have different SP values rather than also being interwoven with the contribution of the NO-detoxifying pathway and/or of co-denitrification.

Adsorption and oxidation of SO₂in a fixed-bed reactor using activated carbon produced from oxytetracycline bacterial residue and impregnated with copper.

PubMed

Zhou, Baohua; Yu, Lei; Song, Hanning; Li, Yaqi; Zhang, Peng; Guo, Bin; Duan, Erhong

2015-02-01

The SO₂removal ability (including adsorption and oxidation ability) of activated carbon produced from oxytetracycline bacterial residue and impregnated with copper was investigated. The activated carbon produced from oxytetracycline bacterial residue and modified with copper was characterized by x-ray diffraction, scanning electron microscopy, and energy-dispersive spectroscopy. The effects of the catalysts, SO₂concentration, weight hourly space velocity, and temperature on the SO₂adsorption and oxidation activity were evaluated. Activated carbon produced from oxytetracycline bacterial residue and used as catalyst supports for copper oxide catalysts provided high catalytic activity for the adsorbing and oxidizing of SO₂from flue gases.

Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation.

PubMed

Saramago, Margarida; Peregrina, Alexandra; Robledo, Marta; Matos, Rute G; Hilker, Rolf; Serrania, Javier; Becker, Anke; Arraiano, Cecilia M; Jiménez-Zurdo, José I

2017-02-17

Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.

Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation

PubMed Central

Saramago, Margarida; Peregrina, Alexandra; Robledo, Marta; Matos, Rute G.; Hilker, Rolf; Serrania, Javier; Becker, Anke; Arraiano, Cecilia M.

2017-01-01

Abstract Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme. PMID:28180335

Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome

PubMed Central

Ilyas, Bushra; Tsai, Caressa N.; Coombes, Brian K.

2017-01-01

Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella. Here, we review the latest understanding of these elements and their contributions to pathogenesis, emphasizing the regulatory circuitry that controls niche-specific gene expression. In addition to an overview of the importance of SPI-1 and SPI-2 to host invasion and colonization, we describe the recently characterized contributions of other SPIs, including the antibacterial activity of SPI-6 and adhesion and invasion mediated by SPI-4. We further discuss how these fitness traits have been integrated into the regulatory circuitry of the bacterial cell through cis-regulatory evolution and by a careful balance of silencing and counter-silencing by regulatory proteins. Detailed understanding of regulatory evolution within Salmonella is uncovering novel aspects of infection biology that relate to host-pathogen interactions and evasion of host immunity. PMID:29034217

Functional Analysis of a Bacterial Antifreeze Protein Indicates a Cooperative Effect between Its Two Ice-Binding Domains.

PubMed

Wang, Chen; Oliver, Erin E; Christner, Brent C; Luo, Bing-Hao

2016-07-19

Antifreeze proteins make up a class of ice-binding proteins (IBPs) that are possessed and expressed by certain cold-adapted organisms to enhance their freezing tolerance. Here we report the biophysical and functional characterization of an IBP discovered in a bacterium recovered from a deep glacial ice core drilled at Vostok Station, Antarctica (IBPv). Our study showed that the recombinant protein rIBPv exhibited a thermal hysteresis of 2 °C at concentrations of >50 μM, effectively inhibited ice recrystallization, and enhanced bacterial viability during freeze-thaw cycling. Circular dichroism scans indicated that rIBPv mainly consists of β strands, and its denaturing temperature was 53.5 °C. Multiple-sequence alignment of homologous IBPs predicted that IBPv contains two ice-binding domains, a feature unique among known IBPs. To examine functional differences between the IBPv domains, each domain was cloned, expressed, and purified. The second domain (domain B) expressed greater ice binding activity. Data from thermal hysteresis and gel filtration assays supported the idea that the two domains cooperate to achieve a higher ice binding effect by forming heterodimers. However, physical linkage of the domains was not required for this effect.

An in vivo library-versus-library selection of optimized protein-protein interactions.

PubMed

Pelletier, J N; Arndt, K M; Plückthun, A; Michnick, S W

1999-07-01

We describe a rapid and efficient in vivo library-versus-library screening strategy for identifying optimally interacting pairs of heterodimerizing polypeptides. Two leucine zipper libraries, semi-randomized at the positions adjacent to the hydrophobic core, were genetically fused to either one of two designed fragments of the enzyme murine dihydrofolate reductase (mDHFR), and cotransformed into Escherichia coli. Interaction between the library polypeptides reconstituted enzymatic activity of mDHFR, allowing bacterial growth. Analysis of the resulting colonies revealed important biases in the zipper sequences relative to the original libraries, which are consistent with selection for stable, heterodimerizing pairs. Using more weakly associating mDHFR fragments, we increased the stringency of selection. We enriched the best-performing leucine zipper pairs by multiple passaging of the pooled, selected colonies in liquid culture, as the best pairs allowed for better bacterial propagation. This competitive growth allowed small differences among the pairs to be amplified, and different sequence positions were enriched at different rates. We applied these selection processes to a library-versus-library sample of 2.0 x 10(6) combinations and selected a novel leucine zipper pair that may be appropriate for use in further in vivo heterodimerization strategies.

[Study on anti-bacterium activity of ginkgolic acids and their momomers].

PubMed

Yang, Xiaoming; Zhu, Wei; Chen, Jun; Qian, Zhiyu; Xie, Jimin

2004-09-01

Ginkgolic acids and their three monomers were separated from ginkgo sarcotestas. The anti-bacterium activity of ginkgolic acids were tested. The relation between the anti-bacterium activity and side chain of ginkgolic acid were studied. The MIC of ginkgolic acids and their three monomers and salicylic acid were tested. Ginkgolic acid has strong inhibitive effect on G+-bacterium. Salicylic acid has no side chain, so no anti-bacterial activity. When the length of gingkolic acid side chain is C13:0, it has the strongest anti-bacterial activity in three monomers. The side chain of ginkgolic acid is the key functional group that possessed anti-bacterial activity. The length of Ginkgolic acid was the main effective factor of anti-bacterial activity.

Effects of Bacterial Microflora of the Lower Digestive Tract of Free-Range Waterfowl on Influenza Virus Activation ▿

PubMed Central

King, Marcus D.; Guentzel, M. Neal; Arulanandam, Bernard P.; Bodour, Adria A.; Brahmakshatriya, Vinayak; Lupiani, Blanca; Chambers, James P.

2011-01-01

Proteolytic cleavage activation of influenza virus hemagglutinin (HA0) is required for cell entry via receptor-mediated endocytosis. Despite numerous studies describing bacterial protease-mediated influenza A viral activation in mammals, very little is known about the role of intestinal bacterial flora of birds in hemagglutinin cleavage/activation. Therefore, the cloaca of wild waterfowl was examined for (i) representative bacterial types and (ii) their ability to cleave in a “trypsin-like” manner the precursor viral hemagglutinin molecule (HA0). Using radiolabeled HA0, bacterial secretion-mediated trypsin-like conversion of HA0 to HA1 and HA2 peptide products was observed to various degrees in 42 of 44 bacterial isolates suggestive of influenza virus activation in the cloaca of wild waterfowl. However, treatment of uncleaved virus with all bacterial isolates gave rise to substantially reduced emergent virus progeny compared with what was expected. Examination of two isolates exhibiting pronounced trypsin-like conversion of HA0 to HA1 and HA2 peptide products and low infectivity revealed lipase activity to be present. Because influenza virus possesses a complex lipid envelope, the presence of lipid hydrolase activity could in part account for the observed less-than-expected level of viable progeny. A thorough characterization of respective isolate protease HA0 hydrolysis products as well as other resident activities (i.e., lipase) is ongoing such that the role of these respective contributors in virus activation/inactivation can be firmly established. PMID:21531837

Genomes of the T4-related bacteriophages as windows on microbial genome evolution.

PubMed

Petrov, Vasiliy M; Ratnayaka, Swarnamala; Nolan, James M; Miller, Eric S; Karam, Jim D

2010-10-28

The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.

Genomes of the T4-related bacteriophages as windows on microbial genome evolution

PubMed Central

2010-01-01

The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature. PMID:21029436

Inflammation and regeneration in the dentin-pulp complex: a double-edged sword.

PubMed

Cooper, Paul R; Holder, Michelle J; Smith, Anthony J

2014-04-01

Dental tissue infection and disease result in acute and chronic activation of the innate immune response, which is mediated by molecular and cellular signaling. Different cell types within the dentin-pulp complex are able to detect invading bacteria at all stages of the infection. Indeed, at relatively early disease stages, odontoblasts will respond to bacterial components, and as the disease progresses, core pulpal cells including fibroblasts, stems cells, endothelial cells, and immune cells will become involved. Pattern recognition receptors, such as Toll-like receptors expressed on these cell types, are responsible for detecting bacterial components, and their ligand binding leads to the activation of the nuclear factor-kappa B and p38 mitogen-activated protein (MAP) kinase intracellular signaling cascades. Subsequent nuclear translocation of the transcription factor subunits from these pathways will lead to proinflammatory mediator expression, including increases in cytokines and chemokines, which trigger host cellular defense mechanisms. The complex molecular signaling will result in the recruitment of immune system cells targeted at combating the invading microbes; however, the trafficking and antibacterial activity of these cells can lead to collateral tissue damage. Recent evidence suggests that if inflammation is resolved relatively low levels of proinflammatory mediators may promote tissue repair, whereas if chronic inflammation ensues repair mechanisms become inhibited. Thus, the effects of mediators are temporal context dependent. Although containment and removal of the infection are keys to enable dental tissue repair, it is feasible that the development of anti-inflammatory and immunomodulatory approaches, based on molecular, epigenetic, and photobiomodulatory technologies, may also be beneficial for future endodontic treatments. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

PubMed Central

Figuerola, Eva L. M.; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

Different Types of Dietary Fibers Trigger Specific Alterations in Composition and Predicted Functions of Colonic Bacterial Communities in BALB/c Mice

PubMed Central

Luo, Yuheng; Zhang, Ling; Li, Hua; Smidt, Hauke; Wright, André-Denis G.; Zhang, Keying; Ding, Xuemei; Zeng, Qiufeng; Bai, Shiping; Wang, Jianping; Li, Jian; Zheng, Ping; Tian, Gang; Cai, Jingyi; Chen, Daiwen

2017-01-01

Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice (n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake (p < 0.05) but no change on the average body weight gain (p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate (p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups (p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased (p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides, Dehalobacterium, and Prevotella, including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group M, whereas Oscillospira, Desulfovibrio, and Ruminoccaceae, typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM (p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria, Betaproteobacteria, Gammaproteobacteria (including Enterobacteriaceae) and Deltaproteobacteria, were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of “Energy metabolism” and “Carbohydrate metabolism” pathways in mice from group G and M, suggesting that the altered bacterial community in the colon of mice with the two dietary fibers probably resulted in a more efficient degradation of dietary polysaccharides. Our result suggests that the influence of dietary β-glucan (SDF) on colonic bacterial community of mice was more extensively than MCC (IDF). Co-supplementation of the two fibers may help to increase the bacterial diversity and reduce the conditional pathogens in the colon of mice. PMID:28611761

Controlled release of Pantoea agglomerans E325 for biocontrol of fire blight

USDA-ARS?s Scientific Manuscript database

Microencapsulation and controlled release of Pantoea agglomerans strain E325 (E325), which is an antagonist to bacterial pathogen (Erwinia amylovora) of fire blight, a devastating disease of apple and pear, have been investigated. Uniform core-shell alginate microcapsules (AMCs), 60-300 µm in diamet...

76 FR 51036 - Proposed Data Collections Submitted for Public Comment and Recommendations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-17

... questions to take about 5 minutes and the telephone interview 20 minutes per respondent. Table--Estimated... Bacterial Core surveillance (ABCs), to add supplemental questions for invasive methicillin-resistant... population remain uncertain. The goal of the supplemental questions to be added to ABCs MRSA surveillance is...

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota.

PubMed

Katsimichas, Themistoklis; Ohtani, Tomohito; Motooka, Daisuke; Tsukamoto, Yasumasa; Kioka, Hidetaka; Nakamoto, Kei; Konishi, Shozo; Chimura, Misato; Sengoku, Kaoruko; Miyawaki, Hiroshi; Sakaguchi, Taiki; Okumura, Ryu; Theofilis, Konstantinos; Iida, Tetsuya; Takeda, Kiyoshi; Nakamura, Shota; Sakata, Yasushi

2018-05-25

Research suggests that heart failure with reduced ejection fraction (HFrEF) is a state of systemic inflammation that may be triggered by microbial products passing into the bloodstream through a compromised intestinal barrier. However, whether the intestinal microbiota exhibits dysbiosis in HFrEF patients is largely unknown.Methods and Results:Twenty eight non-ischemic HFrEF patients and 19 healthy controls were assessed by 16S rRNA analysis of bacterial DNA extracted from stool samples. After processing of sequencing data, bacteria were taxonomically classified, diversity indices were used to examine microbial ecology, and relative abundances of common core genera were compared between groups. Furthermore, we predicted gene carriage for bacterial metabolic pathways and inferred microbial interaction networks on multiple taxonomic levels.Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups wasBacteroides. Although α diversity did not differ between groups, ordination by β diversity metrics revealed a separation of the groups across components of variation.StreptococcusandVeillonellawere enriched in the common core microbiota of patients, whileSMB53was depleted. Gene families in amino acid, carbohydrate, vitamin, and xenobiotic metabolism showed significant differences between groups. Interaction networks revealed a higher degree of correlations between bacteria in patients. Non-ischemic HFrEF patients exhibited multidimensional differences in intestinal microbial communities compared with healthy subjects.

New Amphiphilic Neamine Derivatives Active against Resistant Pseudomonas aeruginosa and Their Interactions with Lipopolysaccharides

PubMed Central

Sautrey, Guillaume; Zimmermann, Louis; Deleu, Magali; Delbar, Alicia; Souza Machado, Luiza; Jeannot, Katy; Van Bambeke, Françoise; Buyck, Julien M.; Decout, Jean-Luc

2014-01-01

The development of novel antimicrobial agents is urgently required to curb the widespread emergence of multidrug-resistant bacteria like colistin-resistant Pseudomonas aeruginosa. We previously synthesized a series of amphiphilic neamine derivatives active against bacterial membranes, among which 3′,6-di-O-[(2″-naphthyl)propyl]neamine (3′,6-di2NP), 3′,6-di-O-[(2″-naphthyl)butyl]neamine (3′,6-di2NB), and 3′,6-di-O-nonylneamine (3′,6-diNn) showed high levels of activity and low levels of cytotoxicity (L. Zimmermann et al., J. Med. Chem. 56:7691–7705, 2013). We have now further characterized the activity of these derivatives against colistin-resistant P. aeruginosa and studied their mode of action; specifically, we characterized their ability to interact with lipopolysaccharide (LPS) and to alter the bacterial outer membrane (OM). The three amphiphilic neamine derivatives were active against clinical colistin-resistant strains (MICs, about 2 to 8 μg/ml), The most active one (3′,6-diNn) was bactericidal at its MIC and inhibited biofilm formation at 2-fold its MIC. They cooperatively bound to LPSs, increasing the outer membrane permeability. Grafting long and linear alkyl chains (nonyl) optimized binding to LPS and outer membrane permeabilization. The effects of amphiphilic neamine derivatives on LPS micelles suggest changes in the cross-bridging of lipopolysaccharides and disordering in the hydrophobic core of the micelles. The molecular shape of the 3′,6-dialkyl neamine derivatives induced by the nature of the grafted hydrophobic moieties (naphthylalkyl instead of alkyl) and the flexibility of the hydrophobic moiety are critical for their fluidifying effect and their ability to displace cations bridging LPS. Results from this work could be exploited for the development of new amphiphilic neamine derivatives active against colistin-resistant P. aeruginosa. PMID:24867965

Bacterial Communities of Surface Mixed Layer in the Pacific Sector of the Western Arctic Ocean during Sea-Ice Melting

PubMed Central

Ha, Ho Kyung; Kim, Hyun Cheol; Kim, Ok-Sun; Lee, Bang Yong; Cho, Jang-Cheon; Hur, Hor-Gil; Lee, Yoo Kyung

2014-01-01

From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting. PMID:24497990

Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting.

PubMed

Han, Dukki; Kang, Ilnam; Ha, Ho Kyung; Kim, Hyun Cheol; Kim, Ok-Sun; Lee, Bang Yong; Cho, Jang-Cheon; Hur, Hor-Gil; Lee, Yoo Kyung

2014-01-01

From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.

Geomicrobial characterization of a 60 m long permafrost core from Svalbard

NASA Astrophysics Data System (ADS)

Fromreide, Siren; Tore Mørkved, Pål; Gilbert, Graham Lewis; Christiansen, Hanne H.; Reigstad, Laila

2014-05-01

In connection with a planned CO2 storage pilot project in the Arctic, a 60 m long permafrost core was drilled in Adventdalen, Svalbard. The on-shore drilling was performed through mainly marine and deltafront sediments, ending at the bedrock. The core has undergone detailed analyses of sedimentary stratigraphy, age, as well as the permafrost ice and carbon content at The University Centre in Svalbard (UNIS), and at the Center for Permafrost (CENPERM), Copenhagen. The main aim of the study presented here is to link the geochemical properties of the permafrost to the microbial community structure and its potential functions. As little is known about microbial life in permafrost at such depths this study will contribute to the understanding of these inaccessible ecosystems. A baseline geomicrobial description of 7 different depths in the 3 - 60 m interval of the permafrost core was done by culture independent methods such as 16S rRNA amplicon 454 pyrosequencing and functional and ribosomal gene quantifications. Additionally, geochemical analyses of the extracted pore water have been performed, as well as measurements of carbon content and major elements. The enumeration of the total prokaryotic community indicated similar numbers of bacteria and archaea down to approximately 50 m depth, while below this depth there was a dominance of archaeal cells. The bacterial 16S rRNA copy numbers ranged between 108 copies per gram sediment at 3 m depth to 104 copies per gram at the bedrock. Concerning the archaeal cells, the 16S rRNA copy numbers per gram sediment were in the range of 107 at the top of the core, ending at 105in the top of the bedrock. Detection and quantification of selected functional marker genes indicated high numbers of sulphate reducing bacteria at certain sediment depths, and a significant potential for microbial methanogenic activity throughout the core. Correlations studies between geochemical data and microbial community composition are currently ongoing.

Transcriptome landscape of a bacterial pathogen under plant immunity.

PubMed

Nobori, Tatsuya; Velásquez, André C; Wu, Jingni; Kvitko, Brian H; Kremer, James M; Wang, Yiming; He, Sheng Yang; Tsuda, Kenichi

2018-03-27

Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta We identified specific "immune-responsive" bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.

Volatiles in Inter-Specific Bacterial Interactions

PubMed Central

Tyc, Olaf; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

2015-01-01

The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities. PMID:26733959

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

PubMed Central

Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

2014-01-01

Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host–microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization. PMID:24335825

Sequence Elements Upstream of the Core Promoter Are Necessary for Full Transcription of the Capsule Gene Operon in Streptococcus pneumoniae Strain D39

PubMed Central

Wen, Zhensong; Sertil, Odeniel; Cheng, Yongxin; Zhang, Shanshan; Liu, Xue; Wang, Wen-Ching

2015-01-01

Streptococcus pneumoniae is a major bacterial pathogen in humans. Its polysaccharide capsule is a key virulence factor that promotes bacterial evasion of human phagocytic killing. While S. pneumoniae produces at least 94 antigenically different types of capsule, the genes for biosynthesis of almost all capsular types are arranged in the same locus. The transcription of the capsular polysaccharide (cps) locus is not well understood. This study determined the transcriptional features of the cps locus in the type 2 virulent strain D39. The initial analysis revealed that the cps genes are cotranscribed from a major transcription start site at the −25 nucleotide (G) upstream of cps2A, the first gene in the locus. Using unmarked chromosomal truncations and a luciferase-based transcriptional reporter, we showed that the full transcription of the cps genes not only depends on the core promoter immediately upstream of cps2A, but also requires additional elements upstream of the core promoter, particularly a 59-bp sequence immediately upstream of the core promoter. Unmarked deletions of these promoter elements in the D39 genome also led to significant reduction in CPS production and virulence in mice. Lastly, common cps gene (cps2ABCD) mutants did not show significant abnormality in cps transcription, although they produced significantly less CPS, indicating that the CpsABCD proteins are involved in the encapsulation of S. pneumoniae in a posttranscriptional manner. This study has yielded important information on the transcriptional characteristics of the cps locus in S. pneumoniae. PMID:25733517

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time.

PubMed

Torres, Sheila; Clayton, Jonathan B; Danzeisen, Jessica L; Ward, Tonya; Huang, Hu; Knights, Dan; Johnson, Timothy J

2017-01-01

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs' microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis . This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

USGS Publications Warehouse

Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

2016-01-01

Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down hydrocarbons. Identifying microorganisms involved in coal degradation and the hydrogeochemical conditions that promote their activity is crucial to understanding and improving in situ CBM production.

Crystalline-gel-molten phase transitions of water in calcium dipicolinate (Ca-DPA)

NASA Astrophysics Data System (ADS)

Tiwari, Subodh; Mishra, Ankit; Sheng, Chunyang; Rajak, Pankaj; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

The heat resistance of bacterial spores directly correlates to the protoplast dehydration and presence of dipicolinic acid (DPA) and its associated metal salts at the core. Bacteria's structural integrity in moist heat conferred by high concentration of DPA and calcium DPA salts depends on the properties are additional water molecules and temperature. In our reactive MD simulations, we characterize different possible phases and the transport properties of water molecules. We observed solid-gel and gel-liquid phase transitions of the hydrated Ca-DPA system. These simulations reveal monotonically decreasing solid-gel-liquid transition temperatures with increasing cell hydration, reflecting the experimental trend of moist-heat resistance of bacterial spores. We also observed that the calcification of bacterial spores further increases the transition temperatures. This research is supported by DTRA Grant No. HDTRA1-14-1-0074.

Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure

PubMed Central

Pérez, María Teresa; Sommaruga, Ruben

2007-01-01

We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24–48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition. PMID:17686018

Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure.

PubMed

Pérez, María Teresa; Sommaruga, Ruben

2007-09-01

We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24-48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition.

Evaluation of culture techniques and bacterial cultures from uroliths.

PubMed

Perry, Leigh A; Kass, Philip H; Johnson, Dee L; Ruby, Annette L; Shiraki, Ryoji; Westropp, Jodi L

2013-03-01

The association between urolithiasis and growth of bacteria in the urine or urolith has not been recently evaluated in the past 15 years, and the effects of antimicrobial administration on urolith cultures have not been reported. As well, laboratory techniques for urolith cultures have not been critically evaluated. The objectives of the current study were to 1) report bacterial isolates from uroliths and their association with signalment, urolith composition, antimicrobial use, and urine cultures and 2) evaluate laboratory techniques for urolith cultures. For the first objective, a retrospective search of bacterial isolates cultured from uroliths submitted to the laboratory as well as the signalment, urine culture results, and antimicrobial use were recorded. For the second objective, 50 urolith pairs were cultured by washing each urolith either 1or 4 times and culturing the core. Five hundred twenty canine and 168 feline uroliths were reviewed. Struvite-containing uroliths had an increased prevalence of a positive culture compared to nonstruvite-containing uroliths (P < 0.0001, odds ratio [OR] = 5.4), as did uroliths from female dogs (P < 0.0001, OR = 2.9). No significant difference between culture results and previous antimicrobial administration was found (P = 0.41). Eighteen percent of cases with negative urine cultures had positive urolith cultures. There was no significant difference in core culture results whether the urolith was washed 1 or 4 times (P = 0.07). Urolith culture outcome was not always influenced by previous antimicrobial administration, and bacterial culture of a urolith may not yield the same results as those obtained from the urine. The modified protocol, which requires less time and expense for urolith cultures, may be an acceptable alternative.

Evaluating the 4-hour and 30-minute rules: effects of room temperature exposure on red blood cell quality and bacterial growth.

PubMed

Ramirez-Arcos, Sandra; Mastronardi, Cherie; Perkins, Heather; Kou, Yuntong; Turner, Tracey; Mastronardi, Emily; Hansen, Adele; Yi, Qi-Long; McLaughlin, Natasha; Kahwash, Eiad; Lin, Yulia; Acker, Jason

2013-04-01

A 30-minute rule was established to limit red blood cell (RBC) exposure to uncontrolled temperatures during storage and transportation. Also, RBC units issued for transfusion should not remain at room temperature (RT) for more than 4 hours (4-hour rule). This study was aimed at determining if single or multiple RT exposures affect RBC quality and/or promote bacterial growth. Growth and RT exposure experiments were performed in RBCs inoculated with Serratia liquefaciens and Serratia marcescens. RBCs were exposed once to RT for 5 hours (S. liquefaciens) or five times to RT for 30 minutes (S. marcescens) with periodic sampling for bacterial counts. Noncontaminated units were exposed to RT once (5 hr) or five times (30 min each) and sampled to measure in vitro quality variables. RBC core temperature was monitored using mock units with temperature loggers. Growth and RT exposure experiments were repeated three and at least six times, respectively. Statistical analysis was done using mixed-model analysis. RBC core temperature ranged from 7.3 to 11.6°C during 30-minute RT exposures and the time to reach 10°C varied from 22 to 55 minutes during 5-hour RT exposures. RBC quality was preserved after single or multiple RT exposures. Increased growth of S. liquefaciens was only observed after 2 hours of continuous RT exposure. S. marcescens concentration increased significantly in multiple-exposed units compared to the controls but did not reach clinically important levels. Single or multiple RT exposures did not affect RBC quality but slightly promoted bacterial growth in contaminated units. The clinical significance of these results remains unclear and needs further investigation. © 2012 American Association of Blood Banks.

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

PubMed Central

Kable, Mary E.; Srisengfa, Yanin; Laird, Miles; Zaragoza, Jose; McLeod, Jeremy; Heidenreich, Jessie

2016-01-01

ABSTRACT Currently, the bacterial composition of raw milk in tanker trucks and the outcomes of transfer and storage of that milk at commercial processing facilities are not well understood. We set out to identify the bacteria in raw milk collected for large-scale dairy product manufacturing. Raw bovine milk samples from 899 tanker trucks arriving at two dairy processors in San Joaquin Valley of California during three seasons (spring, summer, and fall) were analyzed by community 16S rRNA gene sequencing. This analysis revealed highly diverse bacterial populations, which exhibited seasonal differences. Raw milk collected in the spring contained the most diverse bacterial communities, with the highest total cell numbers and highest proportions being those of Actinobacteria. Even with this complexity, a core microbiota was present, consisting of 29 taxonomic groups and high proportions of Streptococcus and Staphylococcus and unidentified members of Clostridiales. Milk samples were also collected from five large-volume silos and from 13 to 25 tankers whose contents were unloaded into each of them during 2 days in the summer. Transfer of the milk to storage silos resulted in two community types. One group of silos contained a high proportion of Streptococcus spp. and was similar in that respect to the tankers that filled them. The community found in the other group of silos was distinct and dominated by Acinetobacter. Overall, despite highly diverse tanker milk community structures, distinct milk bacterial communities were selected within the processing facility environment. This knowledge can inform the development of new sanitation procedures and process controls to ensure the consistent production of safe and high-quality dairy products on a global scale. PMID:27555305

Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide.

PubMed

Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M; Corsaro, Maria Michela

2017-03-04

Erwinia amylovora ( E. amylovora ) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae . In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry.

Native structure of a type IV secretion system core complex essential for Legionella pathogenesis.

PubMed

Kubori, Tomoko; Koike, Masafumi; Bui, Xuan Thanh; Higaki, Saori; Aizawa, Shin-Ichi; Nagai, Hiroki

2014-08-12

Bacterial type IV secretion systems are evolutionarily related to conjugation systems and play a pivotal role in infection by delivering numerous virulence factors into host cells. Using transmission electron microscopy, we report the native molecular structure of the core complex of the Dot/Icm type IV secretion system encoded by Legionella pneumophila, an intracellular human pathogen. The biochemically isolated core complex, composed of at least five proteins--DotC, DotD, DotF, DotG, and DotH--has a ring-shaped structure. Intriguingly, morphologically distinct premature complexes are formed in the absence of DotG or DotF. Our data suggest that DotG forms a central channel spanning inner and outer membranes. DotF, a component dispensable for type IV secretion, plays a role in efficient embedment of DotG into the functional core complex. These results highlight a common scheme for the biogenesis of transport machinery.

Expression and Characterization of an Ice Binding Protein from a Bacterium Isolated at a Depth of 3,519 Meters in the Vostok Ice Core, Antarctica

NASA Astrophysics Data System (ADS)

Christner, B. C.; Achberger, A.; Brox, T. I.; Skidmore, M. L.

2011-12-01

The cryopreservation of microorganisms in ancient glacial ice is possible if lethal levels of macromolecular damage are not incurred and cellular integrity is not compromised via intracellular ice formation or recrystallization. There are numerous examples of cold-adapted species that prevent or limit ice crystal growth by producing ice-binding proteins (IBP). Previously, a bacterium (isolate 3519-10; Flavobacteriaceae family) recovered from a depth of 3,519 meters below the surface in the Vostok ice core was shown to produce and secrete an IBP that inhibits the recrystallization of ice. To explore the phenotypic advantage that IBPs confer to ice-entrapped cells, experiments were designed to examine the expression of 3519-10's IBP gene and protein at different temperatures, assess the effect of the IBP on bacterial viability in ice, and determine how the IBP influences the physical structure of the ice. Total RNA isolated from aerobic cultures grown at temperatures between 4C to 25C and analyzed by reverse transcription-PCR indicated constitutive expression of the IBP gene. Additionally, SDS-PAGE analysis of 3519-10's extracellular proteins revealed a polypeptide corresponding to the predicted size of the 54 kDa IBP at all temperatures tested. The total extracellular protein fraction was subsequently used in assays with Escherichia coli to examine the effect of the IBP on bacterial survival in warm ice (-5C) and after freeze-thaw cycling. In the presence of 100 μg mL-1 of extracellular protein from 3519-10, the survival of E. coli was increased by greater than 100-fold; however, the survival of E. coli suspensions containing the same concentration of bovine serum albumin was not significantly different than controls (p<0.05). Microscopic analysis of ice formed in the presence of the IBP indicated that in a mm^2 field of view, there were 5 times as many crystals as in ice formed in the presence of washed 3519-10 cells and non-IBP producing bacteria, and 10 times as many crystals as in particle-free deionized water. Presumably, the effect that the IBP has on bacterial viability and ice crystal structure is due to its activity as an inhibitor of ice recrystallization. Although a myriad of molecular adaptations are likely to play a role in bacterial persistence under frozen conditions, the ability of 3519-10's IBP to control ice crystal structure may provide one explanation for its successful survival deep within the Antarctic ice sheet for thousands of years.

12 CFR 1265.3 - Core mission activities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 7 2011-01-01 2011-01-01 false Core mission activities. 1265.3 Section 1265.3 Banks and Banking FEDERAL HOUSING FINANCE AGENCY FEDERAL HOME LOAN BANKS CORE MISSION ACTIVITIES § 1265.3 Core mission activities. The following Bank activities qualify as core mission activities: (a...

12 CFR 940.3 - Core mission activities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Core mission activities. 940.3 Section 940.3 Banks and Banking FEDERAL HOUSING FINANCE BOARD FEDERAL HOME LOAN BANK MISSION CORE MISSION ACTIVITIES § 940.3 Core mission activities. The following Bank activities qualify as core mission activities: (a...

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-10-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

Influence of zinc on bacterial populations and their proteolytic enzyme activities in freshwater environments: a cross-site comparison.

PubMed

Rasmussen, Lauren; Olapade, Ola A

2016-04-01

Temporal responses of indigenous bacterial populations and proteolytic enzyme (i.e., aminopeptidase) activities in the bacterioplankton assemblages from 3 separate freshwater environments were examined after exposure to various zinc (Zn) concentrations under controlled microcosm conditions. Zn concentrations (ranging from 0 to 10 μmol/L) were added to water samples collected from the Kalamazoo River, Rice Creek, and Huron River and examined for bacterial abundance and aminopeptidase activities at various time intervals over a 48 h incubation period in the dark. The results showed that the Zn concentrations did not significantly influence total bacterial counts directly; however, aminopeptidase activities varied significantly to increasing zinc treatments over time. Also, analysis of variance and linear regression analyses revealed significant positive relationships between bacterial numbers and their hydrolytic enzyme activities, suggesting that both probably co-vary with increasing Zn concentrations in aquatic systems. The results from this study serve as additional evidence of the ecological role of Zn as an extracellular peptidase cofactor on the dynamics of bacterial assemblages in aquatic environments.

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

PubMed Central

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-01-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults. PMID:27762306

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz.

PubMed

Coelho, Francisco J R C; Louvado, António; Domingues, Patrícia M; Cleary, Daniel F R; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R; Cunha, Ângela; Gomes, Newton C M

2016-10-20

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

Bacterial diversity in different regions of gastrointestinal tract of Giant African snail (Achatina fulica).

PubMed

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-12-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. © 2012 The Authors. Published by Blackwell Publishing Ltd.

Bacterial diversity in different regions of gastrointestinal tract of Giant African Snail (Achatina fulica)

PubMed Central

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-01-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. PMID:23233413

Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest

PubMed Central

Cabugao, Kristine G.; Timm, Collin M.; Carrell, Alyssa A.; Childs, Joanne; Lu, Tse-Yuan S.; Pelletier, Dale A.; Weston, David J.; Norby, Richard J.

2017-01-01

Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result in soils lacking orthophosphate, the form of P most easily metabolized by plants and microbes. In these soils, mineralization of organic P can be the major source for orthophosphate. Both plants and microbes encode for phosphatases capable of mineralizing a range of organic P compounds. However, the activity of these enzymes depends on several edaphic factors including P availability, tree species, and microbial communities. Thus, phosphatase activity in both roots and the root microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. To relate phosphatase activity of roots and bacteria in tropical forests, we measured phosphatase activity in roots and bacterial isolates as well as bacterial community composition from the rhizosphere. Three forests in the Luquillo Mountains of Puerto Rico were selected to represent a range of soil P availability as measured using the resin P method. Within each site, a minimum of three tree species were chosen to sample. Root and bacterial phosphatase activity were both measured using a colorimetric assay with para-nitrophenyl phosphate as a substrate for the phosphomonoesterase enzyme. Both root and bacterial phosphatase were chiefly influenced by tree species. Though tree species was the only significant factor in root phosphatase activity, there was a negative trend between soil P availability and phosphatase activity in linear regressions of average root phosphatase and resin P. Permutational multivariate analysis of variance of bacterial community composition based on 16S amplicon sequencing indicated that bacterial composition was strongly controlled by soil P availability (p-value < 0.05). These results indicate that although root and bacterial phosphatase activity were influenced by tree species; bacterial community composition was chiefly influenced by P availability. Although the sample size is limited given the tremendous diversity of tropical forests, our study indicates the importance of roots and bacterial function to understanding phosphatase activity. Future work will broaden the diversity of tree species and microbial members sampled to provide insight into P mineralization and model representation of tropical forests. PMID:29163572

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

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

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

DOE PAGES

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy; ...

2016-05-11

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Synthesis and characterization of bactericidal oligopeptides designed on the basis of an insect anti-bacterial peptide.

PubMed Central

Saido-Sakanaka, H; Ishibashi, J; Sagisaka, A; Momotani, E; Yamakawa, M

1999-01-01

Defensin from a beetle, Allomyrina dichotoma, is known to have anti-bacterial activity against Gram-positive bacteria. This peptide, which comprises 43 amino acid residues, was effective against methicillin-resistant Staphylococcus aureus. We identified the active site of beetle defensin by measuring anti-bacterial activity against S. aureus of 64 overlapping 12-mer peptides with either a free carboxylate or a free amide group at their C-termini. An LCAAHCLAIGRR-NH2 (19L-30R-NH2) fragment showed the greatest activity of the synthetic oligopeptides. The 19L-30R-NH2 fragment was effective against both Gram-positive and Gram-negative bacteria. CD spectra showed that the 19L-30R-NH2 fragment formed an alpha-helical structure in the lipidic environment. The anti-bacterial effect of the 19L-30R-NH2 fragment was due to its interaction with bacterial membranes, judging from the leakage of liposome-entrapped glucose. Its anti-bacterial activity was increased when certain amino acid residues were replaced. Truncated peptides having had some amino acids removed from the N-terminus of the 19L-30R-NH2 fragment (8-10-mer peptides) still had strong anti-bacterial activity. Deleting some amino acids from the C-terminal region of the fragment dramatically reduced activity, indicating that the C-terminal region of the 19L-30R-NH2 fragment, i.e. RR-NH2, is important for exerting anti-bacterial activity. The AHCLAIGRR-NH2 (22A-30R-NH2) fragment and its analogues exhibited about 3-fold and 9-12-fold higher activity against S. aureus than did the 19L-30R-NH2 fragment, and these analogues were effective against methicillin-resistant S. aureus and Pseudomonas aeruginosa isolated from patients. These oligopeptides showed no haemolytic activity and did not inhibit the growth of murine fibroblast cells. PMID:9931294

Determining the culturability of the rumen bacterial microbiome

PubMed Central

Creevey, Christopher J; Kelly, William J; Henderson, Gemma; Leahy, Sinead C

2014-01-01

The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000. PMID:24986151

Activity and growth efficiency of heterotrophic bacteria in a salt marsh (Ria de Aveiro, Portugal).

PubMed

Cunha, M A; Pedro, R; Almeida, M A; Silva, M H

2005-01-01

Bacterial utilization of monomers is recognized as an important step in the biogeochemical cycling of organic matter. In this study we have compared the heterotrophic activity of bacterial communities from different micro-habitats within a salt marsh environment (Ria de Aveiro, Portugal) in order to establish spatial patterns of bacterial abundance, monomer turnover rates (Tr) and bacterial growth efficiency (BGE). Differences in bacterial abundance and activity could be found between distinct plant rhizospheres. BGE tended to be lower at Halimione portulacoides banks, when compared to Sarcocornia perennis subsp. perennis banks which, on the contrary, showed the highest bacterial densities. Experiments of amendment of natural samples with organic and inorganic supplements indicated that salt marsh bacteria are not strongly regulated by salinity but the increased availability of labile organic matter causes a significant metabolic shift towards mineralization.

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China.

PubMed

Su, Jian-Qiang; An, Xin-Li; Li, Bing; Chen, Qing-Lin; Gillings, Michael R; Chen, Hong; Zhang, Tong; Zhu, Yong-Guan

2017-07-19

Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known. Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively. In total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 10 11 and 1.79 × 10 12 copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal. This study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship.

Flagellar motility is a key determinant of the magnitude of the inflammasome response to Pseudomonas aeruginosa.

PubMed

Patankar, Yash R; Lovewell, Rustin R; Poynter, Matthew E; Jyot, Jeevan; Kazmierczak, Barbara I; Berwin, Brent

2013-06-01

We previously demonstrated that bacterial flagellar motility is a fundamental mechanism by which host phagocytes bind and ingest bacteria. Correspondingly, loss of bacterial motility, consistently observed in clinical isolates from chronic Pseudomonas aeruginosa infections, enables bacteria to evade association and ingestion of P. aeruginosa by phagocytes both in vitro and in vivo. Since bacterial interactions with the phagocyte cell surface are required for type three secretion system-dependent NLRC4 inflammasome activation by P. aeruginosa, we hypothesized that reduced bacterial association with phagocytes due to loss of bacterial motility, independent of flagellar expression, will lead to reduced inflammasome activation. Here we report that inflammasome activation is reduced in response to nonmotile P. aeruginosa. Nonmotile P. aeruginosa elicits reduced IL-1β production as well as caspase-1 activation by peritoneal macrophages and bone marrow-derived dendritic cells in vitro. Importantly, nonmotile P. aeruginosa also elicits reduced IL-1β levels in vivo in comparison to those elicited by wild-type P. aeruginosa. This is the first demonstration that loss of bacterial motility results in reduced inflammasome activation and antibacterial IL-1β host response. These results provide a critical insight into how the innate immune system responds to bacterial motility and, correspondingly, how pathogens have evolved mechanisms to evade the innate immune system.

Flagellar Motility Is a Key Determinant of the Magnitude of the Inflammasome Response to Pseudomonas aeruginosa

PubMed Central

Patankar, Yash R.; Lovewell, Rustin R.; Poynter, Matthew E.; Jyot, Jeevan; Kazmierczak, Barbara I.

2013-01-01

We previously demonstrated that bacterial flagellar motility is a fundamental mechanism by which host phagocytes bind and ingest bacteria. Correspondingly, loss of bacterial motility, consistently observed in clinical isolates from chronic Pseudomonas aeruginosa infections, enables bacteria to evade association and ingestion of P. aeruginosa by phagocytes both in vitro and in vivo. Since bacterial interactions with the phagocyte cell surface are required for type three secretion system-dependent NLRC4 inflammasome activation by P. aeruginosa, we hypothesized that reduced bacterial association with phagocytes due to loss of bacterial motility, independent of flagellar expression, will lead to reduced inflammasome activation. Here we report that inflammasome activation is reduced in response to nonmotile P. aeruginosa. Nonmotile P. aeruginosa elicits reduced IL-1β production as well as caspase-1 activation by peritoneal macrophages and bone marrow-derived dendritic cells in vitro. Importantly, nonmotile P. aeruginosa also elicits reduced IL-1β levels in vivo in comparison to those elicited by wild-type P. aeruginosa. This is the first demonstration that loss of bacterial motility results in reduced inflammasome activation and antibacterial IL-1β host response. These results provide a critical insight into how the innate immune system responds to bacterial motility and, correspondingly, how pathogens have evolved mechanisms to evade the innate immune system. PMID:23529619

Nitrogen sources of Oligoporus placenta and Trametes versicolor evaluated in a 2(3) experimental plan.

PubMed

Weisshaupt, Petra; Pritzkow, Wolfgang; Noll, Matthias

2012-01-01

Four full-factorial 2(3) experimental plans were applied to evaluate the nitrogen (N) sources of Oligoporus placenta and Trametes versicolor and their interaction with the atmospheric N(2)-assimilating bacterium Beijerinckia acida. The effects of N from peptone, of sapwood and of N from gaseous N(2) on fungal, bacterial and fungal-bacterial activity were investigated. The activities were determined by quantification of biomass, formation of CO(2), consumption of O(2) and laccase activity. The significance of each effect was tested according to t-test recommendation. The activity of both fungi was enhanced by peptone rather than sapwood or gaseous N(2). Nevertheless, comparative studies under an N(2)-free gas mixture as well as under air revealed that the presence of N(2) affected bacterial growth and bacterial-fungal cocultivations. Elemental analysis isotope ratio mass spectrometry (IRMS) of the bacterial and fungal biomass enabled estimation of N transfer and underlined gaseous N(2) as requisite for fungal-bacterial interactions. Combining full-factorial experimental plans with an analytical set-up comprising gas chromatography, IRMS and enzymatic activity allowed synergistic effects to be revealed, fungal N sources to be traced, and symbiotic fungal-bacterial interactions to be investigated. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Effect of flow and active mixing on bacterial growth in a colon-like geometry

NASA Astrophysics Data System (ADS)

Cremer, Jonas; Segota, Igor; Arnoldini, Markus; Groisman, Alex; Hwa, Terence

The large intestine harbors bacteria from hundreds of species, with bacterial densities reaching up to 1012 cells per gram. Many different factors influence bacterial growth dynamics and thus bacterial density and microbiota composition. One dominant force is flow which can in principle lead to a washout of bacteria from the proximal colon. Active mixing by Contractions of the colonic wall together with bacterial growth might counteract such flow-forces and allow high bacterial densities to occur. As a step towards understanding bacterial growth in the presence of mixing and flow, we constructed an in-vitro setup where controlled wall-deformations of a channel emulate Contractions. We investigate growth along the channel under a steady nutrient inflow. In the limits of no or very frequent Contractions, the device behaves like a plug-flow reactor and a chemostat respectively. Depending on mixing and flow, we observe varying spatial gradients in bacterial density along the channel. Active mixing by deformations of the channel wall is shown to be crucial in maintaining a steady-state bacterial population in the presence of flow. The growth-dynamics is quantitatively captured by a simple mathematical model, with the effect of mixing described by an effective diffusion term.

Role of Mutant CFTR in Hypersusceptibility of Cystic Fibrosis Patients to Lung Infections

NASA Astrophysics Data System (ADS)

Pier, Gerald B.; Grout, Martha; Zaidi, Tanweer S.; Olsen, John C.; Johnson, Larry G.; Yankaskas, James R.; Goldberg, Joanna B.

1996-01-01

Cystic fibrosis (CF) patients are hypersusceptible to chronic Pseudomonas aeruginosa lung infections. Cultured human airway epithelial cells expressing the ΔF508 allele of the cystic fibrosis transmembrane conductance regulator (CFTR) were defective in uptake of P. aeruginosa compared with cells expressing the wild-type allele. Pseudomonas aeruginosa lipopolysaccharide (LPS)-core oligosaccharide was identified as the bacterial ligand for epithelial cell ingestion; exogenous oligosaccharide inhibited bacterial ingestion in a neonatal mouse model, resulting in increased amounts of bacteria in the lungs. CFTR may contribute to a host-defense mechanism that is important for clearance of P. aeruginosa from the respiratory tract.

Parasaccharibacter apium, gen. nov., sp. nov., improves honey bee (Hymenoptera: Apidae) resistance to Nosema

USDA-ARS?s Scientific Manuscript database

The honey bee, Apis mellifera, is host to a variety of microorganisms. The bacterial community that occupies the adult worker gut contains a core group of approximately seven taxa, while the hive environment contains its own distribution of bacteria that is in many ways distinct from the gut. Parasa...

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics.

PubMed

Tarnecki, A M; Burgos, F A; Ray, C L; Arias, C R

2017-02-07

The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next-generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host-microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome. Journal of Applied Microbiology © 2017 The Society for Applied Microbiology.

Production of the catalytic core of human peptidylglycine α-hydroxylating monooxygenase (hPHMcc) in Escherichia coli

PubMed Central

Handa, Sumit; Spradling, Tyler J.; Dempsey, Daniel R.; Merkler, David J.

2013-01-01

Most mammalian bioactive peptides possess a C-terminal amino acid amide moiety. The presence of the C-terminal amide is a significant impediment to the recombinant production of α-amidated peptides. α-Amidated peptides are produced in vivo by the enzymatic cleavage of a precursor with a C-terminal glycine residue. Peptidylglycine α-hydroxylating monooxygenase catalyzes the key step in the oxidation of the glycine-extended precursors to the α-amidated peptide. Herein, we detail the production of the catalytic core of human peptidylglycine α-hydroxylating monooxygenase (hPHMcc) in Escherichia coli possessing a N-terminal fusion to thioredoxin (Trx). Trx was fused to hPHMcc to enhance the yield of the resulting 52 kDa protein as a soluble and catalytically active enzyme. The Trx-hPHMcc-His6 fusion was purified to homogeneity and exhibited steady-state kinetic parameters that were similar to purified rat PHMcc. The bacterial production of recombinant hPHMcc will foster efforts to generate α-amidated peptides by the co-expression of hPHMcc and the α-amidated peptide precursors in E. coli or the in vitro amidation of recombinantly expressed α-amidated peptide precursors. PMID:22554821

Localization of yeast RNA polymerase I core subunits by immunoelectron microscopy.

PubMed Central

Klinger, C; Huet, J; Song, D; Petersen, G; Riva, M; Bautz, E K; Sentenac, A; Oudet, P; Schultz, P

1996-01-01

Immunoelectron microscopy was used to determine the spatial organization of the yeast RNA polymerase I core subunits on a three-dimensional model of the enzyme. Images of antibody-labeled enzymes were compared with the native enzyme to determine the localization of the antibody binding site on the surface of the model. Monoclonal antibodies were used as probes to identify the two largest subunits homologous to the bacterial beta and beta' subunits. The epitopes for the two monoclonal antibodies were mapped using subunit-specific phage display libraries, thus allowing a direct correlation of the structural data with functional information on conserved sequence elements. An epitope close to conserved region C of the beta-like subunit is located at the base of the finger-like domain, whereas a sequence between conserved regions C and D of the beta'-like subunit is located in the apical region of the enzyme. Polyclonal antibodies outlined the alpha-like subunit AC40 and subunit AC19 which were found co-localized also in the apical region of the enzyme. The spatial location of the subunits is correlated with their biological activity and the inhibitory effect of the antibodies. Images PMID:8887555

Molecular Characterization of Lipopolysaccharide Binding to Human α-1-Acid Glycoprotein

PubMed Central

Huang, Johnny X.; Azad, Mohammad A. K.; Yuriev, Elizabeth; Baker, Mark A.; Nation, Roger L.; Li, Jian; Cooper, Matthew A.; Velkov, Tony

2012-01-01

The ability of AGP to bind circulating lipopolysaccharide (LPS) in plasma is believed to help reduce the proinflammatory effect of bacterial lipid A molecules. Here, for the first time we have characterized human AGP binding characteristics of the LPS from a number of pathogenic Gram-negative bacteria: Escherichia coli, Salmonella typhimurium, Klebsiella pneumonia, Pseudomonas aeruginosa, and Serratia marcescens. The binding affinity and structure activity relationships (SAR) of the AGP-LPS interactions were characterized by surface plasma resonance (SPR). In order to dissect the contribution of the lipid A, core oligosaccharide and O-antigen polysaccharide components of LPS, the AGP binding affinity of LPS from smooth strains, were compared to lipid A, Kdo2-lipid A, Ra, Rd, and Re rough LPS mutants. The SAR analysis enabled by the binding data suggested that, in addition to the important role played by the lipid A and core components of LPS, it is predominately the unique species- and strain-specific carbohydrate structure of the O-antigen polysaccharide that largely determines the binding affinity for AGP. Together, these data are consistent with the role of AGP in the binding and transport of LPS in plasma during acute-phase inflammatory responses to invading Gram-negative bacteria. PMID:23316371

Bacterial Standing Stock, Activity, and Carbon Production during Formation and Growth of Sea Ice in the Weddell Sea, Antarctica.

PubMed

Grossmann, S; Dieckmann, G S

1994-08-01

Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 x 10 to 3 x 10 liter, were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [H]leucine incorporation into proteins to [H]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained lower than in open water. Bacterial concentrations of up to 2.8 x 10 cells liter along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 mug of C liter h. In thick ice, bacterial secondary production exceeded primary production of microalgae.

Assessment of pollution impact on biological activity and structure of seabed bacterial communities in the Port of Livorno (Italy).

PubMed

Iannelli, Renato; Bianchi, Veronica; Macci, Cristina; Peruzzi, Eleonora; Chiellini, Carolina; Petroni, Giulio; Masciandaro, Grazia

2012-06-01

The main objective of this study was to assess the impact of pollution on seabed bacterial diversity, structure and activity in the Port of Livorno. Samples of seabed sediments taken from five selected sites within the port were subjected to chemical analyses, enzymatic activity detection, bacterial count and biomolecular analysis. Five different statistics were used to correlate the level of contamination with the detected biological indicators. The results showed that the port is mainly contaminated by variable levels of petroleum hydrocarbons and heavy metals, which affect the structure and activity of the bacterial population. Irrespective of pollution levels, the bacterial diversity did not diverge significantly among the assessed sites and samples, and no dominance was observed. The type of impact of hydrocarbons and heavy metals was controversial, thus enforcing the supposition that the structure of the bacterial community is mainly driven by the levels of nutrients. The combined use of chemical and biological essays resulted in an in-depth observation and analysis of the existing links between pollution macro-indicators and biological response of seabed bacterial communities. Copyright © 2012 Elsevier B.V. All rights reserved.

Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation.

PubMed

Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David; Findeisen, Felix; Stein, Richard A; Nurva, Shailika Reddy; Mishra, Smriti; Mchaourab, Hassane S; Minor, Daniel L

2016-02-25

Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel. Copyright © 2016 Elsevier Inc. All rights reserved.

Unfolding of a temperature-sensitive domain controls voltage-gated channel activation

PubMed Central

Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David; Findeisen, Felix; Stein, Richard A.; Nurva, Shailika Reddy; Mishra, Smriti; Mchaourab, Hassane S.; Minor, Daniel L.

2016-01-01

Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNaV) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNaV CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNaV CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNaV voltage dependencies, and demonstrate that a discrete domain can encode the temperature dependent response of a channel. PMID:26919429

Preparation and characterization of biocompatible magnetic carbon nanotubes

NASA Astrophysics Data System (ADS)

Shan, Yan; Chen, Kezheng; Yu, Xuegang; Gao, Lian

2010-11-01

Magnetic carbon nanotubes consisting of multi-wall carbon nanotubes (MWNTs) core and Fe3O4 shell were successfully prepared by in situ thermal decomposition of Fe(acac)3 or FeCl3 or Fe(CO)5 in 2-pyrrolidone containing acid treated MWNTs at 240 °C with the protection of nitrogen gas. The samples were characterized by TEM, XRD, SEAD, XPS and superconducting quantum interference device. Also, their biocompatibility was compared with naked carbon nanotubes. The results showed that after coated with Fe3O4 nanoparticles, the obtained magnetic carbon nanotubes show superparamagnetic characteristic at room temperature, and their blocking temperature is about 80 K. The magnetic properties of the nanotubes are relevant to the content of magnetic particles, increasing content of magnetic nanoparticles leads to higher blocking temperature and saturation magnetization. The results of antimicrobial activities to bacterial cells (Escherichia coli) showed that the MWNTs have antimicrobial activity, while the magnetic nanotubes are biocompatible even with a higher concentration than that of MWNTs.

Isolation of bacterial metabolites as natural inducers for larval settlement in the marine polychaete Hydroides elegans (Haswell).

PubMed

Harder, Tilmann; Lau, Stanley Chun Kwan; Dahms, Hans-Uwe; Qian, Pei-Yuan

2002-10-01

The bacterial component of marine biofilms plays an important role in the induction of larval settlement in the polychaete Hydroides elegans. In this study, we provide experimental evidence that bacterial metabolites comprise the chemical signal for larval settlement. Bacteria were isolated from biofilms, purified and cultured according to standard procedures. Bacterial metabolites were isolated from spent culture broth by chloroform extraction as well as by closed-loop stripping and adsorption of volatile components on surface-modified silica gel. A pronounced biological activity was exclusively observed when concentrated metabolites were adsorbed on activated charcoal. Larvae did not respond to waterbome metabolites when prevented from contacting the bacterial film surface. These results indicate that an association of the chemical signal with a sorbent-like substratum may be an essential cofactor for the expression of biological activity. The functional role of bacterial exopolymers as an adsorptive matrix for larval settlement signals is discussed.

Connecting the dots between bacterial biofilms and ice cream

NASA Astrophysics Data System (ADS)

Stanley-Wall, Nicola R.; MacPhee, Cait E.

2015-12-01

Emerging research is revealing a diverse array of interfacially-active proteins that are involved in varied biological process from foaming horse sweat to bacterial raincoat formation. We describe an interdisciplinary approach to study the molecular and biophysical mechanisms controlling the activity of an unusual bacterial protein called BslA. This protein is needed for biofilm formation and forms a protective layer or raincoat over the bacterial community, but also has a multitude of potential applications in multiphase formulations. Here we document our journey from fundamental research to an examination of the applications for this surface-active protein in ice cream.

Connecting the dots between bacterial biofilms and ice cream.

PubMed

Stanley-Wall, Nicola R; MacPhee, Cait E

2015-12-18

Emerging research is revealing a diverse array of interfacially-active proteins that are involved in varied biological process from foaming horse sweat to bacterial raincoat formation. We describe an interdisciplinary approach to study the molecular and biophysical mechanisms controlling the activity of an unusual bacterial protein called BslA. This protein is needed for biofilm formation and forms a protective layer or raincoat over the bacterial community, but also has a multitude of potential applications in multiphase formulations. Here we document our journey from fundamental research to an examination of the applications for this surface-active protein in ice cream.

Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA).

PubMed

Davis, James P; Struchtemeyer, Christopher G; Elshahed, Mostafa S

2012-11-01

We monitored the bacterial communities in the gas-water separator and water storage tank of two newly drilled natural gas wells in the Barnett Shale in north central Texas, using a 16S rRNA gene pyrosequencing approach over a period of 6 months. Overall, the communities were composed mainly of moderately halophilic and halotolerant members of the phyla Firmicutes and Proteobacteria (classes Βeta-, Gamma-, and Epsilonproteobacteria) in both wells at all sampling times and locations. Many of the observed lineages were encountered in prior investigations of microbial communities from various fossil fluid formations and production facilities. In all of the samples, multiple H(2)S-producing lineages were encountered; belonging to the sulfate- and sulfur-reducing class Deltaproteobacteria, order Clostridiales, and phylum Synergistetes, as well as the thiosulfate-reducing order Halanaerobiales. The bacterial communities from the separator and tank samples bore little resemblance to the bacterial communities in the drilling mud and hydraulic-fracture waters that were used to drill these wells, suggesting the in situ development of the unique bacterial communities in such well components was in response to the prevalent geochemical conditions present. Conversely, comparison of the bacterial communities on temporal and spatial scales suggested the establishment of a core microbial community in each sampled location. The results provide the first overview of bacterial dynamics and colonization patterns in newly drilled, thermogenic natural gas wells and highlights patterns of spatial and temporal variability observed in bacterial communities in natural gas production facilities.

Ultrastructure of Bacterial Cells Infected with Bacteriophage PM2, a Lipid-containing Bacterial Virus

PubMed Central

Cota-Robles, Eugene; Espejo, Romilio Torres; Haywood, Patricia Williams

1968-01-01

The cytological pattern of infection of a host pseudomonad with PM2, a lipid-containing bacterial virus, was investigated by electron microscopy. Normal and infected cells frequently contain a myelin figure, which is found in the nucleoid region or at the periphery of the cell. The most striking finding in this investigation was that completed virions are found in the cell adjacent to or in association with the cytoplasmic membrane. This localization is precise; virions are not found elsewhere in infected cells. The completed virions occasionally appear to be attached to the cytoplasmic membrane. The virus contains a darkly staining core surrounded by a tripartite envelope of a thickness of approximately 70 A, which is identical to the thickness of the cytoplasmic membrane. Lysing cells appear to undergo extensive damage of the cytoplasmic membrane prior to rupture of the L layer of the cell wall. Images PMID:5742028

Sensory deprivation in Staphylococcus aureus.

PubMed

Villanueva, Maite; García, Begoña; Valle, Jaione; Rapún, Beatriz; Ruiz de Los Mozos, Igor; Solano, Cristina; Martí, Miguel; Penadés, José R; Toledo-Arana, Alejandro; Lasa, Iñigo

2018-02-06

Bacteria use two-component systems (TCSs) to sense and respond to environmental changes. The core genome of the major human pathogen Staphylococcus aureus encodes 16 TCSs, one of which (WalRK) is essential. Here we show that S. aureus can be deprived of its complete sensorial TCS network and still survive under growth arrest conditions similarly to wild-type bacteria. Under replicating conditions, however, the WalRK system is necessary and sufficient to maintain bacterial growth, indicating that sensing through TCSs is mostly dispensable for living under constant environmental conditions. Characterization of S. aureus derivatives containing individual TCSs reveals that each TCS appears to be autonomous and self-sufficient to sense and respond to specific environmental cues, although some level of cross-regulation between non-cognate sensor-response regulator pairs occurs in vivo. This organization, if confirmed in other bacterial species, may provide a general evolutionarily mechanism for flexible bacterial adaptation to life in new niches.

Predictors of serious bacterial infections in pediatric burn patients with fever.

PubMed

Vyles, David; Sinha, Madhumita; Rosenberg, David I; Foster, Kevin N; Tran, Melissa; Drachman, David

2014-01-01

To determine predictors of serious bacterial infections in pediatric burn patients with fever (core temp ≥38.5°C), the authors conducted a retrospective review of medical records of pediatric (0-18 years) patients admitted to the Arizona Burn Center between 2008 and 2011 with greater than 5% TBSA and inpatient hospitalization for ≥72 hours. The study group comprised patients with a febrile episode during their inpatient stay. Serious bacterial infection (the primary outcome variable) was defined as: bacteremia, urinary tract infection, meningitis (blood, urine, or cerebrospinal fluid culture positive for a pathogen respectively), pneumonia, line, and wound infection. A generalized estimating equation analysis was done to predict the presence or absence of serious bacterial infection. Of 1082 pediatric burn patients hospitalized during the study period, 353 met the study eligibility criteria. A total of 108 patients (30.6%) had at least one fever episode (fever group). No difference in demographic characteristics was noted between the fever and no-fever groups; significant differences were observed for: third-degree TBSA, second-degree TBSA, total operating room visits, length of stay, Injury Severity Score, and death. A total of 47.2% of the patients had one or more episodes of fever with serious bacterial infection. In a generalized estimating equation predictive model, presence of a central line, second-, and third-degree TBSA were predictive of serious bacterial infection in burn patients with fever. In this study, individual clinical variables such as tachypnea and tachycardia were not predictive of serious bacterial infections, but the presence of a central line, and larger TBSA were significant predictors of serious bacterial infections. Younger age (P =.08) and ventilator support (P =.057) also approached significance as predictors of serious bacterial infections.

Effects of bacterial pollution caused by a strong typhoon event and the restoration of a recreational beach: Transitions of fecal bacterial counts and bacterial flora in beach sand.

PubMed

Suzuki, Yoshihiro; Teranishi, Kotaro; Matsuwaki, Tomonori; Nukazawa, Kei; Ogura, Yoshitoshi

2018-05-28

To determine the effects of bacteria pollution associated with a strong typhoon event and to assess the restoration of the normal bacterial flora, we used conventional filtration methods and nextgeneration sequencing of 16S rRNA genes to analyze the transition of fecal and total bacterial counts in water and core sand samples collected from a recreational beach. Immediately after the typhoon event, Escherichia coli counts increased to 82 CFU/100 g in the surface beach sand. E. coli was detected through the surface to sand 85-cm deep at the land side point (10-m land side from the high-water line). However, E. coli disappeared within a month from the land side point. The composition of the bacterial flora in the beach sand at the land point was directly influenced by the typhoon event. Pseudomonas was the most prevalent genus throughout the sand layers (0-102-cm deep) during the typhoon event. After 3 months, the population of Pseudomonas significantly decreased, and the predominant genus in the surface layer was Kaistobacter, although Pseudomonas was the major genus in the 17- to 85-cm layer. When the beach conditions stabilized, the number of pollutant Pseudomonas among the 10 most abundant genera decreased to lower than the limit of detection. The bacterial population of the sand was subsequently restored to the most populous pre-event orders at the land point. A land-side beach, where users directly contact the sand, was significantly affected by bacterial pollution caused by a strong typhoon event. We show here that the normal bacterial flora of the surface sand was restored within 1 month. Copyright © 2018 Elsevier B.V. All rights reserved.

Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome.

PubMed

Becker, C G; Longo, A V; Haddad, C F B; Zamudio, K R

2017-08-30

Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus Batrachochytrium dendrobatidis ( Bd ) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats. Bd infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and Bd loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from Bd infection, we also evaluated the bi-directional microbiome- Bd link but failed to find a significant effect of skin bacterial diversity reducing Bd infections. Although weak, we found support for Bd increasing bacterial diversity and/or for core bacteria dominance reducing Bd loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host-pathogen-microbiome triangle. © 2017 The Author(s).

Characterization of CCN and IN activity of bacterial isolates collected in Atlanta, GA

NASA Astrophysics Data System (ADS)

Purdue, Sara; Waters, Samantha; Karthikeyan, Smruthi; Konstantinidis, Kostas; Nenes, Athanasios

2016-04-01

Characterization of CCN activity of bacteria, other than a few select types such as Pseudomonas syringae, is limited, especially when looked at in conjunction with corresponding IN activity. The link between these two points is especially important for bacteria as those that have high CCN activity are likely to form an aqueous phase required for immersion freezing. Given the high ice nucleation temperature of bacterial cells, especially in immersion mode, it is important to characterize the CCN and IN activity of many different bacterial strains. To this effect, we developed a droplet freezing assay (DFA) which consists of an aluminum cold plate, cooled by a continuous flow of an ethylene glycol-water mixture, in order to observe immersion freezing of the collected bacteria. Here, we present the initial results on the CCN and IN activities of bacterial samples we have collected in Atlanta, GA. Bacterial strains were collected and isolated from rainwater samples taken from different storms throughout the year. We then characterized the CCN activity of each strain using a DMT Continuous Flow Streamwise Thermal Gradient CCN Counter by exposing the aerosolized bacteria to supersaturations ranging from 0.05% to 0.6%. Additionally, using our new DFA, we characterized the IN activity of each bacterial strain at temperatures ranging from -20oC to 0oC. The combined CCN and IN activity gives us valuable information on how some uncharacterized bacteria contribute to warm and mixed-phase cloud formation in the atmosphere.

The source of high signal cooperativity in bacterial chemosensory arrays

PubMed Central

Piñas, Germán E.; Frank, Vered; Vaknin, Ady; Parkinson, John S.

2016-01-01

The Escherichia coli chemosensory system consists of large arrays of transmembrane chemoreceptors associated with a dedicated histidine kinase, CheA, and a linker protein, CheW, that couples CheA activity to receptor control. The kinase activity responses to receptor ligand occupancy changes can be highly cooperative, reflecting allosteric coupling of multiple CheA and receptor molecules. Recent structural and functional studies have led to a working model in which receptor core complexes, the minimal units of signaling, are linked into hexagonal arrays through a unique interface 2 interaction between CheW and the P5 domain of CheA. To test this array model, we constructed and characterized CheA and CheW mutants with amino acid replacements at key interface 2 residues. The mutant proteins proved defective in interface 2-specific in vivo cross-linking assays, and formed signaling complexes that were dispersed around the cell membrane rather than clustered at the cell poles as in wild type chemosensory arrays. Interface 2 mutants down-regulated CheA activity in response to attractant stimuli in vivo, but with much less cooperativity than the wild type. Moreover, mutant cells containing fluorophore-tagged receptors exhibited greater basal anisotropy that changed rapidly in response to attractant stimuli, consistent with facile changes in loosely packed receptors. We conclude that interface 2 lesions disrupt important network connections between core complexes, preventing receptors from operating in large, allosteric teams. This work confirms the critical role of interface 2 in organizing the chemosensory array, in directing the clustered array to the cell poles, and in producing its highly cooperative signaling properties. PMID:26951681

[Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

PubMed

Li, Min; Wu, Feng-zhi

2014-12-01

Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition.

PubMed

Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; Zhang, Li-Mei

2016-02-01

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

Bacterial diversity and active biomass in full-scale granular activated carbon filters operated at low water temperatures.

PubMed

Kaarela, Outi E; Härkki, Heli A; Palmroth, Marja R T; Tuhkanen, Tuula A

2015-01-01

Granular activated carbon (GAC) filtration enhances the removal of natural organic matter and micropollutants in drinking water treatment. Microbial communities in GAC filters contribute to the removal of the biodegradable part of organic matter, and thus help to control microbial regrowth in the distribution system. Our objectives were to investigate bacterial community dynamics, identify the major bacterial groups, and determine the concentration of active bacterial biomass in full-scale GAC filters treating cold (3.7-9.5°C), physicochemically pretreated, and ozonated lake water. Three sampling rounds were conducted to study six GAC filters of different operation times and flow modes in winter, spring, and summer. Total organic carbon results indicated that both the first-step and second-step filters contributed to the removal of organic matter. Length heterogeneity analysis of amplified 16S rRNA genes illustrated that bacterial communities were diverse and considerably stable over time. α-Proteobacteria, β-Proteobacteria, and Nitrospira dominated in all of the GAC filters, although the relative proportion of dominant phylogenetic groups in individual filters differed. The active bacterial biomass accumulation, measured as adenosine triphosphate, was limited due to low temperature, low flux of nutrients, and frequent backwashing. The concentration of active bacterial biomass was not affected by the moderate seasonal temperature variation. In summary, the results provided an insight into the biological component of GAC filtration in cold water temperatures and the operational parameters affecting it.

Leaky RAG Deficiency in Adult Patients with Impaired Antibody Production against Bacterial Polysaccharide Antigens

PubMed Central

Geier, Christoph B.; Piller, Alexander; Linder, Angela; Sauerwein, Kai M. T.; Eibl, Martha M.; Wolf, Hermann M.

2015-01-01

Loss of function mutations in the recombination activating genes RAG1 and RAG2 have been reported to cause a T-B-NK+ type of severe combined immunodeficiency. In addition identification of hypomorphic mutations in RAG1 and RAG2 has led to an expansion of the spectrum of disease to include Omenn syndrome, early onset autoimmunity, granuloma, chronic cytomegalovirus- or EBV-infection with expansion of gamma/delta T-cells, idiophatic CD4 lymphopenia and a phenotype resembling common variable immunodeficiency. Herein we describe a novel presentation of leaky RAG1 and RAG2 deficiency in two unrelated adult patients with impaired antibody production against bacterial polysaccharide antigens. Clinical manifestation included recurrent pneumonia, sinusitis, otitis media and in one patient recurrent cutaneous vasculitis. Both patients harbored a combination of a null mutation on one allele with a novel hypomorphic RAG1/2 mutation on the other allele. One of these novel mutations affected the start codon of RAG1 and resulted in an aberrant gene and protein expression. The second novel RAG2 mutation leads to a truncated RAG2 protein, lacking the C-terminus with intact core RAG2 and reduced VDJ recombination capacity as previously described in a mouse model. Both patients presented with severely decreased numbers of naïve CD4+ T cells and defective T independent IgG responses to bacterial polysaccharide antigens, while T cell-dependent IgG antibody formation e.g. after tetanus or TBEV vaccination was intact. In conclusion, hypomorphic mutations in genes responsible for SCID should be considered in adults with predominantly antibody deficiency. PMID:26186701

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.

PubMed

Galperin, Michael Y; Higdon, Roger; Kolker, Eugene

2010-04-01

Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats.

PubMed

Hernandez-Agreda, Alejandra; Leggat, William; Bongaerts, Pim; Ainsworth, Tracy D

2016-07-26

For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts' environment. Corals have been proposed as the most diverse microbial biosphere. The high variability of microbial communities has hampered the identification of bacteria playing key functional roles that contribute to coral survival. Exploring the bacterial community in a coral with a broad environmental distribution, we found a group of bacteria present across all environments and a higher number of bacteria consistently associated with mesophotic corals (60 to 80 m). These results provide evidence of consistent and ubiquitous coral-bacterial partnerships and support the consideration of corals as metaorganisms hosting three functionally distinct microbiomes: a ubiquitous core microbiome, a microbiome filling functional niches, and a highly variable bacterial community. Copyright © 2016 Hernandez-Agreda et al.

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes.

PubMed

Clarke, Thomas H; Brinkac, Lauren M; Inman, Jason M; Sutton, Granger; Fouts, Derrick E

2018-06-27

Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regions. Multiple software packages are available to visualize pan-genomes, but currently their ability to address these concerns are limited by using only pre-computed data sets, prioritizing core over variable gene clusters, or by not accounting for pan-chromosome positioning in the viewer. We introduce PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer), which utilizes locally-computed interactive web-pages to view ordered pan-genome data. It consists of multi-tiered, hierarchical display pages that extend from pan-chromosomes to both core and variable regions to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated. PanACEA's memory and time requirements are within the capacities of standard laptops. The capability of PanACEA as a research tool is demonstrated by highlighting a variable region important in differentiating strains of Enterobacter hormaechei. PanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation. It will empower researchers to visually explore and identify regions of the pan-chromosome that are most biologically interesting, and to obtain publication quality images of these regions.

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

PubMed Central

Carter, Kelsey R.; Carrell, Alyssa A.; Jun, Se-Ran; Jawdy, Sara S.; Vélez, Jessica M.; Gunter, Lee E.; Yang, Zamin; Nookaew, Intawat; Engle, Nancy L.; Lu, Tse-Yuan S.; Schadt, Christopher W.; Tschaplinski, Timothy J.; Tuskan, Gerald A.; Pelletier, Dale A.; Weston, David J.

2018-01-01

ABSTRACT Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress. IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth. PMID:29404422

Abiotic Stresses Shift Belowground Populus -Associated Bacteria Toward a Core Stress Microbiome

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

Timm, Collin M.; Carter, Kelsey R.; Carrell, Alyssa A.

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome ofPopulus deltoideschanges in response to diverse environmental conditions, including water limitation, light limitation (shading),more » and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.« less

Abiotic Stresses Shift Belowground Populus -Associated Bacteria Toward a Core Stress Microbiome

DOE PAGES

Timm, Collin M.; Carter, Kelsey R.; Carrell, Alyssa A.; ...

2018-01-23

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome ofPopulus deltoideschanges in response to diverse environmental conditions, including water limitation, light limitation (shading),more » and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.« less

Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization1

PubMed Central

Yim, Young-Sun; Davis, Georgia L.; Duru, Ngozi A.; Musket, Theresa A.; Linton, Eric W.; Messing, Joachim W.; McMullen, Michael D.; Soderlund, Carol A.; Polacco, Mary L.; Gardiner, Jack M.; Coe, Edward H.

2002-01-01

Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage λ. The results indicate that the libraries are of high quality with low contamination by organellar and λ-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6× coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 × Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 ± 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction. PMID:12481051

Bacterial components are the major contributors to the macrophage stimulating activity exhibited by extracts of common edible mushrooms.

PubMed

Tyler, Heather L; Haron, Mona H; Pugh, Nirmal D; Zhang, Jin; Jackson, Colin R; Pasco, David S

2016-10-12

Recent studies have indicated that a major contributor to the innate immune enhancing properties of some medicinal plants is derived from the cell wall components of bacteria colonizing these plants. The purpose of the current study was to assess if the bacteria present within edible and medicinal mushrooms substantially contribute to the innate immune stimulating potential of these mushrooms. Whole mushrooms from thirteen types of edible fungi and individual parts from Agaricus bisporus were analyzed for in vitro macrophage activation as well as bacterial lipopolysaccharides (LPS) content, cell load, and community composition. Substantial variation between samples was observed in macrophage activation (over 500-fold), total bacterial load (over 200-fold), and LPS content (over 10 million-fold). Both LPS content (ρ = 0.832, p < 0.0001) and total bacterial load (ρ = 0.701, p < 0.0001) correlated significantly with macrophage activation in the whole mushroom extracts. Extract activity was negated by treatment with NaOH, conditions that inactivate LPS and other bacterial components. Significant correlations between macrophage activation and total bacterial load (ρ = 0.723, p = 0.0001) and LPS content (ρ = 0.951, p < 0.0001) were also observed between different tissues of Agaricus bisporus. Pseudomonas and Flavobacterium were the most prevalent genera identified in the different tissue parts and these taxa were significantly correlated with in vitro macrophage activation (ρ = 0.697, p < 0.0001 and ρ = 0.659, p = 0.0001, respectively). These results indicate that components derived from mushroom associated bacteria contribute substantially to the innate immune enhancing activity exhibited by mushrooms and may result in similar therapeutic actions as reported for ingestion of bacterial preparations such as probiotics.

Flow and active mixing have a strong impact on bacterial growth dynamics in the proximal large intestine

NASA Astrophysics Data System (ADS)

Cremer, Jonas; Segota, Igor; Yang, Chih-Yu; Arnoldini, Markus; Groisman, Alex; Hwa, Terence

2016-11-01

More than half of fecal dry weight is bacterial mass with bacterial densities reaching up to 1012 cells per gram. Mostly, these bacteria grow in the proximal large intestine where lateral flow along the intestine is strong: flow can in principal lead to a washout of bacteria from the proximal large intestine. Active mixing by contractions of the intestinal wall together with bacterial growth might counteract such a washout and allow high bacterial densities to occur. As a step towards understanding bacterial growth in the presence of mixing and flow, we constructed an in-vitro setup where controlled wall-deformations of a channel emulate contractions. We investigate growth along the channel under a steady nutrient inflow. Depending on mixing and flow, we observe varying spatial gradients in bacterial density along the channel. Active mixing by deformations of the channel wall is shown to be crucial in maintaining a steady-state bacterial population in the presence of flow. The growth-dynamics is quantitatively captured by a simple mathematical model, with the effect of mixing described by an effective diffusion term. Based on this model, we discuss bacterial growth dynamics in the human large intestine using flow- and mixing-behavior having been observed for humans.

Purification of CD47-streptavidin fusion protein from bacterial lysate using biotin-agarose affinity chromatography.

PubMed

Salehi, Nasrin; Peng, Ching-An

2016-07-08

CD47 is a widely expressed transmembrane glycoprotein that modulates the activity of a plethora of immune cells via its extracellular domain. Therefore, CD47 plays important roles in the regulation of immune responses and may serve as targets for the development of immunotherapeutic agents. To make sure CD47 functionality is intact under the process of protein conjugation, CD47-streptavidin fusion protein was expressed and purified because it can easily bind to biotin-tagged materials via the unique biotin-streptavidin affinity. In this study, gene sequences of CD47 extracellular domain (CD47ECD) and core streptavidin (coreSA) with a total 834 bp were inserted into pET20b plasmid to construct recombinant plasmid encoding CD47-SA fusion gene. After bacteria transformation, the CD47-SA fusion protein was expressed by isopropyl-β-d-thiogalactopyranoside (IPTG) induction. The collected bacteria lysate was loaded on biotinylated agarose to proceed the purification of CD47-SA fusion protein. Due to the unexpected high affinity between biotin and coreSA, standard washing and elution approaches (e.g., varying pH, using biotin, and applying guanidine hydrochloride) reported for biotin-streptavidin affinity chromatography were not able to separate the target fusion protein. Instead, using low concentration of the non-ionic detergent Triton X-100 followed with alkaline buffer could efficiently weaken the binding between biotin and coreSA, thereby eluting out CD47-SA fusion protein from the biotin agarose column. The purified CD47-SA fusion protein was further characterized by molecular biology methods and its antiphagocytic functionality was confirmed by the phagocytosis assay. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:949-958, 2016. © 2016 American Institute of Chemical Engineers.

Oligomerization of the E. coli Core RNA Polymerase: Formation of (α2ββ'ω)2–DNA Complexes and Regulation of the Oligomerization by Auxiliary Subunits

PubMed Central

Kansara, Seema G.; Sukhodolets, Maxim V.

2011-01-01

In this work, using multiple, dissimilar physico-chemical techniques, we demonstrate that the Escherichia coli RNA polymerase core enzyme obtained through a classic purification procedure forms stable (α2ββ'ω)2 complexes in the presence or absence of short DNA probes. Multiple control experiments indicate that this self-association is unlikely to be mediated by RNA polymerase-associated non-protein molecules. We show that the formation of (α2ββ'ω)2 complexes is subject to regulation by known RNA polymerase interactors, such as the auxiliary SWI/SNF subunit of RNA polymerase RapA, as well as NusA and σ70. We also demonstrate that the separation of the core RNA polymerase and RNA polymerase holoenzyme species during Mono Q chromatography is likely due to oligomerization of the core enzyme. We have analyzed the oligomeric state of the polymerase in the presence or absence of DNA, an aspect that was missing from previous studies. Importantly, our work demonstrates that RNA polymerase oligomerization is compatible with DNA binding. Through in vitro transcription and in vivo experiments (utilizing a RapAR599/Q602 mutant lacking transcription-stimulatory function), we demonstrate that the formation of tandem (α2ββ'ω)2–DNA complexes is likely functionally significant and beneficial for the transcriptional activity of the polymerase. Taken together, our findings suggest a novel structural aspect of the E. coli elongation complex. We hypothesize that transcription by tandem RNA polymerase complexes initiated at hypothetical bidirectional “origins of transcription” may explain recurring switches of the direction of transcription in bacterial genomes. PMID:21533049

The sedimentary organic matter from a Lake Ichkeul core (far northern Tunisia): Rock-Eval and biomarker approach

NASA Astrophysics Data System (ADS)

Affouri, Hassène; Sahraoui, Olfa

2017-05-01

The vertical distributions of bulk and molecular biomarker composition in samples from a ca. 156 cm sediment core from Lake Ichkeul were determined. Bulk analysis (Rock-Eval pyrolysis, carbonate, lipid extraction) and molecular analysis of saturated fractions were used to characterize the nature, preservation conditions and input of sedimentary organic matter (OM) to this sub-wet lake environment. The sediments are represented mainly by gray-black silty-clay facies where the carbonate (CaCO3) content varies in a range of 10-30% dry sediment. Rock-Eval pyrolysis revealed a homogeneous total organic carbon (TOC) content of ca. 1% sediment, but with down core fluctuation, indicating different anoxic conditions at different depths and material source variation. The values show three periods of relative enrichment, exceeding ca. 1%, at 146-134 cm, 82 cm and 14-0 cm depth. The low Hydrogen Index (HI) values [<119 mg hydrocarbon (HC)/g TOC)] were characteristic of continental Type III OM. The Tmax values in the range 415-420 °C were characteristic of immature OM at an early diagenetic stage. The distributions of n-alkanes (C17 to C34), isoprenoid (iso) alkanes (pristane and phytane), terpanes and steranes showed that the OM is a mixture of marine algal and bacterial source and emergent and floating higher plant origin. In addition, the distributions, as well as several biomarker ratios (n-alkanes, iso-alkanes/n-alkanes), showed that the OM is a mixture of immature and mature. Significant downcore fluctuation was observed in the molecular composition. This indicates intense microbial activity below ca. 50 cm core depth under an anoxic and brackish environment.

A Comparison of Naturally-Occurring and Artificially Stimulated Uranium(VI) Bioreduction in Sediment from a Field-scale Experiment in Rifle, CO

NASA Astrophysics Data System (ADS)

Campbell, K. M.; Williams, K. H.; Lesher, E.; Davis, J. A.; Long, P. E.

2007-12-01

Long-term remediation of uranium (U)-contaminated groundwater poses one of the greatest challenges in the clean-up of impacted sites. One solution is to reduce dissolved U(VI) to insoluble U(IV) precipitates by stimulating indigenous metal reducing bacterial populations in situ. Contamination from a former U mine tailings repository (Rifle, CO) provides a research site to study the efficacy of biostimulated U(VI) reduction at the field scale. Several cores were drilled in June 2007 across a region of naturally-occurring U(VI) bioreduction. The cores represent a cross section of sediment that ranges from minimally reducing to highly reducing. Anaerobic sediment samples from the cores were analyzed for labile U(VI) content by carbonate extraction in anoxic conditions (pH 9.4, 14 mM NaHCO3, 2.8 mM Na2CO¬3). A subset of the same core sections were dried and oxidized by exposure to air for 2 weeks. The carbonate extraction was repeated, and the amount of U(IV) present in the anaerobic sample was calculated by difference between the anoxic and oxidized extractions. An acid extraction was also performed on the oxidized sediments to compare the carbonate extractable and the acid extractable U fractions. The highest U concentrations were found in the highly bioreduced sediment, with the majority of U present as U(IV) (66-92%). The regions of highest bioreduction also correspond to elevated concentrations of solid phase organic carbon, suggesting that natural bioreduction is stimulated by zones of increased organic carbon content. The same field site was then used for an artificially stimulated bioreduction experiment, where the indigenous bacterial community was stimulated by injecting acetate upgradient of the core collection location. Carbonate and acid extractions were performed on core samples taken after the completion of the acetate injection. This work evaluates the composition of the sediment before and after biostimulation as a way of directly comparing the extent of natural U(VI) bioreduction to acetate-stimulated bioreduction in order to facilitate the design of a more effective bioremediation strategy for this site.

Apoptosis-Like Death in Bacteria Induced by HAMLET, a Human Milk Lipid-Protein Complex

PubMed Central

Hakansson, Anders P.; Roche-Hakansson, Hazeline; Mossberg, Ann-Kristin; Svanborg, Catharina

2011-01-01

Background Apoptosis is the primary means for eliminating unwanted cells in multicellular organisms in order to preserve tissue homeostasis and function. It is characterized by distinct changes in the morphology of the dying cell that are orchestrated by a series of discrete biochemical events. Although there is evidence of primitive forms of programmed cell death also in prokaryotes, no information is available to suggest that prokaryotic death displays mechanistic similarities to the highly regulated programmed death of eukaryotic cells. In this study we compared the characteristics of tumor and bacterial cell death induced by HAMLET, a human milk complex of alpha-lactalbumin and oleic acid. Methodology/Principal Findings We show that HAMLET-treated bacteria undergo cell death with mechanistic and morphologic similarities to apoptotic death of tumor cells. In Jurkat cells and Streptococcus pneumoniae death was accompanied by apoptosis-like morphology such as cell shrinkage, DNA condensation, and DNA degradation into high molecular weight fragments of similar sizes, detected by field inverse gel electrophoresis. HAMLET was internalized into tumor cells and associated with mitochondria, causing a rapid depolarization of the mitochondrial membrane and bound to and induced depolarization of the pneumococcal membrane with similar kinetic and magnitude as in mitochondria. Membrane depolarization in both systems required calcium transport, and both tumor cells and bacteria were found to require serine protease activity (but not caspase activity) to execute cell death. Conclusions/Significance Our results suggest that many of the morphological changes and biochemical responses associated with apoptosis are present in prokaryotes. Identifying the mechanisms of bacterial cell death has the potential to reveal novel targets for future antimicrobial therapy and to further our understanding of core activation mechanisms of cell death in eukaryote cells. PMID:21423701

Apoptosis-like death in bacteria induced by HAMLET, a human milk lipid-protein complex.

PubMed

Hakansson, Anders P; Roche-Hakansson, Hazeline; Mossberg, Ann-Kristin; Svanborg, Catharina

2011-03-10

Apoptosis is the primary means for eliminating unwanted cells in multicellular organisms in order to preserve tissue homeostasis and function. It is characterized by distinct changes in the morphology of the dying cell that are orchestrated by a series of discrete biochemical events. Although there is evidence of primitive forms of programmed cell death also in prokaryotes, no information is available to suggest that prokaryotic death displays mechanistic similarities to the highly regulated programmed death of eukaryotic cells. In this study we compared the characteristics of tumor and bacterial cell death induced by HAMLET, a human milk complex of alpha-lactalbumin and oleic acid. We show that HAMLET-treated bacteria undergo cell death with mechanistic and morphologic similarities to apoptotic death of tumor cells. In Jurkat cells and Streptococcus pneumoniae death was accompanied by apoptosis-like morphology such as cell shrinkage, DNA condensation, and DNA degradation into high molecular weight fragments of similar sizes, detected by field inverse gel electrophoresis. HAMLET was internalized into tumor cells and associated with mitochondria, causing a rapid depolarization of the mitochondrial membrane and bound to and induced depolarization of the pneumococcal membrane with similar kinetic and magnitude as in mitochondria. Membrane depolarization in both systems required calcium transport, and both tumor cells and bacteria were found to require serine protease activity (but not caspase activity) to execute cell death. Our results suggest that many of the morphological changes and biochemical responses associated with apoptosis are present in prokaryotes. Identifying the mechanisms of bacterial cell death has the potential to reveal novel targets for future antimicrobial therapy and to further our understanding of core activation mechanisms of cell death in eukaryote cells.

The multifunctional wound dressing with core-shell structured fibers prepared by coaxial electrospinning

NASA Astrophysics Data System (ADS)

Wei, Qilin; Xu, Feiyang; Xu, Xingjian; Geng, Xue; Ye, Lin; Zhang, Aiying; Feng, Zengguo

2016-06-01

The non-woven wound dressing with core-shell structured fibers was prepared by coaxial electrospinning. The polycaprolactone (PCL) was electrospun as the fiber's core to provide mechanical strength whereas collagen was fabricated into the shell in order to utilize its good biocompatibility. Simultaneously, the silver nanoparticles (Ag-NPs) as anti-bacterial agent were loaded in the shell whereas the vitamin A palmitate (VA) as healing-promoting drug was encapsulated in the core. Resulting from the fiber's core-shell structure, the VA released from the core and Ag-NPs present in the shell can endow the dressing both heal-promoting and anti-bacteria ability simultaneously, which can greatly enhance the dressing's clinical therapeutic effect. The dressing can maintain high swelling ratio of 190% for 3 d indicating its potential application as wet dressing. Furthermore, the dressing's anti-bacteria ability against Staphylococcus aureus was proved by in vitro anti-bacteria test. The in vitro drug release test showed the sustainable release of VA within 72 h, while the cell attachment showed L929 cells can well attach on the dressing indicating its good biocompatibility. In conclusion, the fabricated nanofibrous dressing possesses multiple functions to benefit wound healing and shows promising potential for clinical application.

Design of a low cost spinneret assembly for coaxial electrospinning

NASA Astrophysics Data System (ADS)

Raheja, Anant; Chandra, T. S.; Natarajan, T. S.

2015-06-01

Coaxial electrospinning makes use of a concentric arrangement of spinneret orifices for synthesis of core-shell polymer nanofibers. Most laboratories purchase the spinneret from commercial manufacturers at a significant expense, or design it indigenously to save costs but compromise on manufacturing precision. Therefore, the present work suggests the use of a relatively lower priced McIntyre cannula needle, conventionally used for ophthalmic surgeries, as a coaxial spinneret for electrospinning. The McIntyre cannula needle was modified to synthesize hollow fibers of nylon 6, which acted as sheath with hydrogen peroxide as core during electrospinning. In addition, encapsulation of bioactives, viz., red blood cells, bacterial cells, and lysozyme (enzyme protein) was attempted, using their aqueous suspensions as core, with polycaprolactone solution as sheath. Resulting fibers had an integral core-shell structure with the bioactives encapsulated in the core. This indicated that the modified McIntyre cannula functions suitably as a spinneret for coaxial electrospinning. Thus, apart from being a clinical device, the modified McIntyre cannula needle provides an economic alternative to conventional coaxial spinneret assemblies.

Antibacterial effect of composite resin foundation material incorporating quaternary ammonium polyethyleneimine nanoparticles.

PubMed

Pietrokovski, Yoav; Nisimov, Ilana; Kesler-Shvero, Dana; Zaltsman, Natan; Beyth, Nurit

2016-10-01

As caries is the most frequent cause of the failure of composite resin-based restorations, composite resins with antibacterial properties are desirable. However, whether quaternary ammonium polyethyleneimine nanoparticles can be effectively incorporated is unknown. The purpose of this in vitro study was to evaluate the antibacterial activity against Streptococcus mutans and Actinomyces viscosus of a foundation material incorporating quaternary ammonium polyethyleneimine (QPEI) nanoparticles. QPEI antimicrobial nanoparticles were incorporated in a commercially available foundation material (Q Core; BJM Laboratories Ltd) at 1% wt/wt. Antibacterial efficacy against S mutans (10 6 colony-forming units [CFU]/mL) and A viscosus (10 6 CFU/mL) was examined by the direct contact test (DCT), and the agar diffusion test (ADT) with and without surface polishing. Bacterial outgrowth was recorded with a spectrophotometer. Growth of S mutans and A viscosus was inhibited, showing a decrease by 6 orders of magnitude in bacterial viability in specimens incorporating the nanoparticles, even after polishing the foundation material (P<.05). Growth inhibition was not observed in specimens without nanoparticles. Antibacterial properties can be achieved in a commercially available foundation material by incorporating polycationic antibacterial nanoparticles. This antibacterial effect did not diminish after surface polishing. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Response of Bacterial Metabolic Activity to Riverine Dissolved Organic Carbon and Exogenous Viruses in Estuarine and Coastal Waters: Implications for CO2 Emission

PubMed Central

Xu, Jie; Sun, Mingming; Shi, Zhen; Harrison, Paul J.; Liu, Hongbin

2014-01-01

A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO2 degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7–12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary. PMID:25036641

Response of bacterial metabolic activity to riverine dissolved organic carbon and exogenous viruses in estuarine and coastal waters: implications for CO2 emission.

PubMed

Xu, Jie; Sun, Mingming; Shi, Zhen; Harrison, Paul J; Liu, Hongbin

2014-01-01

A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO2 degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7-12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary.

A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei

PubMed Central

2013-01-01

Background Pseudomyxoma peritonei (PMP) is a malignancy characterized by dissemination of mucus-secreting cells throughout the peritoneum. This disease is associated with significant morbidity and mortality and despite effective treatment options for early-stage disease, patients with PMP often relapse. Thus, there is a need for additional treatment options to reduce relapse rate and increase long-term survival. A previous study identified the presence of both typed and non-culturable bacteria associated with PMP tissue and determined that increased bacterial density was associated with more severe disease. These findings highlighted the possible role for bacteria in PMP disease. Methods To more clearly define the bacterial communities associated with PMP disease, we employed a sequenced-based analysis to profile the bacterial populations found in PMP tumor and mucin tissue in 11 patients. Sequencing data were confirmed by in situ hybridization at multiple taxonomic depths and by culturing. A pilot clinical study was initiated to determine whether the addition of antibiotic therapy affected PMP patient outcome. Main results We determined that the types of bacteria present are highly conserved in all PMP patients; the dominant phyla are the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. A core set of taxon-specific sequences were found in all 11 patients; many of these sequences were classified into taxonomic groups that also contain known human pathogens. In situ hybridization directly confirmed the presence of bacteria in PMP at multiple taxonomic depths and supported our sequence-based analysis. Furthermore, culturing of PMP tissue samples allowed us to isolate 11 different bacterial strains from eight independent patients, and in vitro analysis of subset of these isolates suggests that at least some of these strains may interact with the PMP-associated mucin MUC2. Finally, we provide evidence suggesting that targeting these bacteria with antibiotic treatment may increase the survival of PMP patients. Conclusions Using 16S amplicon-based sequencing, direct in situ hybridization analysis and culturing methods, we have identified numerous bacterial taxa that are consistently present in all PMP patients tested. Combined with data from a pilot clinical study, these data support the hypothesis that adding antimicrobials to the standard PMP treatment could improve PMP patient survival. PMID:23844722

Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.

PubMed

Rubio-Portillo, Esther; Santos, Fernando; Martínez-García, Manuel; de Los Ríos, Asunción; Ascaso, Carmen; Souza-Egipsy, Virginia; Ramos-Esplá, Alfonso A; Anton, Josefa

2016-12-01

Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells

PubMed Central

2010-01-01

Background In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry. To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process. To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. Results In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared. During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation. During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity. High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. Conclusions The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells. PMID:20831775

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells.

PubMed

Peternel, Spela; Komel, Radovan

2010-09-10

In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry.To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process.To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared.During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation.During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity.High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells.

Temperature-driven adaptation of the bacterial community in peat measured by using thymidine and leucine incorporation.

PubMed

Ranneklev, S B; Bååth, E

2001-03-01

The temperature-driven adaptation of the bacterial community in peat was studied, by altering temperature to simulate self-heating and a subsequent return to mesophilic conditions. The technique used consisted of extracting the bacterial community from peat using homogenization-centrifugation and measuring the rates of thymidine (TdR) or leucine (Leu) incorporation by the extracted bacterial community at different temperatures. Increasing the peat incubation temperature from 25 degrees C to 35, 45, or 55 degrees C resulted in a selection of bacterial communities whose optimum temperatures for activity correlated to the peat incubation temperatures. Although TdR and Leu incorporations were significantly correlated, the Leu/TdR incorporation ratios were affected by temperature. Higher Leu/TdR incorporation ratios were found at higher temperatures of incubation of the extracted bacterial community. Higher Leu/TdR incorporation ratios were also found for bacteria in peat samples incubated at higher temperatures. The reappearance of the mesophilic community and disappearance of the thermophilic community when the incubation temperature of the peat was shifted down were monitored by measuring TdR incorporation at 55 degrees C (thermophilic activity) and 25 degrees C (mesophilic activity). Shifting the peat incubation temperature from 55 to 25 degrees C resulted in a recovery of the mesophilic activity, with a subsequent disappearance of the thermophilic activity. The availability of substrate for bacterial growth varied over time and among different peat samples. To avoid confounding effects of substrate availability, a temperature adaptation index was calculated. This index consisted of the log(10) ratio of TdR incorporation at 55 and 25 degrees C. The temperature index decreased linearly with time, indicating that no thermophilic activity would be detected by the TdR technique 1 month after the temperature downshift. There were no differences between the slopes of the temperature adaptation indices over time for peat samples incubated at 55 degrees C 3 or 11 days before incubation at 25 degrees C. Thus, different levels of bacterial activity did not affect the temperature-driven adaptation of the bacterial community.

Temperature-Driven Adaptation of the Bacterial Community in Peat Measured by Using Thymidine and Leucine Incorporation

PubMed Central

Ranneklev, Sissel Brit; Bååth, Erland

2001-01-01

The temperature-driven adaptation of the bacterial community in peat was studied, by altering temperature to simulate self-heating and a subsequent return to mesophilic conditions. The technique used consisted of extracting the bacterial community from peat using homogenization-centrifugation and measuring the rates of thymidine (TdR) or leucine (Leu) incorporation by the extracted bacterial community at different temperatures. Increasing the peat incubation temperature from 25°C to 35, 45, or 55°C resulted in a selection of bacterial communities whose optimum temperatures for activity correlated to the peat incubation temperatures. Although TdR and Leu incorporations were significantly correlated, the Leu/TdR incorporation ratios were affected by temperature. Higher Leu/TdR incorporation ratios were found at higher temperatures of incubation of the extracted bacterial community. Higher Leu/TdR incorporation ratios were also found for bacteria in peat samples incubated at higher temperatures. The reappearance of the mesophilic community and disappearance of the thermophilic community when the incubation temperature of the peat was shifted down were monitored by measuring TdR incorporation at 55°C (thermophilic activity) and 25°C (mesophilic activity). Shifting the peat incubation temperature from 55 to 25°C resulted in a recovery of the mesophilic activity, with a subsequent disappearance of the thermophilic activity. The availability of substrate for bacterial growth varied over time and among different peat samples. To avoid confounding effects of substrate availability, a temperature adaptation index was calculated. This index consisted of the log10 ratio of TdR incorporation at 55 and 25°C. The temperature index decreased linearly with time, indicating that no thermophilic activity would be detected by the TdR technique 1 month after the temperature downshift. There were no differences between the slopes of the temperature adaptation indices over time for peat samples incubated at 55°C 3 or 11 days before incubation at 25°C. Thus, different levels of bacterial activity did not affect the temperature-driven adaptation of the bacterial community. PMID:11229900

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

PubMed

Kim, Hye Min; Lee, Min Jin; Jung, Ji Young; Hwang, Chung Yeon; Kim, Mincheol; Ro, Hee-Myong; Chun, Jongsik; Lee, Yoo Kyung

2016-11-01

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Ray Meta: scalable de novo metagenome assembly and profiling

PubMed Central

2012-01-01

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

Collective chemotaxis and segregation of active bacterial colonies

NASA Astrophysics Data System (ADS)

Amar, M. Ben

2016-02-01

Still recently, bacterial fluid suspensions have motivated a lot of works, both experimental and theoretical, with the objective to understand their collective dynamics from universal and simple rules. Since some species are active, most of these works concern the strong interactions that these bacteria exert on a forced flow leading to instabilities, chaos and turbulence. Here, we investigate the self-organization of expanding bacterial colonies under chemotaxis, proliferation and eventually active-reaction. We propose a simple model to understand and quantify the physical properties of these living organisms which either give cohesion or on the contrary dispersion to the colony. Taking into account the diffusion and capture of morphogens complicates the model since it induces a bacterial density gradient coupled to bacterial density fluctuations and dynamics. Nevertheless under some specific conditions, it is possible to investigate the pattern formation as a usual viscous fingering instability. This explains the similarity and differences of patterns according to the physical bacterial suspension properties and explain the factors which favor compactness or branching.

[Effects of traditional Chinese medicine on oral bacteria biofilm].

PubMed

Zhao, Jin; Li, Ji-yao; Zhu, Bing; Zhou, Xue-dong

2007-10-01

To investigate the effects of compounds of Galla chinensis extract (GCE) and Nidus vespae extract-1 (WVE1) on oral bacteria biofilm structure and activity and to determine the possibility of caries prevention by the compounds. The morphology and activity of treated-oral bacterial biofilm and untreated-oral bacterial biofilm were observed by using fluorescence microscope in combination of idio-fluorochrome to label the died and living bacteria. The visible light semiquantitative method was used to measure biomass glucosyltransferase (GTF, A620) values and to determine the effects of active compounds of GCE and NVE1 on GTF of oral bacteria biofilm. The living bacteria in the untreated 24 h bacterial biofilm was dominant, and only a small number of died bacteria were found, the biofilm structure was regular and clear. GCE, GCE-B and NVE1 could inhibit the bacteria in the dental biofilm, which showed significant difference with the negative control. GCE and NVE1 could also inhibit GTF activity of 24 h bacterial biofilm in comparison with the negative control. The traditional Chinese medicine Galla chinensis and Nidus vespae could not only inhibit bacteria growth on oral bacterial biofilm, but also function by adjusting biofilm structure, composition and GTF activity of 24 h bacterial biofilm.

Chronic rhinosinusitis and antibiotics: the good, the bad, and the ugly.

PubMed

Kennedy, Joshua L; Borish, Larry

2013-01-01

Despite the recognition that bacteria are universally present in the sinuses of patients with chronic rhinosinusitis (CRS) no compelling role for a primary infectious etiology of CRS has been elucidated. CRS is a constellation of inflammatory diseases that typically involve either noneosinophilic or eosinophilic processes, distinct conditions that must be treated individually. The bacteria that are present in the sinuses may be innocuous bystanders but alternatively may contribute to the presence and severity of the disease through their ability to influence immune responses, function as immune adjuvants, provide antigens or superantigens that contribute to adaptive immune activation, or in forming the basis for the frequent acute superinfections. However, those bacteria that do contribute to the persistence and severity of CRS primarily reside in biofilms, and, as such, are not capable of being eradicated with antibiotics at the doses at which they can be used, even when local irrigation is considered. Biofilms create an inhospitable environment for antibiotic potency by down-regulating the metabolic activity of their "core" bacteria, decreasing the oxygen concentration, and altering the pH at the core of the biofilm. Ultimately, if topical antibiotics are considered, they should be primarily focused on treating acute exacerbations and choices of antibiotics should optimally be based on endoscopic culture. This should be done with the recognition that while under certain circumstances antibiotics can ameliorate the severity of CRS, even if bacterial eradication were possible, this would not eliminate the underlying primary pathogenic mechanism or the natural history of these conditions.

Cellular Uptake and Localization of Polymyxins in Renal Tubular Cells Using Rationally Designed Fluorescent Probes

PubMed Central

Yun, Bo; Azad, Mohammad A. K.; Nowell, Cameron J.; Nation, Roger L.; Thompson, Philip E.; Roberts, Kade D.

2015-01-01

Polymyxins are cyclic lipopeptide antibiotics that serve as a last line of defense against Gram-negative bacterial superbugs. However, the extensive accumulation of polymyxins in renal tubular cells can lead to nephrotoxicity, which is the major dose-limiting factor in clinical use. In order to gain further insights into the mechanism of polymyxin-induced nephrotoxicity, we have rationally designed novel fluorescent polymyxin probes to examine the localization of polymyxins in rat renal tubular (NRK-52E) cells. Our design strategy focused on incorporating a dansyl fluorophore at the hydrophobic centers of the polymyxin core structure. To this end, four novel regioselectively labeled monodansylated polymyxin B probes (MIPS-9541, MIPS-9542, MIPS-9543, and MIPS-9544) were designed, synthesized, and screened for their antimicrobial activities and apoptotic effects against rat kidney proximal tubular cells. On the basis of the assessment of antimicrobial activities, cellular uptake, and apoptotic effects on renal tubular cells, incorporation of a dansyl fluorophore at either position 6 or 7 (MIPS-9543 and MIPS-9544, respectively) of the polymyxin core structure appears to be an appropriate strategy for generating representative fluorescent polymyxin probes to be utilized in intracellular imaging and mechanistic studies. Furthermore, confocal imaging experiments utilizing these probes showed evidence of partial colocalization of the polymyxins with both the endoplasmic reticulum and mitochondria in rat renal tubular cells. Our results highlight the value of these new fluorescent polymyxin probes and provide further insights into the mechanism of polymyxin-induced nephrotoxicity. PMID:26392495

Nosiheptide Biosynthesis Featuring a Unique Indole Side Ring Formation on the Characteristic Thiopeptide Framework

PubMed Central

Yu, Yi; Duan, Lian; Zhang, Qi; Liao, Rijing; Ding, Ying; Pan, Haixue; Wendt-Pienkowski, Evelyn; Tang, Gongli; Shen, Ben; Liu, Wen

2009-01-01

Nosiheptide (NOS), belonging to the e series of thiopeptide antibiotics that exhibit potent activity against various bacterial pathogens, bears a unique indole side ring system and regiospecific hydroxyl groups on the characteristic macrocyclic core. Here, cloning, sequencing and characterization of the nos gene cluster from Streptomyces actuosus ATCC 25421 as a model for this series of thiopeptides has unveiled new insights into their biosynthesis. Bioinformatics-based sequence analysis and in vivo investigation into the gene functions show that NOS biosynthesis shares a common strategy with recently characterized b or c series thiopeptides for forming the characteristic macrocyclic core, which features a ribosomally synthesized precursor peptide with conserved posttranslational modifications. However, it apparently proceeds via a different route for tailoring the thiopeptide framework, allowing the final product to exhibit the distinct structural characteristics of e series thiopeptides, such as the indole side ring system. Chemical complementation supports the notion that the S-adenosylmethionine (AdoMet)-dependent protein NosL may play a central role in converting Trp to the key 3-methylindole moiety by an unusual carbon side chain rearrangement, most likely via a radical-initiated mechanism. Characterization of the indole side ring-opened analog of NOS from the nosN mutant strain is consistent with the proposed methyltransferase activity of its encoded protein, shedding light into the timing of the individual steps for indole side ring biosynthesis. These results also suggest the feasibility of engineering novel thiopeptides for drug discovery by manipulating the NOS biosynthetic machinery. PMID:19678698

A common core microbiota between obese individuals and their lean relatives? Evaluation of the predisposition to obesity on the basis of the fecal microflora profile.

PubMed

Elli, M; Colombo, O; Tagliabue, A

2010-10-01

Obesity represents a crucial social problem in developed countries as a cause of multiple metabolic abnormalities. The exact etiology of this multifactorial disease is still unknown. The impact of dietary habits and lifestyle is currently under investigation but the role of other predisposing factors, such as genetic determinants and familial history, needs still to be elucidated. Significant alterations in the composition of the intestinal microbiota have been recently identified in obese mice, suggesting an involvement of gut microbes in obesity. In humans, obese subjects are supposed to have a more efficient flora in energy extraction from food, due to the detection of quantitative differences in the major bacterial groups in obese subjects compared to lean ones. Despite these observations, the homologies in gut microbiota between obese adults and their lean relatives have never been investigated in details. Few reports about the detection of common microbial profiles between members of the same family have been published in the past but only one recent scientific article, investigating the presence of a common core microbiota between obese and lean twins, correlates genetic background and gut microflora as significant variables in obesity. The hypothesis suggested herein is that the identification of a familial-specific core microbiota could be precious in order to identify key-bacterial groups to be used as biomarkers for the evaluation of predisposition to obesity. Copyright 2010 Elsevier Ltd. All rights reserved.

Mixed response in bacterial and biochemical variables to simulated sand mining in placer-rich beach sediments, Ratnagiri, West coast of India.

PubMed

Fernandes, Christabelle E G; Das, Anindita; Nath, B N; Faria, Daphne G; Loka Bharathi, P A

2012-05-01

We investigated the influence on bacterial community and biochemical variables through mechanical disturbance of sediment-akin to small-scale mining in Kalbadevi beach, Ratnagiri, a placer-rich beach ecosystem which is a potential mining site. Changes were investigated by comparing three periods, namely phase I before disturbance, phase II just after disturbance, and phase III 24 h after disturbance as the bacterial generation time is ≤7 h. Cores from dune, berm, high-, mid-, and low-tide were examined for changes in distribution of total bacterial abundance, total direct viability (counts under aerobic and anaerobic conditions), culturability and biochemical parameters up to 40 cm depth. Results showed that bacterial abundance decreased by an order from 10(6) cells g(-1) sediment, while, viability reduced marginally. Culturability on different-strength nutrient broth increased by 155% during phase II. Changes in sedimentary proteins, carbohydrates, and lipids were marked at berm and dune and masked at other levels by tidal influence. Sedimentary ATP reduced drastically. During phase III, Pearson's correlation between these variables evolved from non-significant to significant level. Thus, simulated disturbance had a mixed effect on bacterial and biochemical variables of the sediments. It had a negative impact on bacterial abundance, viability and ATP but positive impact on culturability. Viability, culturability, and ATP could act as important indicators reflecting the disturbance in the system at short time intervals. Culturability, which improved by an order, could perhaps be a fraction that contributes to restoration of the system at bacterial level. This baseline information about the potential mining site could help in developing rational approach towards sustainable harnessing of resources with minimum damage to the ecosystem.

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

PubMed

Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

2015-11-25

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile

PubMed Central

Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

2015-01-01

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800–2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400–1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today. PMID:26601753

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing.

PubMed

Ismail, Anisa S; Valastyan, Julie S; Bassler, Bonnie L

2016-04-13

Host-microbial symbioses are vital to health; nonetheless, little is known about the role crosskingdom signaling plays in these relationships. In a process called quorum sensing, bacteria communicate with one another using extracellular signal molecules called autoinducers. One autoinducer, AI-2, is proposed to promote interspecies bacterial communication, including in the mammalian gut. We show that mammalian epithelia produce an AI-2 mimic activity in response to bacteria or tight-junction disruption. This AI-2 mimic is detected by the bacterial AI-2 receptor, LuxP/LsrB, and can activate quorum-sensing-controlled gene expression, including in the enteric pathogen Salmonella typhimurium. AI-2 mimic activity is induced when epithelia are directly or indirectly exposed to bacteria, suggesting that a secreted bacterial component(s) stimulates its production. Mutagenesis revealed genes required for bacteria to both detect and stimulate production of the AI-2 mimic. These findings uncover a potential role for the mammalian AI-2 mimic in fostering crosskingdom signaling and host-bacterial symbioses. Copyright © 2016 Elsevier Inc. All rights reserved.

Pyrosequencing analysis of bacterial diversity in dental unit waterlines.

PubMed

Costa, Damien; Mercier, Anne; Gravouil, Kevin; Lesobre, Jérôme; Delafont, Vincent; Bousseau, Anne; Verdon, Julien; Imbert, Christine

2015-09-15

Some infections cases due to exposure to output water from dental unit waterlines (DUWL) have been reported in the literature. However, this type of healthcare-associated risk has remained unclear and up until now the overall bacterial composition of DUWL has been poorly documented. In this study, 454 high-throughput pyrosequencing was used to investigate the bacterial community in seven dental offices (N = 7) and to identify potential bacterial pathogenic sequences. Dental unit waters (DUW) were collected from the tap water supplying units (Incoming Water; IW) to the output exposure point of the turbine handpiece (Output water; OW) following a stagnation period (OWS), and immediately after the last patient of the sampling day (OWA). A high bacterial diversity was revealed in DUW with 394 operational taxonomic units detected at the genus level. In addition to the inter-unit variability observed, results showed increased total bacterial cell concentration and shifts in bacterial community composition and abundance at the genus level, mainly within the Gamma- and Alpha-Proteobacteria class, as water circulated in the dental unit (DU). Results showed that 96.7%, 96.8% and 97.4% of the total sequences from IW, OWS and OWA respectively were common to the 3 defined water groups, thereby highlighting a common core microbiome. Results also suggested that stagnation and DU maintenance practices were critical to composition of the bacterial community. The presence of potentially pathogenic genera was detected, including Pseudomonas and Legionella spp. Emerging and opportunistic pathogenic genera such as Mycobacterium, Propionibacterium and Stenotrophomonas were likewise recovered in DUW. For the first time, an exhaustive evaluation of the bacterial communities present in DUW was performed taking into account the circulation of water within the DU. This study highlights an ignored diversity of the DUWL bacterial community. Our findings also contribute to a better appreciation of the potential infectious risk associated with dental care and suggest the importance of better managing microbial quality in DUW. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optical fiber sensor having an active core

NASA Technical Reports Server (NTRS)

Egalon, Claudio Oliveira (Inventor); Rogowski, Robert S. (Inventor)

1993-01-01

An optical fiber is provided. The fiber is comprised of an active fiber core which produces waves of light upon excitation. A factor ka is identified and increased until a desired improvement in power efficiency is obtained. The variable a is the radius of the active fiber core and k is defined as 2 pi/lambda wherein lambda is the wavelength of the light produced by the active fiber core. In one embodiment, the factor ka is increased until the power efficiency stabilizes. In addition to a bare fiber core embodiment, a two-stage fluorescent fiber is provided wherein an active cladding surrounds a portion of the active fiber core having an improved ka factor. The power efficiency of the embodiment is further improved by increasing a difference between the respective indices of refraction of the active cladding and the active fiber core.

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

PubMed Central

Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

2012-01-01

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009–2010 crop cycle. Total bacterial populations averaged between 105 and 106 per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial ‘core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment. PMID:22534606

Hepatitis C virus core protein potentiates proangiogenic activity of hepatocellular carcinoma cells.

PubMed

Shao, Yu-Yun; Hsieh, Min-Shu; Wang, Han-Yu; Li, Yong-Shi; Lin, Hang; Hsu, Hung-Wei; Huang, Chung-Yi; Hsu, Chih-Hung; Cheng, Ann-Lii

2017-10-17

Increased angiogenic activity has been demonstrated in hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC), but the mechanism was unclear. To study the role of HCV core protein, we used tube formation and Matrigel plug assays to assess the proangiogenic activity of an HCC cell line, HuH7, and 2 of its stable clones-HuH7-core-high and HuH7-core-low, with high and low HCV core protein expression, respectively. In both assays, HuH7-core-high and HuH7-core-low cells dose-dependently induced stronger angiogenesis than control cells. HuH7 cells with HCV core protein expression showed increased mRNA and protein expression of vascular endothelial growth factor (VEGF). VEGF inhibition by bevacizumab reduced the proangiogenic activity of HuH7-core-high cells. The promotor region of VEGF contains the binding site of activator protein-1 (AP-1). Compared with controls, HuH7-core-high cells had an increased AP-1 activity and nuclear localization of phospho-c-jun. AP-1 inhibition using either RNA knockdown or AP-1 inhibitors reduced the VEGF mRNA expression and the proangiogenic activity of HuH7-core-high cells. Among 131 tissue samples from HCC patients, HCV-related HCC revealed stronger VEGF expression than did hepatitis B virus-related HCC. In conclusion, increased VEGF expression through AP-1 activation is a crucial mechanism underlying the proangiogenic activity of the HCV core protein in HCC cells.

Hepatitis C virus core protein potentiates proangiogenic activity of hepatocellular carcinoma cells

PubMed Central

Shao, Yu-Yun; Hsieh, Min-Shu; Wang, Han-Yu; Li, Yong-Shi; Lin, Hang; Hsu, Hung-Wei; Huang, Chung-Yi; Hsu, Chih-Hung; Cheng, Ann-Lii

2017-01-01

Increased angiogenic activity has been demonstrated in hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC), but the mechanism was unclear. To study the role of HCV core protein, we used tube formation and Matrigel plug assays to assess the proangiogenic activity of an HCC cell line, HuH7, and 2 of its stable clones—HuH7-core-high and HuH7-core-low, with high and low HCV core protein expression, respectively. In both assays, HuH7-core-high and HuH7-core-low cells dose-dependently induced stronger angiogenesis than control cells. HuH7 cells with HCV core protein expression showed increased mRNA and protein expression of vascular endothelial growth factor (VEGF). VEGF inhibition by bevacizumab reduced the proangiogenic activity of HuH7-core-high cells. The promotor region of VEGF contains the binding site of activator protein-1 (AP-1). Compared with controls, HuH7-core-high cells had an increased AP-1 activity and nuclear localization of phospho-c-jun. AP-1 inhibition using either RNA knockdown or AP-1 inhibitors reduced the VEGF mRNA expression and the proangiogenic activity of HuH7-core-high cells. Among 131 tissue samples from HCC patients, HCV-related HCC revealed stronger VEGF expression than did hepatitis B virus-related HCC. In conclusion, increased VEGF expression through AP-1 activation is a crucial mechanism underlying the proangiogenic activity of the HCV core protein in HCC cells. PMID:29156827

Anti-bacterial activity of intermittent preventive treatment of malaria in pregnancy: comparative in vitro study of sulphadoxine-pyrimethamine, mefloquine, and azithromycin

PubMed Central

2010-01-01

Background Intermittent preventive treatment of malaria with sulphadoxine-pyrimethamine (SP) is recommended for the prevention of malaria in pregnancy in sub-Saharan Africa. Increasing drug resistance necessitates the urgent evaluation of alternative drugs. Currently, the most promising candidates in clinical development are mefloquine and azithromycin. Besides the anti-malarial activity, SP is also a potent antibiotic and incurs significant anti-microbial activity when given as IPTp - though systematic clinical evaluation of this action is still lacking. Methods In this study, the intrinsic anti-bacterial activity of mefloquine and azithromycin was assessed in comparison to sulphadoxine-pyrimethamine against bacterial pathogens with clinical importance in pregnancy in a standard microdilution assay. Results SP was highly active against Staphylococcus aureus and Streptococcus pneumoniae. All tested Gram-positive bacteria, except Enterococcus faecalis, were sensitive to azithromycin. Additionally, azithromycin was active against Neisseria gonorrhoeae. Mefloquine showed good activity against pneumococci but lower in vitro action against all other tested pathogens. Conclusion These data indicate important differences in the spectrum of anti-bacterial activity for the evaluated anti-malarial drugs. Given the large scale use of IPTp in Africa, the need for prospective clinical trials evaluating the impact of antibiotic activity of anti-malarials on maternal and foetal health and on the risk of promoting specific drug resistance of bacterial pathogens is discussed. PMID:21029476

Impact of environmental factors on couplings between bacterial community composition and ectoenzymatic activities in a lacustrine ecosystem.

PubMed

Boucher, Delphine; Debroas, Didier

2009-10-01

This study examined the effects of temporal changes in bacterial community composition (BCC) and environmental factors on potential ectoenzymatic activities (alpha-glucosidase, beta-glucosidase, alkaline phosphatase and leucine aminopeptidase) in a lacustrine ecosystem (Sep reservoir, France). BCC was assessed by terminal restriction fragment length polymorphism. Physical parameters, and inorganic and organic nutrient concentrations (dissolved carbohydrates and proteins) were measured in lakes and tributaries. According to the multivariate statistics (redundancy analysis), physical and chemical factors explained the largest part of leucine aminopeptidase activity, whereas the temporal changes of other ectoenzymatic activities were partly dependent on the variations in the BCC. In particular, the occurrence of occasional bacterial populations seemed to explain a lot of the variation in rates and patterns of polymer hydrolysis. The relation observed in this study between the bacterial structure and activity is discussed within the framework of biodiversity-ecosystem functioning.

Non-homogeneous flow profiles in sheared bacterial suspensions

NASA Astrophysics Data System (ADS)

Samanta, Devranjan; Cheng, Xiang

Bacterial suspensions under shear exhibit interesting rheological behaviors including the remarkable ``superfluidic'' state with vanishing viscosity at low shear rates. Theoretical studies have shown that such ``superfluidic'' state is linked with non-homogeneous shear flows, which are induced by coupling between nematic order of active fluids and hydrodynamics of shear flows. However, although bulk rheology of bacterial suspensions has been experimentally studied, shear profiles within bacterial suspensions have not been explored so far. Here, we experimentally investigate the flow behaviors of E. coli suspensions under planar oscillatory shear. Using confocal microscopy and PIV, we measure velocity profiles across gap between two shear plates. We find that with increasing shear rates, high-concentration bacterial suspensions exhibit an array of non-homogeneous flow behaviors like yield-stress flows and shear banding. We show that these non-homogeneous flows are due to collective motion of bacterial suspensions. The phase diagram of sheared bacterial suspensions is systematically mapped as functions of shear rates an bacterial concentrations. Our experiments provide new insights into rheology of bacterial suspensions and shed light on shear induced dynamics of active fluids. Chemical Engineering and Material Science department.

In-situ carbon and nitrogen turnover dynamics and the role of soil functional biodiversity therein; a climate warming simulation study in Alpine ecosystems

NASA Astrophysics Data System (ADS)

Djukic, Ika

2010-05-01

Climate change affects a variety of soil properties and processes. Alpine soils take an extraordinary position in this context because of the vulnerability of mountain regions to climatic changes. We used altitudinal soil translocation to simulate the combined effects of changing climatic conditions and shifting vegetation zones in order to study short- to medium-term soil changes in the Austrian Limestone Alps. We translocated 160 soil cores from an alpine grassland site (1900 m asl) down to a sub-alpine spruce forest (1300 m asl) and a montane beech forest site (900m asl), including reference soil cores at each site to estimate artifacts arising from the method. 15N-labeled maize straw was added (1 kg/m2) to translocated and control soil cores and sampled over a period of 2 years for the analysis of δ13C and δ15N in the bulk soil and extracted phospholipid fatty acids (PLFAs). Additionally, 20 litter bags (at each of the three climatic zones) containing Fagus sylvatica or Pinus nigra litter were inserted into the soil, and decomposition was studied over a two-year period. The basic soil parameters (organic C, total N and pH) were unaffected by translocation within the observation time. Overall, decomposition of Pinus nigra litter was significantly slower compared to Fagus sylvatica, and the decomposition rate of both litter types was inversely related to elevation. The decomposition of the maize straw carbon was significantly faster in the translocated soil cores (sites at 900 and 1300 m asl) than at the original site (1900 m asl). The labelled nitrogen contents in the translocated soil cores showed just marginal differences to the soil cores at the original site. The maize straw application promptly increased the amount of bacterial and fungal PLFAs at all studied sites. Downslope translocated soil cores showed an increase in total microbial biomass and sum of bacteria. The fungal PLFA biomarker 18:2ω6,9 was slightly lower at the new (host) sites compared to the original site. The bacterial to fungal ratio of the translocated soil cores showed a rapid acclimatization to the new (host) soil conditions. Our study demonstrates that rising temperatures in Alpine ecosystems will accelerate decomposition of fresh C pools but also lead to rapid adaptation of the microbial community to the new conditions.

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels.

PubMed

Liu, Han; Guo, Xianwu; Gooneratne, Ravi; Lai, Ruifang; Zeng, Cong; Zhan, Fanbin; Wang, Weimin

2016-04-13

Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels

PubMed Central

Liu, Han; Guo, Xianwu; Gooneratne, Ravi; Lai, Ruifang; Zeng, Cong; Zhan, Fanbin; Wang, Weimin

2016-01-01

Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity. PMID:27072196

Gallic acid conjugated with gold nanoparticles: antibacterial activity and mechanism of action on foodborne pathogens.

PubMed

Rattanata, Narintorn; Klaynongsruang, Sompong; Leelayuwat, Chanvit; Limpaiboon, Temduang; Lulitanond, Aroonlug; Boonsiri, Patcharee; Chio-Srichan, Sirinart; Soontaranon, Siriwat; Rugmai, Supagorn; Daduang, Jureerut

2016-01-01

Foodborne pathogens, including Plesiomonas shigelloides and Shigella flexneri B, are the major cause of diarrheal endemics worldwide. Antibiotic drug resistance is increasing. Therefore, bioactive compounds with antibacterial activity, such as gallic acid (GA), are needed. Gold nanoparticles (AuNPs) are used as drug delivery agents. This study aimed to conjugate and characterize AuNP-GA and to evaluate the antibacterial activity. AuNP was conjugated with GA, and the core-shell structures were characterized by small-angle X-ray scattering and transmission electron microscopy. Antibacterial activity of AuNP-GA against P. shigelloides and S. flexneri B was evaluated by well diffusion method. AuNP-GA bactericidal mechanism was elucidated by Fourier transform infrared microspectroscopic analysis. The results of small-angle X-ray scattering showed that AuNP-GA conjugation was successful. Antibacterial activity of GA against both bacteria was improved by conjugation with AuNP because the minimum inhibitory concentration value of AuNP-GA was significantly decreased (P<0.0001) compared to that of GA. Fourier transform infrared analysis revealed that AuNP-GA resulted in alterations of lipids, proteins, and nucleic acids at the bacterial cell membrane. Our findings show that AuNP-GA has potential for further application in biomedical sciences.

The intrinsic resistome of bacterial pathogens

PubMed Central

Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B. Sanchez, Maria; Martinez, Jose L.

2013-01-01

Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice. PMID:23641241

The intrinsic resistome of bacterial pathogens.

PubMed

Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B Sanchez, Maria; Martinez, Jose L

2013-01-01

Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

[Core muscle chains activation during core exercises determined by EMG-a systematic review].

PubMed

Rogan, Slavko; Riesen, Jan; Taeymans, Jan

2014-10-15

Good core muscles strength is essential for daily life and sports activities. However, the mechanism how core muscles may be effectively triggered by exercises is not yet precisely described in the literature. The aim of this systematic review was to evaluate the rate of activation as measured by electromyography of the ventral, lateral and dorsal core muscle chains during core (trunk) muscle exercises. A total of 16 studies were included. Exercises with a vertical starting position, such as the deadlift or squat activated significantly more core muscles than exercises in the horizontal initial position.

Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope

PubMed Central

2011-01-01

Background A decline in the discovery of new antibacterial drugs, coupled with a persistent rise in the occurrence of drug-resistant bacteria, has highlighted antibiotics as a diminishing resource. The future development of new drugs with novel antibacterial activities requires a detailed understanding of adaptive responses to existing compounds. This study uses Streptomyces coelicolor A3(2) as a model system to determine the genome-wide transcriptional response following exposure to three antibiotics (vancomycin, moenomycin A and bacitracin) that target distinct stages of cell wall biosynthesis. Results A generalised response to all three antibiotics was identified which involves activation of transcription of the cell envelope stress sigma factor σE, together with elements of the stringent response, and of the heat, osmotic and oxidative stress regulons. Attenuation of this system by deletion of genes encoding the osmotic stress sigma factor σB or the ppGpp synthetase RelA reduced resistance to both vancomycin and bacitracin. Many antibiotic-specific transcriptional changes were identified, representing cellular processes potentially important for tolerance to each antibiotic. Sensitivity studies using mutants constructed on the basis of the transcriptome profiling confirmed a role for several such genes in antibiotic resistance, validating the usefulness of the approach. Conclusions Antibiotic inhibition of bacterial cell wall biosynthesis induces both common and compound-specific transcriptional responses. Both can be exploited to increase antibiotic susceptibility. Regulatory networks known to govern responses to environmental and nutritional stresses are also at the core of the common antibiotic response, and likely help cells survive until any specific resistance mechanisms are fully functional. PMID:21569315

Biophysical characterization of the Lactobacillus delbrueckii subsp. bulgaricus membrane during cold and osmotic stress and its relevance for cryopreservation.

PubMed

Meneghel, Julie; Passot, Stéphanie; Dupont, Sébastien; Fonseca, Fernanda

2017-02-01

Freezing lactic acid bacteria often leads to cell death and loss of technological properties. Our objective was to provide an in-depth characterization of the biophysical properties of the Lactobacillus delbrueckii subsp. bulgaricus membrane in relation to its freeze resistance. Freezing was represented as a combination of cold and osmotic stress. This work investigated the relative incidence of increasing sucrose concentrations coupled or not with subzero temperatures without ice nucleation on the biological and biophysical responses of two strains with different membrane fatty acid compositions and freeze resistances. Following exposure of bacterial cells to the highest sucrose concentration, the sensitive strain exhibited a survival rate of less than 10 % and 5 h of acidifying activity loss. Similar biological activity losses were observed upon freeze-thawing and after osmotic treatment for each strain thus highlighting osmotic stress as the main source of cryoinjury. The direct measurement of membrane fluidity by fluorescence anisotropy was linked to membrane lipid organization characterized by FTIR spectroscopy. Both approaches made it possible to investigate the specific contributions of the membrane core and the bilayer external surface to cell degradation caused by cold and osmotic stress. Cold-induced membrane rigidification had no significant implication on bacterial freeze-thaw resistance. Interactions between extracellular sucrose and membrane phospholipid headgroups under osmotic stress were also observed. Such interactions were more evident in the sensitive strain and when increasing sucrose concentration, thus suggesting membrane permeabilization. The relevance of biophysical properties for elucidating mechanisms of cryoinjury and cryoprotection is discussed.

Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades.

PubMed

Chauhan, Ashvini; Pathak, Ashish; Ogram, Andrew

2012-10-01

Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.

Lab-on-fiber optofluidic platform for in-situ study of therapeutic peptides and bacterial response (Rising Researcher Presentation) (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tian, Fei; Yang, Fan; Liang, Junfeng

2017-05-01

Hospital acquired infections in indwelling device have become a life-threatening issue accompanied by the wide use of medical devices and implants. The infection process typically involves the attachment, growth and eventual assemblage of microbial cells into biofilms, with the latter exhibiting extremely higher antibiotic tolerance than planktonic bacteria. Surface constructed antimicrobial coatings offer a viable solution for bacteria responsive antibiotic strategy in medical devices such as catheter and stents. Therapeutic peptide has pioneered the field for their attractive pharmacological profile with broad antibacterial spectrum, great efficacy and long life-span. It has been a common practice to separately assess bacteria responses through commercially available activity assay kits after their exposure to antibiotic coatings, limiting the assessment of their activity in vitro with a discontinuous fashion. We developed and demonstrated an innovative all-optical lab-on-fiber optofluidic platform (LOFOP) to fill in this technical gap by allowing in situ measurement of the bacteria attachment in a continuous manner. This LOFOP allows for evaluation of drug release and resultant bacterial response by integrating glass capillary with lytic peptide-containing LbL-coated long period graing (LPG) as its core. S. aureus suspension is introduced through the assembled optofluidic platform with the capillary and the peptide-coated LPG. The efficacy of the peptide-containing coating is evaluated in situ by monitoring the attachment of bacteria and the ensuing development of biofilms using the LPG. LPG without antimicrobial coatings will be explored and compared as control.

A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

DOE PAGES

Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.; ...

2014-10-23

Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found inmore » seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.« less

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

PubMed Central

Kerfeld, Cheryl A.

2014-01-01

Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications. PMID:25340524

454-Pyrosequencing survey of microbiota in adult Spotted Wing Drosophila (SWD) corroborates a core microbiome and additional symbiotic and entomopathogenic bacterial associates

USDA-ARS?s Scientific Manuscript database

Complete surveys of insect endosymbionts including species of economic importance have until recently been hampered by a lack of high-throughput genetic assays. We used 454-pyrosequencing of the 16S rRNA gene amplicon of adult spotted wing Drosophila (SWD) Drosophila suzukii (Matsumura) from souther...

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand.

PubMed

Secker, Nick H; Chua, Jocelyn P S; Laurie, Rebecca E; McNoe, Les; Guy, Paul L; Orlovich, David A; Summerfield, Tina C

2016-10-01

New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non-heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%-42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface. © 2016 Phycological Society of America.

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh.

PubMed

Larsen, Andrea M; Bullard, Stephen A; Womble, Matthew; Arias, Covadonga R

2015-08-01

Mucus of fish skin harbors complex bacterial communities that likely contribute to fish homeostasis. When the equilibrium between the host and its external bacterial symbionts is disrupted, bacterial diversity decreases while opportunistic pathogen prevalence increases, making the onset of pathogenic bacterial infection more likely. Because of that relationship, documenting temporal and spatial microbial community changes may be predictive of fish health status. The 2010 Deepwater Horizon oil spill was a potential stressor to the Gulf of Mexico's coastal ecosystem. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze the bacterial communities (microbiome) associated with the skin and mucus of Gulf killifish (Fundulus grandis) that were collected from oiled and non-oiled salt marsh sites in Barataria Bay, LA. Water samples and fin clips were collected to examine microbiome structure. The microbiome of Gulf killifish was significantly different from that of the surrounding water, mainly attributable to shifts in abundances of Cyanobacteria and Proteobacteria. The Gulf killifish's microbiome was dominated by Gammaproteobacteria, specifically members of Pseudomonas. No significant difference was found between microbiomes of fish collected from oiled and non-oiled sites suggesting little impact of oil contamination on fish bacterial assemblages. Conversely, seasonality significantly influenced microbiome structure. Overall, the high similarity observed between the microbiomes of individual fish observed during this study posits that skin and mucus of Gulf killifish have a resilient core microbiome.

Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria

PubMed Central

Forster, Scott; Snape, Jason R.; Lappin-Scott, Hilary M.; Porter, Jonathan

2002-01-01

Wastewater treatment is one of the most important commercial biotechnological processes, and yet the component bacterial populations and their associated metabolic activities are poorly understood. The novel fluorescent dye hexidium iodide allows assessment of Gram status by differential absorption through bacterial cell walls. Differentiation between gram-positive and gram-negative wastewater bacteria was achieved after flow cytometric analysis. This study shows that the relative proportions of gram-positive and gram-negative bacterial cells identified by traditional microscopy and hexidium iodide staining were not significantly different. Dual staining of cells for Gram status and activity proved effective in analyzing mixtures of cultured bacteria and wastewater populations. Levels of highly active organisms at two wastewater treatment plants, both gram positive and gram negative, ranged from 1.5% in activated sludge flocs to 16% in the activated sludge fluid. Gram-positive organisms comprised <5% of the total bacterial numbers but accounted for 19 and 55% of the highly active organisms within flocs at the two plants. Assessment of Gram status and activity within activated sludge samples over a 4-day period showed significant differences over time. This method provides a rapid, quantitative measure of Gram status linked with in situ activity within wastewater systems. PMID:12324319

Simultaneous fluorescent gram staining and activity assessment of activated sludge bacteria.

PubMed

Forster, Scott; Snape, Jason R; Lappin-Scott, Hilary M; Porter, Jonathan

2002-10-01

Wastewater treatment is one of the most important commercial biotechnological processes, and yet the component bacterial populations and their associated metabolic activities are poorly understood. The novel fluorescent dye hexidium iodide allows assessment of Gram status by differential absorption through bacterial cell walls. Differentiation between gram-positive and gram-negative wastewater bacteria was achieved after flow cytometric analysis. This study shows that the relative proportions of gram-positive and gram-negative bacterial cells identified by traditional microscopy and hexidium iodide staining were not significantly different. Dual staining of cells for Gram status and activity proved effective in analyzing mixtures of cultured bacteria and wastewater populations. Levels of highly active organisms at two wastewater treatment plants, both gram positive and gram negative, ranged from 1.5% in activated sludge flocs to 16% in the activated sludge fluid. Gram-positive organisms comprised <5% of the total bacterial numbers but accounted for 19 and 55% of the highly active organisms within flocs at the two plants. Assessment of Gram status and activity within activated sludge samples over a 4-day period showed significant differences over time. This method provides a rapid, quantitative measure of Gram status linked with in situ activity within wastewater systems.

Effect of exposure to diesel exhaust particles on the susceptibility of the lung to infection.

PubMed

Castranova, V; Ma, J Y; Yang, H M; Antonini, J M; Butterworth, L; Barger, M W; Roberts, J; Ma, J K

2001-08-01

There are at least three mechanisms by which alveolar macrophages play a critical role in protecting the lung from bacterial or viral infections: production of inflammatory cytokines that recruit and activate lung phagocytes, production of antimicrobial reactive oxidant species, and production of interferon (an antiviral agent). In this article we summarize data concerning the effect of exposure to diesel exhaust particles on these alveolar macrophage functions and the role of adsorbed organic chemicals compared to the carbonaceous core in the toxicity of diesel particles. In vitro exposure of rat alveolar macrophages to diesel exhaust particles decreased the ability of lipopolysaccharide (LPS), a bacterial product] to stimulate the production of inflammatory cytokines interleukin-1 (IL-1) and tumor necrosis factor-alpha (TNF-alpha). Methanol extract exhibited this potential but methanol-washed diesel particles did not. Exposure of rats to diesel exhaust particles by intratracheal instillation also decreased LPS-induced TNF-alpha and IL-1 production from alveolar macrophages. In contrast, carbon black did not exhibit this inhibitory effect. Exposure of rats to diesel exhaust particles by inhalation decreased the ability of alveolar macrophages to produce antimicrobial reactive oxidant species in response to zymosan (a fungal component). In contrast, exposure to coal dust increased zymosan-stimulated oxidant production. In vivo exposure to diesel exhaust particles but not to carbon black decreased the ability of the lungs to clear bacteria. Inhalation exposure of mice to diesel exhaust particles but not to coal dust depressed the ability of the lung to produce the antiviral agent interferon and increased viral multiplication in the lung. These results support the hypothesis that exposure to diesel exhaust particles increases the susceptibility of the lung to infection by depressing the antimicrobial potential of alveolar macrophages. This inhibitory effect appears to be due to adsorbed organic chemicals rather than the carbonaceous core of the diesel particles.

Effect of exposure to diesel exhaust particles on the susceptibility of the lung to infection.

PubMed Central

Castranova, V; Ma, J Y; Yang, H M; Antonini, J M; Butterworth, L; Barger, M W; Roberts, J; Ma, J K

2001-01-01

There are at least three mechanisms by which alveolar macrophages play a critical role in protecting the lung from bacterial or viral infections: production of inflammatory cytokines that recruit and activate lung phagocytes, production of antimicrobial reactive oxidant species, and production of interferon (an antiviral agent). In this article we summarize data concerning the effect of exposure to diesel exhaust particles on these alveolar macrophage functions and the role of adsorbed organic chemicals compared to the carbonaceous core in the toxicity of diesel particles. In vitro exposure of rat alveolar macrophages to diesel exhaust particles decreased the ability of lipopolysaccharide (LPS), a bacterial product] to stimulate the production of inflammatory cytokines interleukin-1 (IL-1) and tumor necrosis factor-alpha (TNF-alpha). Methanol extract exhibited this potential but methanol-washed diesel particles did not. Exposure of rats to diesel exhaust particles by intratracheal instillation also decreased LPS-induced TNF-alpha and IL-1 production from alveolar macrophages. In contrast, carbon black did not exhibit this inhibitory effect. Exposure of rats to diesel exhaust particles by inhalation decreased the ability of alveolar macrophages to produce antimicrobial reactive oxidant species in response to zymosan (a fungal component). In contrast, exposure to coal dust increased zymosan-stimulated oxidant production. In vivo exposure to diesel exhaust particles but not to carbon black decreased the ability of the lungs to clear bacteria. Inhalation exposure of mice to diesel exhaust particles but not to coal dust depressed the ability of the lung to produce the antiviral agent interferon and increased viral multiplication in the lung. These results support the hypothesis that exposure to diesel exhaust particles increases the susceptibility of the lung to infection by depressing the antimicrobial potential of alveolar macrophages. This inhibitory effect appears to be due to adsorbed organic chemicals rather than the carbonaceous core of the diesel particles. PMID:11544172

Environment shapes the fecal microbiome of invasive carp species.

PubMed

Eichmiller, Jessica J; Hamilton, Matthew J; Staley, Christopher; Sadowsky, Michael J; Sorensen, Peter W

2016-08-12

Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.

Block Copolymer Nanoparticles Remove Biofilms of Drug-Resistant Gram-Positive Bacteria by Nanoscale Bacterial Debridement.

PubMed

Li, Jianghua; Zhang, Kaixi; Ruan, Lin; Chin, Seow Fong; Wickramasinghe, Nirmani; Liu, Hanbin; Ravikumar, Vikashini; Ren, Jinghua; Duan, Hongwei; Yang, Liang; Chan-Park, Mary B

2018-06-26

Biofilms and the rapid evolution of multidrug resistance complicate the treatment of bacterial infections. Antibiofilm agents such as metallic-inorganic nanoparticles or peptides act by exerting antibacterial effects and, hence, do not combat biofilms of antibiotics-resistant strains. In this Letter, we show that the block copolymer DA95B5, dextran- block-poly((3-acrylamidopropyl) trimethylammonium chloride (AMPTMA)- co-butyl methacrylate (BMA)), effectively removes preformed biofilms of various clinically relevant multidrug-resistant Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE V583), and Enteroccocus faecalis (OG1RF). DA95B5 self-assembles into core-shell nanoparticles with a nonfouling dextran shell and a cationic core. These nanoparticles diffuse into biofilms and attach to bacteria but do not kill them; instead, they promote the gradual dispersal of biofilm bacteria, probably because the solubility of the bacteria-nanoparticle complex is enhanced by the nanoparticle dextran shell. DA95B5, when applied as a solution to a hydrogel pad dressing, shows excellent in vivo MRSA biofilm removal efficacy of 3.6 log reduction in a murine excisional wound model, which is significantly superior to that for vancomycin. Furthermore, DA95B5 has very low in vitro hemolysis and negligible in vivo acute toxicity. This new strategy for biofilm removal (nanoscale bacterial debridement) is orthogonal to conventional rapidly developing resistance traits in bacteria so that it is as effective toward resistant strains as it is toward sensitive strains and may have widespread applications.

Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

PubMed Central

Headd, Brendan; Engel, Annette S.

2014-01-01

Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria), up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria) occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria), but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria) occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or climate change. PMID:25250021

Metabarcoding of the kombucha microbial community grown in different microenvironments.

PubMed

Reva, Oleg N; Zaets, Iryna E; Ovcharenko, Leonid P; Kukharenko, Olga E; Shpylova, Switlana P; Podolich, Olga V; de Vera, Jean-Pierre; Kozyrovska, Natalia O

2015-12-01

Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member-lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding.

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands.

PubMed

Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban

2009-07-01

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

JAK kinases are required for the bacterial RNA and poly I:C induced tyrosine phosphorylation of PKR

PubMed Central

Bleiblo, Farag; Michael, Paul; Brabant, Danielle; Ramana, Chilakamarti V; Tai, TC; Saleh, Mazen; Parrillo, Joseph E; Kumar, Anand; Kumar, Aseem

2013-01-01

Discriminating the molecular patterns associated with RNA is central to innate immunity. The protein kinase PKR is a cytosolic sensor involved in the recognition of viral dsRNA and triggering interferon-induced signaling. Here, we identified bacterial RNA as a novel distinct pattern recognized by PKR. We show that the tyrosine phosphorylation of PKR induced by either bacterial RNA or poly I:C is impaired in mutant cells lacking TYK2, JAK1, or JAK2 kinases. PKR was found to be a direct substrate for the activated JAKs. Our results indicated that the double-stranded structures of bacterial RNA are required to fully activate PKR. These results suggest that bacterial RNA signaling is analogous in some respects to that of viral RNA and interferons and may have implications in bacterial immunity. PMID:23236554

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

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

Uehling, J.; Gryganskyi, A.; Hameed, K.

Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. Furthermore, we sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primarymore » metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/ absence of M. cysteinexigens. In independent comparative phylogenomic analyses of fungal and bacterial genomes we find that they are consistent with an ancient origin for M. elongata M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.« less

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

PubMed

Yasir, Muhammad; Azhar, Esam I; Khan, Imran; Bibi, Fehmida; Baabdullah, Rnda; Al-Zahrani, Ibrahim A; Al-Ghamdi, Ahmed K

2015-03-14

Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands. In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples. Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

DOE PAGES

Uehling, J.; Gryganskyi, A.; Hameed, K.; ...

2017-01-11

Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. Furthermore, we sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primarymore » metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/ absence of M. cysteinexigens. In independent comparative phylogenomic analyses of fungal and bacterial genomes we find that they are consistent with an ancient origin for M. elongata M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.« less

Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea.

PubMed

De Tender, Caroline; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Vangeyte, Jürgen; Cattrijsse, André; Dawyndt, Peter; Ruttink, Tom

2017-07-05

Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.

Sediment amino acids as indicators of anthropogenic activities and potential environmental risk in Erhai Lake, Southwest China.

PubMed

Ni, Zhaokui; Wang, Shengrui; Zhang, Mianmian

2016-05-01

Total hydrolysable amino acids (THAAs) constitute the most important fraction of labile nitrogen. Anthropogenic activities directly influence various biogeochemical cycles and then accelerate lake ecosystem deterioration. This is the first study that has established the relationship between sediment THAAs and anthropogenic activities using dated sediment cores, and evaluated the possibility of THAAs release at the sediment interface based on changes in environmental conditions in Erhai Lake. The results showed that historical distribution and fractions of THAAs could be divided into three stages: a stable period before the 1970s, a clear increasing period from the 1970s to 1990s, and a gradually steady period that started after the 1990s. The chemical fraction, aromatic and sulfur amino acids (AAs) accounted for only ≤3% of THAAs. Basic AAs accounted for 5-17% of THAAs, and remained at a relatively stable level. However, acidic and neutral AAs, which accounted for 19-44% and 35-69% of THAAs, respectively, were the predominant factors causing THAAs to increase due to rapid agricultural intensification and intensification of contemporary sedimentation of phytoplankton or macrophytes since the 1970s. These trends were closely related to both anthropogenic activities and natural processes, which implied that sediment THAAs could act as an effective indicator that reflects anthropogenic activities and aquatic environmental characteristics. The current contributions of sediment THAAs on TN and TOC were <5% and 1.5%, respectively. However, the dramatic increase in THAAs in the sediment cores indicated that there was a huge potential source of labile nitrogen for the overlying water under certain environmental conditions. Correlation analysis suggested that the release of THAAs was negatively correlated with pH, whereas positively correlated with bacterial number and degree of OM mineralization, which particularly depend on the stability of HFOM. Therefore, the risk of sediment THAAs release might increase when the sediment environment continuously changes. Copyright © 2016 Elsevier B.V. All rights reserved.

In vivo characteristics of targeted drug-carrying filamentous bacteriophage nanomedicines

PubMed Central

2011-01-01

Background Targeted drug-carrying phage nanomedicines are a new class of nanomedicines that combines biological and chemical components into a modular nanometric drug delivery system. The core of the system is a filamentous phage particle that is produced in the bacterial host Escherichia coli. Target specificity is provided by a targeting moiety, usually an antibody that is displayed on the tip of the phage particle. A large drug payload is chemically conjugated to the protein coat of the phage via a chemically or genetically engineered linker that provides for controlled release of the drug after the particle homed to the target cell. Recently we have shown that targeted drug-carrying phage nanomedicines can be used to eradicate pathogenic bacteria and cultured tumor cells with great potentiation over the activity of the free untargeted drug. We have also shown that poorly water soluble drugs can be efficiently conjugated to the phage coat by applying hydrophilic aminoglycosides as branched solubility-enhancing linkers. Results With an intention to move to animal experimentation of efficacy, we tested anti-bacterial drug-carrying phage nanomedicines for toxicity and immunogenicity and blood pharmacokinetics upon injection into mice. Here we show that anti-bacterial drug-carrying phage nanomedicines that carry the antibiotic chloramphenicol conjugated via an aminoglycoside linker are non-toxic to mice and are greatly reduced in immunogenicity in comparison to native phage particles or particles to which the drug is conjugated directly and are cleared from the blood more slowly in comparison to native phage particles. Conclusion Our results suggest that aminoglycosides may serve as branched solubility enhancing linkers for drug conjugation that also provide for a better safety profile of the targeted nanomedicine. PMID:22185583

Gel phase in hydrated calcium dipicolinate

NASA Astrophysics Data System (ADS)

Rajak, Pankaj; Mishra, Ankit; Sheng, Chunyang; Tiwari, Subodh; Krishnamoorthy, Aravind; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2017-11-01

The mineralization of dipicolinic acid (DPA) molecules in bacterial spore cores with Ca2+ ions to form Ca-DPA is critical to the wet-heat resistance of spores. This resistance to "wet-heat" also depends on the physical properties of water and DPA in the hydrated Ca-DPA-rich protoplasm. Using reactive molecular dynamics simulations, we have determined the phase diagram of hydrated Ca-DPA as a function of temperature and water concentration, which shows the existence of a gel phase along with distinct solid-gel and gel-liquid phase transitions. Simulations reveal monotonically decreasing solid-gel-liquid transition temperatures with increasing hydration, which explains the experimental trend of wet-heat resistance of bacterial spores. Our observation of different phases of water also reconciles previous conflicting experimental findings on the state of water in bacterial spores. Further comparison with an unmineralized hydrated DPA system allows us to quantify the importance of Ca mineralization in decreasing diffusivity and increasing the heat resistance of the spore.

Study of the rhizobacterium Azospirillum brasilense Sp245 using Mössbauer spectroscopy with a high velocity resolution: Implication for the analysis of ferritin-like iron cores

NASA Astrophysics Data System (ADS)

Alenkina, I. V.; Oshtrakh, M. I.; Tugarova, A. V.; Biró, B.; Semionkin, V. A.; Kamnev, A. A.

2014-09-01

The results of a comparative study of two samples of the rhizobacterium Azospirillum brasilense (strain Sp245) prepared in different conditions and of human liver ferritin using Mössbauer spectroscopy with a high velocity resolution demonstrated the presence of ferritin-like iron (i.e. iron similar to that found in ferritin-like proteins) in the bacterium. Mössbauer spectra of these samples were fitted in two ways: as a rough approximation using a one quadrupole doublet fit (the homogeneous iron core model) and using a superposition of quadrupole doublets (the heterogeneous iron core model). Both results demonstrated differences in the Mössbauer parameters for mammalian ferritin and for bacterial ferritin-like iron. Moreover, some differences in the Mössbauer parameters were observed between the two samples of A. brasilense Sp245 related to the differences in their preparation conditions.

Cloning and functional characterization of a p-coumaroyl quinate/shikimate 3'-hydroxylase from potato (Solanum tuberosum).

PubMed

Knollenberg, Benjamin J; Liu, Jingjing; Yu, Shu; Lin, Hong; Tian, Li

2018-02-05

Chlorogenic acid (CGA) plays an important role in protecting plants against pathogens and promoting human health. Although CGA accumulates to high levels in potato tubers, the key enzyme p-coumaroyl quinate/shikimate 3'-hydroxylase (C3'H) for CGA biosynthesis has not been isolated and functionally characterized in potato. In this work, we cloned StC3'H from potato and showed that it catalyzed the formation of caffeoylshikimate and CGA (caffeoylquinate) from p-coumaroyl shikimate and p-coumaroyl quinate, respectively, but was inactive towards p-coumaric acid in in vitro enzyme assays. When the expression of StC3'H proteins was blocked through antisense (AS) inhibition under the control of a tuber-specific patatin promoter, moderate changes in tuber yield as well as phenolic metabolites in the core tuber tissue were observed for several AS lines. On the other hand, the AS and control potato lines exhibited similar responses to a bacterial pathogen Pectobacterium carotovorum. These results suggest that StC3'H is implicated in phenolic metabolism in potato. They also suggest that CGA accumulation in the core tissue of potato tubers is an intricately controlled process and that additional C3'H activity may also be involved in CGA biosynthesis in potato. Copyright © 2018 Elsevier Inc. All rights reserved.

Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout.

PubMed

Yang, Tingting; Speare, Kelly; McKay, Luke; MacGregor, Barbara J; Joye, Samantha B; Teske, Andreas

2016-01-01

A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer of 2011 did not show a consistent bacterial community signature, suggesting that the bacterial community was no longer shaped by the DWH fallout of oil-derived marine snow, but instead by location-specific and seasonal factors.

Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout

PubMed Central

Yang, Tingting; Speare, Kelly; McKay, Luke; MacGregor, Barbara J.; Joye, Samantha B.; Teske, Andreas

2016-01-01

A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer of 2011 did not show a consistent bacterial community signature, suggesting that the bacterial community was no longer shaped by the DWH fallout of oil-derived marine snow, but instead by location-specific and seasonal factors. PMID:27679609

Larval settlement and metamorphosis of the mussel Mytilus coruscus in response to monospecific bacterial biofilms.

PubMed

Yang, Jin-Long; Shen, Pei-Jing; Liang, Xiao; Li, Yi-Feng; Bao, Wei-Yang; Li, Jia-Le

2013-01-01

The effects of bacterial biofilms (BFs) on larval settlement and metamorphosis of the mussel, Mytilus coruscus, were investigated in the laboratory. Of nine different isolates, Shewanella sp.1 BF induced the highest percentage of larval settlement and metamorphosis, whereas seven other isolates had a moderate inducing activity and one isolate, Pseudoalteromonas sp. 4, had a no inducing activity. The inducing activity of individual bacterial isolates was not correlated either with their phylogenetic relationship or with the surfaces from which they were isolated. Among the eight bacterial species that demonstrated inducing activity, bacterial density was significantly correlated with the inducing activity for each strain, with the exception of Vibrio sp. 1. The Shewanella sp. 1 BF cue that was responsible for inducing larval settlement and metamorphosis was further investigated. Treatment of the BFs with formalin, antibiotics, ultraviolet irradiation, heat, and ethanol resulted in a significant decrease in their inducing activities and cell survival. BF-conditioned water (CW) did not induce larval metamorphosis, but it triggered larval settlement behavior. A synergistic effect of CW with formalin-fixed Shewanella sp. 1 BF significantly promoted larval metamorphosis. Thus, a cocktail of chemical cues derived from bacteria may be necessary to stimulate larval settlement and metamorphosis in this species.

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

DOE PAGES

Manthei, Kelly A.; Hill, Morgan C.; Burke, Jordan E.; ...

2015-03-23

RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. In this paper, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ~90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATPmore » hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. Finally, this bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.« less

Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism.

PubMed

Daidone, Isabella; Magliano, Alessandro; Di Nola, Alfredo; Mignogna, Giuseppina; Clarkson, Matilda Manuela; Lizzi, Anna Rita; Oratore, Arduino; Mazza, Fernando

2011-04-01

Lactoferricins are potent antimicrobial peptides released by pepsin cleavage of Lactoferrins. Bovine Lactoferricin (LfcinB) has higher activity than the intact bovine Lactoferrin, and is the most active among the other Lactoferricins of human, murine and caprine origin. In the intact protein the fragment corresponding to LfcinB is in an helical conformation, while in water LfcinB adopts an amphipathic β-hairpin structure. However, whether any of these structural motifs is the antibacterial active conformation, i.e., the one interacting with bacterial membrane components, remains to be seen. Here we present Circular Dichroism (CD) spectra and Molecular Dynamics (MD) simulations indicating that in membrane-mimicking solvents the LfcinB adopts an amphipathic β-hairpin structure similar to that observed in water, but differing in the dynamic behavior of the side-chains of the two tryptophan residues. In the membrane-mimicking solvent these side-chains show a high propensity to point towards the hydrophobic environment, rather than being in the hydrophobic core as seen in water, while the backbone preserves the hairpin conformation as found in water. These results suggest that the tryptophans might act as anchors pulling the stable, solvent-invariant hairpin structure into the membrane.

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

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

Jansson, Janet; Edlund, Anna; Hardeman, Fredrik

Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities weremore » most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.« less

Antimicrobial activity of platelet-rich plasma and other plasma preparations against periodontal pathogens.

PubMed

Yang, Li-Chiu; Hu, Suh-Woan; Yan, Min; Yang, Jaw-Ji; Tsou, Sing-Hua; Lin, Yuh-Yih

2015-02-01

In addition to releasing a pool of growth factors during activation, platelets have many features that indicate their role in the anti-infective host defense. The antimicrobial activities of platelet-rich plasma (PRP) and related plasma preparations against periodontal disease-associated bacteria were evaluated. Four distinct plasma fractions were extracted in the formulation used commonly in dentistry and were tested for their antibacterial properties against three periodontal bacteria: Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Fusobacterium nucleatum. The minimum inhibitory concentration of each plasma preparation was determined, and in vitro time-kill assays were used to detect their abilities to inhibit bacterial growth. Bacterial adhesion interference and the susceptibility of bacterial adherence by these plasma preparations were also conducted. All plasma preparations can inhibit bacterial growth, with PRP showing the superior activity. Bacterial growth inhibition by PRP occurred in the first 24 hours after application in the time-kill assay. PRP interfered with P. gingivalis and A. actinomycetemcomitans attachment and enhanced exfoliation of attached P. gingivalis but had no influences on F. nucleatum bacterial adherence. PRP expressed antibacterial properties, which may be attributed to platelets possessing additional antimicrobial molecules. The application of PRP on periodontal surgical sites is advisable because of its regenerative potential and its antibacterial effects.

Carbonaceous aerosol tracers in ice-cores record multi-decadal climate oscillations

PubMed Central

Seki, Osamu; Kawamura, Kimitaka; Bendle, James A. P.; Izawa, Yusuke; Suzuki, Ikuko; Shiraiwa, Takayuki; Fujii, Yoshiyuki

2015-01-01

Carbonaceous aerosols influence the climate via direct and indirect effects on radiative balance. However, the factors controlling the emissions, transport and role of carbonaceous aerosols in the climate system are highly uncertain. Here we investigate organic tracers in ice cores from Greenland and Kamchatka and find that, throughout the period covered by the records (1550 to 2000 CE), the concentrations and composition of biomass burning-, soil bacterial- and plant wax- tracers correspond to Arctic and regional temperatures as well as the warm season Arctic Oscillation (AO) over multi-decadal time-scales. Specifically, order of magnitude decreases (increases) in abundances of ice-core organic tracers, likely representing significant decreases (increases) in the atmospheric loading of carbonaceous aerosols, occur during colder (warmer) phases in the high latitudinal Northern Hemisphere. This raises questions about causality and possible carbonaceous aerosol feedback mechanisms. Our work opens new avenues for ice core research. Translating concentrations of organic tracers (μg/kg-ice or TOC) from ice-cores, into estimates of the atmospheric loading of carbonaceous aerosols (μg/m3) combined with new model constraints on the strength and sign of climate forcing by carbonaceous aerosols should be a priority for future research. PMID:26411576

Immunopharmacology of lipid A mimetics.

PubMed

Bowen, William S; Gandhapudi, Siva K; Kolb, Joseph P; Mitchell, Thomas C

2013-01-01

The structural core of bacterial lipopolysaccharide, lipid A, has played a role in medicine since the 1890s when William Coley sought to harness its immunostimulatory properties in the form of a crude bacterial extract. Recent decades have brought remarkable clarity to the structure of lipid A and the multicomponent endotoxin receptor system that evolved to detect it. A range of therapeutically useful versions of lipid A now exists, including preparations of detoxified lipid A, synthetic copies of naturally occurring biological intermediates such as lipid IVa, and synthetic mimetics. These agents are finding use as vaccine adjuvants, antagonists and immunostimulants whose structural features have been refined to potentiate efficacy while decreasing the risk of inflammatory side effects. Copyright © 2013 Elsevier Inc. All rights reserved.

The effects of therapeutic hip exercise with abdominal core activation on recruitment of the hip muscles.

PubMed

Chan, Mandy Ky; Chow, Ka Wai; Lai, Alfred Ys; Mak, Noble Kc; Sze, Jason Ch; Tsang, Sharon Mh

2017-07-21

Core stabilization has been utilized for rehabilitation and prevention of lower limb musculoskeletal injuries. Previous studies showed that activation of the abdominal core muscles enhanced the hip muscle activity in hip extension and abduction exercises. However, the lack of the direct measurement and quantification of the activation level of the abdominal core muscles during the execution of the hip exercises affect the level of evidence to substantiate the proposed application of core exercises to promote training and rehabilitation outcome of the hip region. The aim of the present study was to examine the effects of abdominal core activation, which is monitored directly by surface electromyography (EMG), on hip muscle activation while performing different hip exercises, and to explore whether participant characteristics such as gender, physical activity level and contractile properties of muscles, which is assessed by tensiomyography (TMG), have confounding effect to the activation of hip muscles in enhanced core condition. Surface EMG of bilateral internal obliques (IO), upper gluteus maximus (UGMax), lower gluteus maximus (LGMax), gluteus medius (GMed) and biceps femoris (BF) of dominant leg was recorded in 20 young healthy subjects while performing 3 hip exercises: Clam, side-lying hip abduction (HABD), and prone hip extension (PHE) in 2 conditions: natural core activation (NC) and enhanced core activation (CO). EMG signals normalized to percentage of maximal voluntary isometric contraction (%MVIC) were compared between two core conditions with the threshold of the enhanced abdominal core condition defined as >20%MVIC of IO. Enhanced abdominal core activation has significantly promoted the activation level of GMed in all phases of clam exercise (P < 0.05), and UGMax in all phases of PHE exercise (P < 0.05), LGMax in eccentric phases of all 3 exercises (P < 0.05), and BF in all phases of all 3 exercises except the eccentric phase of PHE exercise (P < 0.05). The %MVIC of UGMax was significantly higher than that of LGMax in all phases of clam and HABD exercises under both CO and NC conditions (P < 0.001) while the %MVIC of LGMax was significantly higher than UGMax in concentric phase of PHE exercise under NC condition (P = 0.003). Gender, physical activity level and TMG parameters were not major covariates to activation of hip muscles under enhanced core condition. Abdominal core activation enhances the hip muscles recruitment in Clam, HABD and PHE exercises, and this enhancement is correlated with higher physical activity and stiffer hip muscle. Our results suggest the potential application of abdominal core activation for lower limb rehabilitation since the increased activation of target hip muscles may enhance the therapeutic effects of hip strengthening exercises.

Bacterial Infection of Fly Ovaries Reduces Egg Production and Induces Local Hemocyte Activation

PubMed Central

Brandt, Stephanie M.; Schneider, David S.

2009-01-01

Summary Morbidity, the state of being diseased, is an important aspect of pathogenesis that has gone relatively unstudied in fruit flies. Our interest is in characterizing how bacterial pathogenesis affects various physiologies of the fly. We chose to examine the fly ovary because we found bacterial infection had a striking effect on fly reproduction. We observed decreased egg laying after bacterial infection that correlated with increased bacterial virulence. We also found that bacteria colonized the ovary in a previously undescribed manner; bacteria were found in the posterior of the ovary, adjacent to the lateral oviduct. This local infection in the ovary resulted in melanization and activation of the cellular immune response at the site of infection. PMID:17400292

Treatment With High-Hydrostatic Pressure, Activated Film Packaging With Thymol Plus Enterocin AS-48, and Its Combination Modify the Bacterial Communities of Refrigerated Sea Bream (Sparus aurata) Fillets

PubMed Central

Ortega Blázquez, Irene; Grande Burgos, María J.; Pérez-Pulido, Rubén; Gálvez, Antonio; Lucas, Rosario

2018-01-01

The aim of this study was to determine the impact of activated plastic films with thymol and enterocin AS-48 and high-hydrostatic pressure (HP) treatment on the bacterial load and bacterial diversity of vacuum-packaged sea bream fillets under refrigerated storage for 10 days. The activated film and the HP treatment reduced aerobic mesophiles viable counts by 1.46 and 2.36 log cycles, respectively, while the combined treatment achieved a reduction of 4.13 log cycles. HP and combined treatments resulted in longer delays in bacterial growth. Proteobacteria were the dominant phyla in sea bream fillets. The relative abundance of Firmicutes increased by the end of storage both in controls and in samples treated by HP singly or in combination with the activated films. The predominant operational taxonomic units (OTUs) found at time 0 in control samples (Listeria, Acinetobacter, Pseudomonas, Enterobacteriaceae, Chryseobacterium) rapidly changed during storage (with an increase of Vibrio, Photobacterium, and Shewanella together with Cloacibacterium and Lactobacillales by the end of storage). The activated film and the HP treatment induced drastic changes in bacterial diversity right after treatments (with Comamonadaceae, Methylobacterium, Acidovorax, and Sphingomonas as main OTUs) and also induced further modifications during storage. Bacterial diversity in activated film samples was quite homogeneous during storage (with Vibrio, Photobacterium, and Shewanella as main OTUs) and approached control samples. HP treatments (singly or in combination with activated films) determined a high relative abundance of Acinetobacter (followed by Pseudomonas and Shewanella) during early storage as well as a higher relative abundance of lactic acid bacteria by the end of storage. The results indicate that the complex dynamics of bacterial populations in the refrigerated sea bream fillets are markedly influenced by treatment and antimicrobials applied. PMID:29541064

Treatment With High-Hydrostatic Pressure, Activated Film Packaging With Thymol Plus Enterocin AS-48, and Its Combination Modify the Bacterial Communities of Refrigerated Sea Bream (Sparus aurata) Fillets.

PubMed

Ortega Blázquez, Irene; Grande Burgos, María J; Pérez-Pulido, Rubén; Gálvez, Antonio; Lucas, Rosario

2018-01-01

The aim of this study was to determine the impact of activated plastic films with thymol and enterocin AS-48 and high-hydrostatic pressure (HP) treatment on the bacterial load and bacterial diversity of vacuum-packaged sea bream fillets under refrigerated storage for 10 days. The activated film and the HP treatment reduced aerobic mesophiles viable counts by 1.46 and 2.36 log cycles, respectively, while the combined treatment achieved a reduction of 4.13 log cycles. HP and combined treatments resulted in longer delays in bacterial growth. Proteobacteria were the dominant phyla in sea bream fillets. The relative abundance of Firmicutes increased by the end of storage both in controls and in samples treated by HP singly or in combination with the activated films. The predominant operational taxonomic units (OTUs) found at time 0 in control samples ( Listeria, Acinetobacter, Pseudomonas, Enterobacteriaceae, Chryseobacterium ) rapidly changed during storage (with an increase of Vibrio, Photobacterium , and Shewanella together with Cloacibacterium and Lactobacillales by the end of storage). The activated film and the HP treatment induced drastic changes in bacterial diversity right after treatments (with Comamonadaceae, Methylobacterium, Acidovorax , and Sphingomonas as main OTUs) and also induced further modifications during storage. Bacterial diversity in activated film samples was quite homogeneous during storage (with Vibrio, Photobacterium , and Shewanella as main OTUs) and approached control samples. HP treatments (singly or in combination with activated films) determined a high relative abundance of Acinetobacter (followed by Pseudomonas and Shewanella ) during early storage as well as a higher relative abundance of lactic acid bacteria by the end of storage. The results indicate that the complex dynamics of bacterial populations in the refrigerated sea bream fillets are markedly influenced by treatment and antimicrobials applied.