Killing of Staphylococcus aureus via Magnetic Hyperthermia Mediated by Magnetotactic Bacteria

PubMed Central

Chen, Changyou; Chen, Linjie; Yi, Yong; Chen, Chuanfang

2016-01-01

Staphylococcus aureus is a common hospital and household pathogen. Given the emergence of antibiotic-resistant derivatives of this pathogen resulting from the use of antibiotics as general treatment, development of alternative therapeutic strategies is urgently needed. Here, we assess the feasibility of killing S. aureus cells in vitro and in vivo through magnetic hyperthermia mediated by magnetotactic bacteria that possess magnetic nanocrystals and demonstrate magnetically steered swimming. The S. aureus suspension was added to magnetotactic MO-1 bacteria either directly or after coating with anti-MO-1 polyclonal antibodies. The suspensions were then subjected to an alternating magnetic field (AMF) for 1 h. S. aureus viability was subsequently assessed through conventional plate counting and flow cytometry. We found that approximately 30% of the S. aureus cells mixed with uncoated MO-1 cells were killed after AMF treatment. Moreover, attachment between the magnetotactic bacteria and S. aureus increased the killing efficiency of hyperthermia to more than 50%. Using mouse models, we demonstrated that magnetic hyperthermia mediated by antibody-coated magnetotactic MO-1 bacteria significantly improved wound healing. These results collectively demonstrated the effective eradication of S. aureus both in vitro and in vivo, indicating the potential of magnetotactic bacterium-mediated magnetic hyperthermia as a treatment for S. aureus-induced skin or wound infections. PMID:26873320

Organization of P, S, and Fe Inclusions in a Freshwater Magnetococcus

NASA Technical Reports Server (NTRS)

Cox, Lea; Popa Radu; Douglas, Susanne; Belz, Andrea; Nealson, Kenneth H.

2001-01-01

Magnetotactic bacteria are a heterogeneous group of motile, mainly aquatic procaryotes that align and swim along geomagnetic field lines. They are of interest to astrobiologists because of the magnetite crystals found in the Mars meteorite ALH84001 which share many characteristics with the magnetite produced intracellularly by magnetotactic bacteria. These bacteria are diverse morphologically, physiologically and phylogenetically, sharing a few key characteristics: 1) the presence of intracellular membrane-bound magnetic crystals (magnetosomes), usually but not always arranged in chains; 2) motility by means of flagella; and 3) microaerophillic or anaerobic physiology. The bilophotrichous (having two flagella bundles) magnetotactic cocci (MC) are ubiquitous in aquatic habitats but have proven extremely difficult to cultivate. Because only several marine strains have been isolated and grown in axenic culture, little is known about the physiology and the biogeochemical roles of the MC. We studied the composition and distribution of intracellular structures in an uncultured MC, designated ARB-1. To do this, a combination of light microscopy, environmental scanning electron microscopy (ESEM), transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS) were used. Cells of ARB-1 were separated from sediments collected from Baldwin Lake (Los Angeles Arboretum, Arcadia, CA). They are large spherical to oblate spheroidal Gram-negative cells, ranging from 1 to 4 micrometers along the maximum dimension, which is perpendicular to the direction of swimming. Cells have two large phosphorus-containing inclusions that comprise a large percentage of the cell volume. Many smaller sulfur inclusions are located at the convex end of the cell. Most of the cellular Fe is present in the magnetosomes. These may be arranged as a clump at the concave end of the cell, near the two flagella bundles, or as chains, or as both a clump and chains. The magnetosomes were identified as magnetite (Fe3O4) by selected area electron diffraction (SAED) and high resolution TEM. We saw a trend between cell size and organization of the magnetosomes. Smaller, more spherical cells were more likely to have chains than were larger, more oblate cells. This may indicate different populations of cells, or it may be attributed to variations in cell growth cycle. The size distribution (length) of magnetosomes in chains was similar to that of magnetosomes in clusters, except that there was a larger size range for clustered magnetosomes. Magnetosomes from ARB-1 cells average 82 nm in length. If plotted on a graph of length as a function of aspect ratio, they fall within the single domain region of the plot. If compared with the size distributions of magnetite from ALH84001 and magnetosomes from the cultured magnetotactic vibrio MV-1, the magnetites produced by ARB-1 cells are, on average, larger and have a wider range of aspect ratio. ARB-1 cells have a specific organization of the P, S, and Fe inclusions. The P inclusions always occupy the majority of the cell volume and separate the S inclusions from the disorganized clumps of magnetosomes and the flagella bundles. The P inclusions may contain polyphosphate, which could play several roles in motility, adaptation to stress, growth and division, buoyancy, and energy. The S inclusions might be a way to store S, a potential energy source, when the cells move from sulfide to oxygen zones. The consistency of P, S, and Fe organization in ARB-1 cells suggests that these inclusions have some specific and interactive functions.

Novel Magnetic Nanomaterials Inspired by Magnetotactic Baterial: Topical Review

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

Prozorov, Tanya; Bazylinki, Dennis A.; Mallapragada, Surya K.

2013-05-14

Magnetotactic bacteria, known to produce magnetic nanocrystals with uniform shapes and sizes at physiological conditions, serve as an inspiration and source of a number of biological macromolecules used for the biomimetic synthesis of a variety of magnetic nanomaterials. This review discusses the current state of understanding of magnetosome biomineralization in magnetotactic bacteria, as well as the ways in which iron biomineralization processes can be utilized for tailored in vivo formation of complex magnetic nanomaterials, not occurring in magnetotactic bacteria naturally. The review assesses the current efforts on in vitro synthesis of a variety of magnetic nanoparticles using bioinspired approaches bymore » utilizing mineralization proteins from magnetotactic bacteria, and surveys biomimetic strategies for the rational synthesis of various magnetic nanomaterials under ambient conditions. Finally, this review presents magnetic characterization of nanoparticles, highlighting differences in magnetic behavior between magnetic nanoparticles produced using bioinspired in vivo and in vitro strategies, compared to those produced using conventional methods. This in turn impacts their utility in a wide range of applications for magnetic nanoparticles, which are examined in detail, where bioinspired synthesis methods have potentially provided added advantages.« less

A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria.

PubMed

Lefèvre, Christopher T; Menguy, Nicolas; Abreu, Fernanda; Lins, Ulysses; Pósfai, Mihály; Prozorov, Tanya; Pignol, David; Frankel, Richard B; Bazylinski, Dennis A

2011-12-23

Magnetotactic bacteria contain magnetosomes--intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe(3)O(4)) or greigite (Fe(3)S(4))--that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite.

Simultaneously discrete biomineralization of magnetite and tellurium nanocrystals in magnetotactic bacteria.

PubMed

Tanaka, Masayoshi; Arakaki, Atsushi; Staniland, Sarah S; Matsunaga, Tadashi

2010-08-01

Magnetotactic bacteria synthesize intracellular magnetosomes comprising membrane-enveloped magnetite crystals within the cell which can be manipulated by a magnetic field. Here, we report the first example of tellurium uptake and crystallization within a magnetotactic bacterial strain, Magnetospirillum magneticum AMB-1. These bacteria independently crystallize tellurium and magnetite within the cell. This is also highly significant as tellurite (TeO(3)(2-)), an oxyanion of tellurium, is harmful to both prokaryotes and eukaryotes. Additionally, due to its increasing use in high-technology products, tellurium is very precious and commercially desirable. The use of microorganisms to recover such molecules from polluted water has been considered as a promising bioremediation technique. However, cell recovery is a bottleneck in the development of this approach. Recently, using the magnetic property of magnetotactic bacteria and a cell surface modification technology, the magnetic recovery of Cd(2+) adsorbed onto the cell surface was reported. Crystallization within the cell enables approximately 70 times more bioaccumulation of the pollutant per cell than cell surface adsorption, while utilizing successful recovery with a magnetic field. This fascinating dual crystallization of magnetite and tellurium by magnetotactic bacteria presents an ideal system for both bioremediation and magnetic recovery of tellurite.

Simultaneously Discrete Biomineralization of Magnetite and Tellurium Nanocrystals in Magnetotactic Bacteria▿

PubMed Central

Tanaka, Masayoshi; Arakaki, Atsushi; Staniland, Sarah S.; Matsunaga, Tadashi

2010-01-01

Magnetotactic bacteria synthesize intracellular magnetosomes comprising membrane-enveloped magnetite crystals within the cell which can be manipulated by a magnetic field. Here, we report the first example of tellurium uptake and crystallization within a magnetotactic bacterial strain, Magnetospirillum magneticum AMB-1. These bacteria independently crystallize tellurium and magnetite within the cell. This is also highly significant as tellurite (TeO32−), an oxyanion of tellurium, is harmful to both prokaryotes and eukaryotes. Additionally, due to its increasing use in high-technology products, tellurium is very precious and commercially desirable. The use of microorganisms to recover such molecules from polluted water has been considered as a promising bioremediation technique. However, cell recovery is a bottleneck in the development of this approach. Recently, using the magnetic property of magnetotactic bacteria and a cell surface modification technology, the magnetic recovery of Cd2+ adsorbed onto the cell surface was reported. Crystallization within the cell enables approximately 70 times more bioaccumulation of the pollutant per cell than cell surface adsorption, while utilizing successful recovery with a magnetic field. This fascinating dual crystallization of magnetite and tellurium by magnetotactic bacteria presents an ideal system for both bioremediation and magnetic recovery of tellurite. PMID:20581185

Motility of magnetotactic bacteria/MTB to Geomagnetic fields

NASA Astrophysics Data System (ADS)

Hidajatullah-Maksoed, Fatahillah

2016-03-01

Bacteria with motility directed by a local geomagnetic fields have been observed in marine sediments'' discussed by R. Blakemore, 1975. Magnetotactic bacteria/MTB discovered in 1963 by Salvatore Bellini. For ``off-axis electron holography in the transmission electron microscope was used to correlates the physical & magnetic microstructure of magnetite nanocrystals in magnetotactic bacteria'' sought ``single-domain magnetite in hemopelagic sediments'' from JF Stolz. Otherwise, for potential source of bioproducts- product meant from result to multiplier -of magnetotactic bacteria[ACV Araujo, et.al, 2014 ] of marine drugs retrieved the `measurement of cellular chemotaxis with ECIS/Taxis, from KM Pietrosimone, 2012, whereas after ``earth magnetic field role on small living models'' are other interpretation of ``taxis'' as a movement of a cell instead usual ``tax'' for yew's taxus cuspidate, hired car & taxes in financial realms. Acknowledgements to HE. Mr. H. TUK SETYOHADI, Jl. Sriwijaya Raya 3, South-Jakarta, INDONESIA.

Controlling Magnetotactic Bacteria through an Integrated Nanofabricated Metallic Island and Optical Microscope Approach

PubMed Central

González, Lina M.; Ruder, Warren C.; Leduc, Philip R.; Messner, William C.

2014-01-01

Herein, we demonstrate the control of magnetotactic bacteria through the application of magnetic field gradients with real-time visualization. We accomplish this control by integrating a pair of macroscale Helmholtz coils and lithographically fabricated nanoscale islands composed of permalloy (Ni80Fe20). This system enabled us to guide and steer amphitrichous Magnetospirillum magneticum strain AMB-1 to specific location via magnetic islands. The geometries of the islands allowed us to have control over the specific magnetic field gradients on the bacteria. We estimate that magnetotactic bacteria located less than 1 μm from the edge of a diamond shaped island experience a maximum force of approximately 34 pN, which engages the bacteria without trapping them. Our system could be useful for a variety of applications including magnetic fabrication, self-assembly, and probing the sensing apparatus of magnetotactic bacteria. PMID:24553101

Two Genera of Magnetococci with Bean-like Morphology from Intertidal Sediments of the Yellow Sea, China

PubMed Central

Zhang, Wen-Yan; Zhou, Ke; Pan, Hong-Miao; Yue, Hai-Dong; Jiang, Ming

2012-01-01

Magnetotactic bacteria have the unique capacity of being able to swim along geomagnetic field lines. They are Gram-negative bacteria with diverse morphologies and variable phylogenetic relatedness. Here, we describe a group of uncultivated marine magnetococci collected from intertidal sediments of Huiquan Bay in the Yellow Sea. They were coccoid-ovoid in morphology, with an average size of 2.8 ± 0.3 μm by 2.0 ± 0.2 μm. Differential interference contrast microscopy, fluorescence microscopy, and transmission electron microscopy revealed that each cell was apparently composed of two hemispheres. The cells synthesized iron oxide-type magnetosomes that clustered on one side of the cell at the interface between the two hemispheres. In some cells two chains of magnetosomes were observed across the interface. Each cell had two bundles of flagella enveloped in a sheath and displayed north-seeking helical motion. Two 16S rRNA gene sequences having 91.8% identity were obtained, and their authenticity was confirmed by fluorescence in situ hybridization. Phylogenetic analysis revealed that the magnetococci are affiliated with the Alphaproteobacteria and are most closely related to two uncultured magnetococci with sequence identities of 92.7% and 92.4%, respectively. Because they display a >7% sequence divergence to all bacteria reported, the bean-like magnetococci may represent two novel genera. PMID:22660708

Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae.

PubMed

Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

2014-12-01

Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

Swimming motion of rod-shaped magnetotactic bacteria: the effects of shape and growing magnetic moment

PubMed Central

Kong, Dali; Lin, Wei; Pan, Yongxin; Zhang, Keke

2014-01-01

We investigate the swimming motion of rod-shaped magnetotactic bacteria affiliated with the Nitrospirae phylum in a viscous liquid under the influence of an externally imposed, time-dependent magnetic field. By assuming that fluid motion driven by the translation and rotation of a swimming bacterium is of the Stokes type and that inertial effects of the motion are negligible, we derive a new system of the twelve coupled equations that govern both the motion and orientation of a swimming rod-shaped magnetotactic bacterium with a growing magnetic moment in the laboratory frame of reference. It is revealed that the initial pattern of swimming motion can be strongly affected by the rate of the growing magnetic moment. It is also revealed, through comparing mathematical solutions of the twelve coupled equations to the swimming motion observed in our laboratory experiments with rod-shaped magnetotactic bacteria, that the laboratory trajectories of the swimming motion can be approximately reproduced using an appropriate set of the parameters in our theoretical model. PMID:24523716

Biomagnetic Recovery and Bioaccumulation of Selenium Granules in Magnetotactic Bacteria.

PubMed

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

2016-07-01

Using microorganisms to remove waste and/or neutralize pollutants from contaminated water is attracting much attention due to the environmentally friendly nature of this methodology. However, cell recovery remains a bottleneck and a considerable challenge for the development of this process. Magnetotactic bacteria are a unique group of organisms that can be manipulated by an external magnetic field due to the presence of biogenic magnetite crystals formed within their cells. In this study, we demonstrated an account of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria alongside and independent of magnetite crystal biomineralization when grown in a medium containing selenium oxyanion (SeO3 (2-)). Quantitative analysis shows that magnetotactic bacteria accumulate the largest amount of target molecules (Se) per cell compared with any other previously reported nonferrous metal/metalloid. For example, 2.4 and 174 times more Se is accumulated than Te taken up into cells and Cd(2+) adsorbed onto the cell surface, respectively. Crucially, the bacteria with high levels of Se accumulation were successfully recovered with an external magnetic field. The biomagnetic recovery and the effective accumulation of target elements demonstrate the potential for application in bioremediation of polluted water. The development of a technique for effective environmental water remediation is urgently required across the globe. A biological remediation process of waste removal and/or neutralization of pollutant from contaminated water using microorganisms has great potential, but cell recovery remains a bottleneck. Magnetotactic bacteria synthesize magnetic particles within their cells, which can be recovered by a magnetic field. Herein, we report an example of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria independent of magnetic particle synthesis. The cells were able to accumulate the largest amount of Se compared to other foreign elements. More importantly, the Se-accumulating bacteria were successfully recovered with an external magnetic field. We believe magnetotactic bacteria confer unique advantages of biomagnetic cell recovery and of Se accumulation, providing a new and effective methodology for bioremediation of polluted water. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Statistical Analyses Comparing Prismatic Magnetite Crystals in ALH84001 Carbonate Globules with those from the Terrestrial Magnetotactic Bacteria Strain MV-1

NASA Technical Reports Server (NTRS)

Thomas-Keprta, Kathie L.; Clemett, Simon J.; Bazylinski, Dennis A.; Kirschvink, Joseph L.; McKay, David S.; Wentworth, Susan J.; Vali, H.; Gibson, Everett K.

2000-01-01

Here we use rigorous mathematical modeling to compare ALH84001 prismatic magnetites with those produced by terrestrial magnetotactic bacteria, MV-1. We find that this subset of the Martian magnetites appears to be statistically indistinguishable from those of MV-1.

North-Seeking Magnetotactic Gammaproteobacteria in the Southern Hemisphere

PubMed Central

Leão, Pedro; Teixeira, Lia C. R. S.; Cypriano, Jefferson; Farina, Marcos; Abreu, Fernanda; Bazylinski, Dennis A.

2016-01-01

ABSTRACT Magnetotactic bacteria (MTB) comprise a phylogenetically diverse group of prokaryotes capable of orienting and navigating along magnetic field lines. Under oxic conditions, MTB in natural environments in the Northern Hemisphere generally display north-seeking (NS) polarity, swimming parallel to the Earth's magnetic field lines, while those in the Southern Hemisphere generally swim antiparallel to magnetic field lines (south-seeking [SS] polarity). Here, we report a population of an uncultured, monotrichously flagellated, and vibrioid MTB collected from a brackish lagoon in Brazil in the Southern Hemisphere that consistently exhibits NS polarity. Cells of this organism were mainly located below the oxic-anoxic interface (OAI), suggesting it is capable of some type of anaerobic metabolism. Magnetosome crystalline habit and composition were consistent with elongated prismatic magnetite (Fe3O4) particles. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this organism belongs to a distinct clade of the Gammaproteobacteria class. The presence of NS MTB in the Southern Hemisphere and the previously reported finding of SS MTB in the Northern Hemisphere reinforce the idea that magnetotaxis is more complex than we currently understand and may be modulated by factors other than O2 concentration and redox gradients in sediments and water columns. IMPORTANCE Magnetotaxis is a navigational mechanism used by magnetotactic bacteria to move along geomagnetic field lines and find an optimal position in chemically stratified sediments. For that, magnetotactic bacteria swim parallel to the geomagnetic field lines under oxic conditions in the Northern Hemisphere, whereas those in the Southern Hemisphere swim antiparallel to magnetic field lines. A population of uncultured vibrioid magnetotactic bacteria was discovered in a brackish lagoon in the Southern Hemisphere that consistently swim northward, i.e., the opposite of the overwhelming majority of other Southern Hemisphere magnetotactic bacteria. This finding supports the idea that magnetotaxis is more complex than previously thought. PMID:27401974

Microscopic observation of magnetic bacteria in the magnetic field of a rotating permanent magnet.

PubMed

Smid, Pieter; Shcherbakov, Valeriy; Petersen, Nikolai

2015-09-01

Magnetotactic bacteria are ubiquitous and can be found in both freshwater and marine environments. Due to intracellular chains of magnetic single domain particles, they behave like swimming compass needles. In external magnetic fields like the Earth's magnetic field, a torque is acting on the chain. This will cause the bacterium to be rotated and aligned with the external field. The swimming direction of magnetotactic bacteria can be controlled with external magnetic fields, which makes it convenient to study them under a light microscope. Usually, a special set of coils arranged around a light microscope is used to control the swimming magnetotactic bacteria. Here, we present a simple mechanical system with a permanent magnet, which produces a rotating magnetic field of nearly constant amplitude in the focal plane of a light microscope. The device is placed beside the light microscope and easily adaptable to almost any microscope and thus convenient for field experiments. To describe the trajectories qualitatively, a theoretical model of the trajectories is presented. This device can be used to control the swimming direction of magnetotactic bacteria and also for studying their magnetic and hydrodynamic properties.

Directed transport of active magnetotactic bacteria in porous media flow

NASA Astrophysics Data System (ADS)

Waisbord, Nicolas; Dehkharghani, Amin; Coons, Thomas; Guasto, Jeffrey S.

2017-11-01

Swimming cell migration through porous media is a topic of ecological and technical relevance for understanding sediment ecosystems and bioremediation of soil for decontamination. We focus on magnetotactic bacteria - which align passively with Earth's magnetic field and migrate in such sediment environments - as a model system. The transport properties of magnetotactic bacteria are measured in a 2D microfluidic porous medium as a function of the porous microstructure geometry and under a variety of environmental conditions. In a quiescent fluid and in the absence of an external, guiding magnetic field, the effective diffusion of cells' random walk is unsurprisingly hindered with decreasing porosity due to cell-surface interactions. When guided by a magnetic field, cell trajectories acquire a net direction and form lanes, a behavior that is enhanced with increasing magnetic field. When the directed motility is coupled with an opposing fluid flow through the porous medium, convective cells form and locally trap the swimming bacteria. These results, which are corroborated by Langevin Simulations are an important step toward understanding magnetotactic bacterial ecology as well as for the magnetic guidance of microrobots in complex environments. Supported by NSF Grant CBET-1511340.

How Magnetotactic Bacteria Respond to Radiation Induced Stress and Damage: Comparative Genomics Evidences for Evolutionary Adaptation

NASA Astrophysics Data System (ADS)

Wang, Y.; Pan, Y.

2015-12-01

Solar radiation and galactic cosmic radiation is believed to be major restriction factors influencing survival and evolution of life. On planet earth, geomagnetic field along with atmosphere protect living beings from the harmful radiation. During a geomagnetic reversal or excursion, however, the efflux of charged particles on earth surface would increase as the shielding effect of magnetic field decrease. The stratospheric ozone can also be partially stripped away by solar wind when the strength of the field is weak, leading to an increasing ultraviolet radiation penetration to the earth surface. However, studies on the mechanism of radiation induced stress and damage are focused only on bacteria that have no response to magnetic field. This study was motivated by the need to fill the gap upon knowledge of that on magnetic field sensitive microorganism. Magnetotactic bacteria (MTB) are a group of microbes that are able to synthesis intracellular nano-sized magnetic particles (named magnetosomes). These chain-arranged magnetosomes help MTB sense and swim along the magnetic field to find their optimal living environment efficiently. In this paper, in silico prediction of stress and damage repair genes in response to different radiation were carried out on the complete genome of four nonmagnetotactic and four magnetotactic spirilla. In silico analyses of the genomes of magnetic field sensitive and non-sensitive spirilla revealed: 1) all strains contain genes for regulate responses superoxide and peroxide stress, DNA pyrimidine dimer and string breaks; 2) non-magnetotactic spirilla have more genes dealing with oxidative stress, while magnetotactic spirilla may benefit from magnetotaxis by swimming into oxic-anoxic zone away from oxidative stress and direct radiation damage; yet, the lipid hydroperoxide peroxidase gene in MTB may be responsible for possible ROS generated by the membrane enveloped magnetite magnetosome; 3) magnetotactic spirilla possess SOS recA mediated umuCD genes and double copied ssb gene, these low fidelity DNA polymerase along with Ssb protein may endow MTB high adaptive mutation under stress condition; 4) also, magnetosome crystals (magnetite or greigite) can reduce radiation oxidative damage and protect MTB.

The chemical formula of a magnetotactic bacterium.

PubMed

Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

2012-05-01

Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. Copyright © 2011 Wiley Periodicals, Inc.

Characterization of Eight Kinds of Marine Magnetotactic Bacteria

NASA Astrophysics Data System (ADS)

Du, H.; Pan, H.; Zhang, W.; Wu, L. F.; Xiao, T.

2017-12-01

Eight marine magnetotactic bacteria were isolated from intertidal sediments. Six of them are magnetococci (RO-1, RO-2, RO-3, RO-4, SC-1 and SC-2), and two of them are manetospirilla (SH-1 and HH-1). Strain RO-1, RO-2, RO-3, and RO-4 were from Lake Yuehu, Rongcheng (the Yellow Sea). Strain SC-1, SC-2 and SH-1 were from Sanya (the South China Sea). Strain HH-1 was from Huiquan Bay, Qingdao (the Yellow Sea). Magnetosomes arranged in a disorganized cluster in RO-1 and RO-4, two chains in SC-2, and in one chain in others. All the magnetosome crystals were prismatic magnetites. Phylogenetic analysis revealed that they all belonged to the Alphaproteobacteria. Strain RO-1, RO-2, RO-3, RO-4, SC-2 and SH-1 are novel cultured magnetotactic bacteria.

Quantitative Imaging of Single Unstained Magnetotactic Bacteria by Coherent X-ray Diffraction Microscopy.

PubMed

Fan, Jiadong; Sun, Zhibin; Zhang, Jian; Huang, Qingjie; Yao, Shengkun; Zong, Yunbing; Kohmura, Yoshiki; Ishikawa, Tetsuya; Liu, Hong; Jiang, Huaidong

2015-06-16

Novel coherent diffraction microscopy provides a powerful lensless imaging method to obtain a better understanding of the microorganism at the nanoscale. Here we demonstrated quantitative imaging of intact unstained magnetotactic bacteria using coherent X-ray diffraction microscopy combined with an iterative phase retrieval algorithm. Although the signal-to-noise ratio of the X-ray diffraction pattern from single magnetotactic bacterium is weak due to low-scattering ability of biomaterials, an 18.6 nm half-period resolution of reconstructed image was achieved by using a hybrid input-output phase retrieval algorithm. On the basis of the quantitative reconstructed images, the morphology and some intracellular structures, such as nucleoid, polyβ-hydroxybutyrate granules, and magnetosomes, were identified, which were also confirmed by scanning electron microscopy and energy dispersive spectroscopy. With the benefit from the quantifiability of coherent diffraction imaging, for the first time to our knowledge, an average density of magnetotactic bacteria was calculated to be ∼1.19 g/cm(3). This technique has a wide range of applications, especially in quantitative imaging of low-scattering biomaterials and multicomponent materials at nanoscale resolution. Combined with the cryogenic technique or X-ray free electron lasers, the method could image cells in a hydrated condition, which helps to maintain their natural structure.

The swimming polarity of multicellular magnetotactic prokaryotes can change during an isolation process employing magnets: evidence of a relation between swimming polarity and magnetic moment intensity.

PubMed

de Melo, Roger Duarte; Acosta-Avalos, Daniel

2017-09-01

Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets. The proportion of north- and south-seeking organisms was counted as a function of the magnetic field intensity used during the isolation of the organisms from sediment. It was observed that the proportion of north-seeking organisms increased when the magnetic field was increased. The magnetic moment for north- and south-seeking populations was estimated using the U-turn method. The average magnetic moment was higher for north- than south-seeking organisms. The results suggest that the reversal of swimming polarity must occur during the isolation process in the presence of high magnetic fields and magnetic field gradients. It is shown for the first time that the swimming polarity reversal depends on the magnetic moment intensity of multicellular magnetotactic prokaryotes, and new studies must be undertaken to understand the role of magnetic moment polarity and oxygen gradients in determination of swimming polarity.

Effect of light wavelength on motility and magnetic sensibility of the magnetotactic multicellular prokaryote 'Candidatus Magnetoglobus multicellularis'.

PubMed

de Azevedo, Lyvia Vidinho; de Barros, Henrique Lins; Keim, Carolina Neumann; Acosta-Avalos, Daniel

2013-09-01

'Candidatus Magnetoglobus multicellularis' is a magnetotactic microorganism composed of several bacterial cells. Presently, it is the best known multicellular magnetotactic prokaryote (MMP). Recently, it has been observed that MMPs present a negative photoresponse to high intensity ultraviolet and violet-blue light. In this work, we studied the movement of 'Candidatus Magnetoglobus multicellularis' under low intensity light of different wavelengths, measuring the average velocity and the time to reorient its trajectory when the external magnetic field changes its direction (U-turn time). Our results show that the mean average velocity is higher for red light (628 nm) and lower for green light (517 nm) as compared to yellow (596 nm) and blue (469 nm) light, and the U-turn time decreased for green light illumination. The light wavelength velocity dependence can be understood as variation in flagella rotation speed, being increased by the red light and decreased by the green light relative to yellow and blue light. It is suggested that the dependence of the U-turn time on light wavelength can be considered a form of light-dependent magnetotaxis, because this time represents the magnetic sensibility of the magnetotactic microorganisms. The cellular and molecular mechanisms for this light-dependent velocity and magnetotaxis are unknown and deserve further studies to understand the biochemical interactions and the ecological roles of the different mechanisms of taxis in MMPs.

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

USGS Publications Warehouse

Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

1990-01-01

Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

Gram staining for the treatment of peritonsillar abscess.

PubMed

Takenaka, Yukinori; Takeda, Kazuya; Yoshii, Tadashi; Hashimoto, Michiko; Inohara, Hidenori

2012-01-01

Objective. To examine whether Gram staining can influence the choice of antibiotic for the treatment of peritonsillar abscess. Methods. Between 2005 and 2009, a total of 57 cases of peritonsillar abscess were analyzed with regard to cultured bacteria and Gram staining. Results. Only aerobes were cultured in 16% of cases, and only anaerobes were cultured in 51% of cases. Mixed growth of aerobes and anaerobes was observed in 21% of cases. The cultured bacteria were mainly aerobic Streptococcus, anaerobic Gram-positive cocci, and anaerobic Gram-negative rods. Phagocytosis of bacteria on Gram staining was observed in 9 cases. The bacteria cultured from these cases were aerobic Streptococcus, anaerobic Gram-positive cocci, and anaerobic Gram-negative rods. The sensitivity of Gram staining for the Gram-positive cocci and Gram-negative rods was 90% and 64%, respectively. The specificity of Gram staining for the Gram-positive cocci and Gram-negative rods was 62% and 76%, respectively. Most of the Gram-positive cocci were sensitive to penicillin, but some of anaerobic Gram-negative rods were resistant to penicillin. Conclusion. When Gram staining shows only Gram-positive cocci, penicillin is the treatment of choice. In other cases, antibiotics effective for the penicillin-resistant organisms should be used.

Chocolate agar, a differential medium for gram-positive cocci.

PubMed Central

Gunn, B A

1984-01-01

Reactions incurred on chocolate agar by gram-positive cocci were correlated with species identity. Darkening and clearing of the medium was usually associated with the species Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus simulans, and Streptococcus faecalis. Yellowing of chocolate agar was associated with alpha-hemolytic species of Streptococcus. The study demonstrated that reactions occurring on chocolate agar are useful in identifying gram-positive cocci. PMID:6490866

Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism

USGS Publications Warehouse

Lovley, D.R.; Stolz, J.F.; Nord, G.L.; Phillips, E.J.P.

1987-01-01

The potential contribution of microbial metabolism to the magnetization of sediments has only recently been recognized. In the presence of oxygen, magnetotactic bacteria can form intracellular chains of magnetite while using oxygen or nitrate as the terminal electron acceptor for metabolism1. The production of ultrafine-grained magnetite by magnetotactic bacteria in surficial aerobic sediments may contribute significantly to the natural remanent magnetism of sediments2-4. However, recent studies on iron reduction in anaerobic sediments suggested that bacteria can also generate magnetite in the absence of oxygen5. We report here on a sediment organism, designated GS-15, which produces copious quantities of ultrafine-grained magnetite under anaerobic conditions. GS-15 is not magnetotactic, but reduces amorphic ferric oxide to extracellular magnetite during the reduction of ferric iron as the terminal electron acceptor for organic matter oxidation. This novel metabolism may be the mechanism for the formation of ultrafine-grained magnetite in anaerobic sediments, and couldaccount for the accumulation of magnetite in ancient iron formations and hydrocarbon deposits. ?? 1987 Nature Publishing Group.

Uncultivated Microbial Eukaryotic Diversity: A Method to Link ssu rRNA Gene Sequences with Morphology

PubMed Central

Hirst, Marissa B.; Kita, Kelley N.; Dawson, Scott C.

2011-01-01

Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA “phylotypes” from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH) with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of novel lineages, identified in diverse environments. PMID:22174774

Rapid differentiation of cocci/mixed bacteria from rods in voided urine culture of women with uncomplicated urinary tract infections.

PubMed

Yang, Chun-Chun; Yang, Stephen Shei-Dei; Hung, Hui-Ching; Chiang, I-Ni; Peng, Chiung-Hui; Chang, Shang-Jen

2017-09-01

To evaluate the ability of laser flow cytometry to predict cocci/mixed growth in the pre-analytical phase of urine specimens. We retrospectively reviewed urine samples from women with uncomplicated urinary tract infections from urologic clinics for study. Urine analyses were performed with laser flow cytometry (UF1000i, Sysmex, Kobe, Japan) and then diagrams were generated (forward scatter vs. fluorescent light scatter). Each specimen (bacteria count >357 BACT/μL) was classified as either cocci bacteria or rods/mixed growth according to the diagrams. Standard urine cultures were performed, and the agreement between cultures and the UF1000i interpretations was analyzed with kappa statistics. Finally, 491 specimens met the criteria for analysis. Among the 376 specimens with single bacteria growth, there were 26 gram-positive cocci (13 Streptococci spp., 7 Staphylococci spp., 6 Enterococci spp.), 1 gram-positive rods (Corynebacterium spp.), and 349 gram-negative rods (273 Escherichia coli, 33 Klebsiella spp., 29 Proteus spp., 6 Citrobacter spp., 4 Enterobacter spp., 3 Pseudomonas spp., and 1 Providencia spp.). There were 115 specimens with two bacteria species or more that were regarded as mixed growth. Agreement of rods or cocci/mixed growth between the laser flow cytometry and urine cultures yielded a kappa value of 0.58. The positive and negative predictive rate of the UF1000i for cocci/mixed growth in voided urine culture was 81.8% and 84.7%, respectively. Through laser flow cytometry, we can predict growth of cocci/mixed growth in the pre-analytical phase of urine culture, thus avoiding unnecessary urine culture and waiting time. © 2016 Wiley Periodicals, Inc.

Dietary betaine increases intraepithelial lymphocytes in the duodenum of coccidia-infected chicks and increases functional properties of phagocytes.

PubMed

Klasing, K C; Adler, K L; Remus, J C; Calvert, C C

2002-08-01

Betaine is used by cells to defend against changes in osmolarity. We examined relationships among betaine, osmolarity and coccidiosis. In the first experiment, chicks were fed corn-soy diets containing 0.0, 0.5 or 1.0 g/kg betaine; half were challenged with Eimeria acervulina (Cocci). Cocci decreased weight gain and feed efficiency and increased the osmolarity of the duodenal and jejunal mucosa (P < 0.01). Betaine decreased osmolarity of the duodenum (P < 0.01), especially in Cocci-challenged birds. Cocci increased the thickness (P = 0.04) of and number (P < 0.01) of leukocytes in the duodenal lamina propria especially at high betaine levels (interaction P = 0.05). Villi height was decreased by Cocci (P = 0.05) and this was ameliorated by 1.0 g/kg betaine (interaction P = 0.04). Intraepithelial leukocyte numbers were increased by Cocci (P < 0.01) especially at 0.5 and 1 g/kg betaine. Peritoneal macrophages or peripheral blood heterophils were incubated in media with an osmolarity of 200, 310, 600 or 900 mOsmol and 0.0, 0.1, 0.5 or 1.5 mmol/L betaine (4 x 4 factorial) for 6 h and then E. acervulina were added. In general, phagocytosis and NO release were decreased and interleukin (IL)-1 and IL-6 release were increased in hyperosmotic media compared with isosmotic media. Betaine (0.1 mmol/L) increased NO release by heterophils (P = 0.04) and tended to increase (P < 0.1) NO release from macrophages. The chemotaxis of monocytes toward chemotactic factors released by heterophils was increased by betaine. Increased chemotaxis of monocytes and NO release by macrophages may explain the decreased intestinal pathology but increased leukocyte numbers that were observed when betaine was fed during a Cocci infection.

Magnetotactic bacteria and magnetosomes - Scope and challenges.

PubMed

Jacob, Jobin John; Suthindhiran, K

2016-11-01

Geomagnetism aided navigation has been demonstrated by certain organisms which allows them to identify a particular location using magnetic field. This attractive technique to recognize the course was earlier exhibited in numerous animals, for example, birds, insects, reptiles, fishes and mammals. Magnetotactic bacteria (MTB) are one of the best examples for magnetoreception among microorganisms as the magnetic mineral functions as an internal magnet and aid the microbe to move towards the water columns in an oxic-anoxic interface (OAI). The ability of MTB to biomineralize the magnetic particles (magnetosomes) into uniform nano-sized, highly crystalline structure with uniform magnetic properties has made the bacteria an important topic of research. The superior properties of magnetosomes over chemically synthesized magnetic nanoparticles made it an attractive candidate for potential applications in microbiology, biophysics, biochemistry, nanotechnology and biomedicine. In this review article, the scope of MTB, magnetosomes and its challenges in research and industrial application have been discussed in brief. This article mainly focuses on the application based on the magnetotactic behaviour of MTB and magnetosomes in different areas of modern science. Copyright © 2016 Elsevier B.V. All rights reserved.

Migration of magnetotactic bacteria in porous media.

PubMed

Rismani Yazi, Saeed; Nosrati, Reza; Stevens, Corey A; Vogel, David; Escobedo, Carlos

2018-01-01

Magnetotactic bacteria (MTB) migrate in complex porous sediments where fluid flow is ubiquitous. Here, we demonstrate that magnetotaxis enables MTB to migrate effectively through porous micromodels. Directed MTB can circumvent curved obstacles by traveling along the boundaries and pass flat obstacles by repeatedly switching between forward and backward runs. Magnetotaxis enables directed motion of MTB through heterogeneous porous media, overcoming tortuous flow fields with local velocities as high as 250  μ m s -1 . Our findings bring new insights into the migration behaviour of MTB in their natural habitats and their potential in vivo applications as microbiorobots.

Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

PubMed

Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

2016-04-21

Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain.

Nonmagnetotactic Multicellular Prokaryotes from Low-Saline, Nonmarine Aquatic Environments and Their Unusual Negative Phototactic Behavior▿ †

PubMed Central

Lefèvre, Christopher T.; Abreu, Fernanda; Lins, Ulysses; Bazylinski, Dennis A.

2010-01-01

Magnetotactic multicellular prokaryotes (MMPs) are unique magnetotactic bacteria of the Deltaproteobacteria class and the first found to biomineralize the magnetic mineral greigite (Fe3S4). Thus far they have been reported only from marine habitats. We questioned whether MMPs exist in low-saline, nonmarine environments. MMPs were observed in samples from shallow springs in the Great Boiling Springs geothermal field and Pyramid Lake, both located in northwestern Nevada. The temperature at all sites was ambient, and salinities ranged from 5 to 11 ppt. These MMPs were not magnetotactic and did not contain magnetosomes (called nMMPs here). nMMPs ranged from 7 to 11 μm in diameter, were composed of about 40 to 60 Gram-negative cells, and were motile by numerous flagella that covered each cell on one side, characteristics similar to those of MMPs. 16S rRNA gene sequences of nMMPs show that they form a separate phylogenetic branch within the MMP group in the Deltaproteobacteria class, probably representing a single species. nMMPs exhibited a negative phototactic behavior to white light and to wavelengths of ≤480 nm (blue). We devised a “light racetrack” to exploit this behavior, which was used to photoconcentrate nMMPs for specific purposes (e.g., DNA extraction) even though their numbers were low in the sample. Our results show that the unique morphology of the MMP is not restricted to marine and magnetotactic prokaryotes. Discovery of nonmagnetotactic forms of the MMP might support the hypothesis that acquisition of the magnetosome genes involves horizontal gene transfer. To our knowledge, this is the first report of phototaxis in bacteria of the Deltaproteobacteria class. PMID:20363801

Changes of the Quinolones Resistance to Gram-positive Cocci Isolated during the Past 8 Years in the First Bethune Hospital

NASA Astrophysics Data System (ADS)

Xu, Jiancheng; Chen, Qihui; Yao, Hanxin; Zhou, Qi

This study was to investigate the quinolones resistance to gram-positive cocci isolated in the First Bethune Hospital during the past 8 years. Disk diffusion test was used to study the antimicrobial resistance. The data were analyzed by WHONET 5 software according to Clinical and Laboratory Standards Institute (CLSI). The rates of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococci (MRCNS) were 50.8%∼83.3% and 79.4%∼81.5%during the past 8 years, respectively. In recent 8 years, the quinolones resistance to gram-positive cocci had increased. Monitoring of the quinolones resistance to gram-positive cocci should be strengthened. The change of the antimicrobial resistance should be investigated in order to guide rational drug usage in the clinic and prevent bacterial strain of drug resistance from being transmitted.

RNA-oligonucleotide quantification technique (ROQT) for the enumeration of uncultivated bacterial species in subgingival biofilms

PubMed Central

Teles, F.R.F.; Teles, R.P.; Siegelin, Y.; Paster, B.; Haffajee, A.D.; Socransky, S.S.

2010-01-01

SUMMARY Approximately 35% of the species present in subgingival biofilms are as yet uncultivated, so their role in periodontal pathogenesis is unknown. The aim of the present study was to develop a high throughput method to quantify a wide range of cultivated and uncultivated taxa in subgingival biofilm samples associated with periodontal disease or health. Oligonucleotides targeting the 16S ribosomal DNA gene were designed, synthesized and labeled with digoxigenin. These probes were hybridized with the total nucleic acids of pure cultures or subgingival biofilm samples. Target species included cultivated taxa associated with periodontal health and disease, as well as uncultivated species, such as TM7 sp OT 346, Mitsuokella sp. OT 131 and Desulfobulbus sp. OT 041. Sensitivity and specificity of the probes were determined. A Universal probe was used to assess total bacterial load. Sequences complementary to the probes were used as standards for quantification. Chemiluminescent signals were visualized after film exposure or using a CCD camera. In a pilot clinical study, 266 subgingival plaque samples from eight periodontally healthy people and 11 patients with periodontitis were examined. Probes were specific and sensitivity reached 104 cells. Fusobacterium nucleatum ss polymorphum and Actinomyces gerencseriae were the most abundant cultivated taxa in clinical samples. Among uncultivated/unrecognized species, Mitsuokella sp. OT 131 and Prevotella sp. OT 306 were the most numerous. Porphyromonas gingivalis and Desulfobulbus sp. OT 041 were only detected in patients with periodontitis. Direct hybridization of total nucleic acids using oligonucleotide probes permitted the quantification of multiple cultivated and uncultivated taxa in mixed species biofilm samples. PMID:21375703

Molecular mechanisms of magnetosome formation.

PubMed

Komeili, Arash

2007-01-01

Magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. This unique feat is accomplished with the help of magnetosomes, nanometer-sized magnetic crystals surrounded by a lipid bilayer membrane and organized into chains via a dedicated cytoskeleton within the cell. Because of the special properties of these magnetic crystals, magnetotactic bacteria have been exploited for a variety of applications in diverse disciplines from geobiology to biotechnology. In addition, magnetosomes have served as a powerful model system for the study of biomineralization and cell biology in bacteria. This review focuses on recent advances in understanding the molecular mechanisms of magnetosome formation and magnetite biomineralization.

Controlled manipulation and actuation of micro-objects with magnetotactic bacteria

NASA Astrophysics Data System (ADS)

Martel, Sylvain; Tremblay, Charles C.; Ngakeng, Serge; Langlois, Guillaume

2006-12-01

Bacterial actuation and manipulation are demonstrated where Magnetospirillum gryphiswaldense magnetotactic bacteria (MTB) are used to push 3μm beads at an average velocity of 7.5μms-1 along preplanned paths by modifying the torque on a chain of magnetosomes in the bacterium with a directional magnetic field of at least 0.5G generated from a small programmed electrical current. But measured average thrusts of 0.5 and 4pN of the flagellar motor of a single Magnetospirillum gryphiswaldense and MC-1 MTB suggest that average velocities greater than 16 and 128μms-1, respectively could be achieved.

A Comparison of Methods to Measure the Magnetic Moment of Magnetotactic Bacteria through Analysis of Their Trajectories in External Magnetic Fields

PubMed Central

Fradin, Cécile

2013-01-01

Magnetotactic bacteria possess organelles called magnetosomes that confer a magnetic moment on the cells, resulting in their partial alignment with external magnetic fields. Here we show that analysis of the trajectories of cells exposed to an external magnetic field can be used to measure the average magnetic dipole moment of a cell population in at least five different ways. We apply this analysis to movies of Magnetospirillum magneticum AMB-1 cells, and compare the values of the magnetic moment obtained in this way to that obtained by direct measurements of magnetosome dimension from electron micrographs. We find that methods relying on the viscous relaxation of the cell orientation give results comparable to that obtained by magnetosome measurements, whereas methods relying on statistical mechanics assumptions give systematically lower values of the magnetic moment. Since the observed distribution of magnetic moments in the population is not sufficient to explain this discrepancy, our results suggest that non-thermal random noise is present in the system, implying that a magnetotactic bacterial population should not be considered as similar to a paramagnetic material. PMID:24349185

Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats

NASA Technical Reports Server (NTRS)

Ruff-Roberts, A. L.; Kuenen, J. G.; Ward, D. M.

1994-01-01

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria

PubMed Central

Soro, Valeria; Dutton, Lindsay C.; Sprague, Susan V.; Nobbs, Angela H.; Ireland, Anthony J.; Sandy, Jonathan R.; Jepson, Mark A.; Micaroni, Massimo; Splatt, Peter R.; Dymock, David

2014-01-01

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium. PMID:25107981

Surviving bacterial sibling rivalry: inducible and reversible phenotypic switching in Paenibacillus dendritiformis.

PubMed

Be'er, Avraham; Florin, E-L; Fisher, Carolyn R; Swinney, Harry L; Payne, Shelley M

2011-01-01

Natural habitats vary in available nutrients and room for bacteria to grow, but successful colonization can lead to overcrowding and stress. Here we show that competing sibling colonies of Paenibacillus dendritiformis bacteria survive overcrowding by switching between two distinct vegetative phenotypes, motile rods and immotile cocci. Growing colonies of the rod-shaped bacteria produce a toxic protein, Slf, which kills cells of encroaching sibling colonies. However, sublethal concentrations of Slf induce some of the rods to switch to Slf-resistant cocci, which have distinct metabolic and resistance profiles, including resistance to cell wall antibiotics. Unlike dormant spores of P. dendritiformis, the cocci replicate. If cocci encounter conditions that favor rods, they secrete a signaling molecule that induces a switch to rods. Thus, in contrast to persister cells, P. dendritiformis bacteria adapt to changing environmental conditions by inducible and reversible phenotypic switching. In favorable environments, species may face space and nutrient limits due to overcrowding. Bacteria provide an excellent model for analyzing principles underlying overcrowding and regulation of density in nature, since their population dynamics can be easily and accurately assessed under controlled conditions. We describe a newly discovered mechanism for survival of a bacterial population during overcrowding. When competing with sibling colonies, Paenibacillus dendritiformis produces a lethal protein (Slf) that kills cells at the interface of encroaching colonies. Slf also induces a small proportion of the cells to switch from motile, rod-shaped cells to nonmotile, Slf-resistant, vegetative cocci. When crowding is reduced and nutrients are no longer limiting, the bacteria produce a signal that induces cocci to switch back to motile rods, allowing the population to spread. Genes encoding components of this phenotypic switching pathway are widespread among bacterial species, suggesting that this survival mechanism is not unique to P. dendritiformis.

Virus-associated apoptosis of blood neutrophils as a risk factor for invasive meningococcal disease

PubMed Central

Smith, Harry; Rogers, Sharon L; Smith, Helen V; Gillis, David; Siskind, Victor; Smith, Judith A

2013-01-01

Aims To quantify a range of haematological indicators of viral infection (leucocyte apoptosis, cytopenia of normal lymphocytes, reactive lymphocyte increase, neutropenia) in patients with recent onset invasive meningococcal disease (IMD), with a view to test the association of viral infection with IMD and identify possible haematological risk factors for its development. Subjects and methods 88 patients with recent onset IMD, classified on clinical severity as fatal (n=14), septic shock survived (n=26) and no shock (n=48), and 50 healthy controls were studied. Blood film microscopy and leucocyte counts were used to quantify the virus-associated indicators. Cocci-containing neutrophils were also quantified. Results All viral parameters were significantly more frequent or higher in patients than controls, with leucocyte apoptosis found only in the patients. A significant gradient in accord with clinical severity was found for neutrophil and lymphocyte apoptosis, neutropenia and cocci-containing neutrophils. Crucially, apoptotic neutrophils did not contain cocci, and cocci-containing neutrophils were not apoptotic. Conclusions The correlation between magnitude of neutrophil apoptosis and severity of IMD suggests a cause–effect relationship. We propose that neutrophil apoptosis is more likely a facilitator rather than an effect of IMD for these reasons: (1) apoptotic neutrophils did not contain cocci and cocci-containing neutrophils were not apoptotic, (2) leucocyte apoptosis is a recognised viral effect and (3) Neisseria meningitidis is incapable of producing a Panton–Valentine type leucocidin. The lymphocyte apoptosis which accompanies neutrophil death may contribute to risk by impairing the generation of microbicidal antibody. Leucocyte apoptosis is a morphological expression of viral immunosuppression and, we suggest, is a likely contributor to a range of viral effects. PMID:23801496

A point-source outbreak of Coccidioidomycosis among a highway construction crew.

PubMed

Nicas, Mark

2018-01-01

Coccidioidomycosis is an infection caused by inhaling spores of the soil fungus Coccidioides immitis (hereafter termed Cocci). Cocci is endemic in certain areas of California. When soil containing the fungus is disturbed, as during earth-moving activities, respirable Cocci spores can become airborne and be inhaled by persons in the vicinity. This article describes a cluster of seven Cocciodioidomycosis cases among a highway construction crew that occurred in June/July 2008 in Kern County, CA, which is among the most highly endemic regions for Cocci in California. The exposures spanned no more than seven work days, and illness developed within two to three weeks of the exposures. Given the common source of exposure (soil dust generated at the work site) and the multiple cases occurring close in time, the cluster can also be termed a "point-source outbreak." The contractor was not informed of the infection risk and did not take adequate precautions against dust exposure. Appropriate engineering/administrative controls and respiratory protection are discussed.

Desulfamplus magnetovallimortis gen. nov., sp. nov., a magnetotactic bacterium from a brackish desert spring able to biomineralize greigite and magnetite, that represents a novel lineage in the Desulfobacteraceae.

PubMed

Descamps, Elodie C T; Monteil, Caroline L; Menguy, Nicolas; Ginet, Nicolas; Pignol, David; Bazylinski, Dennis A; Lefèvre, Christopher T

2017-07-01

A magnetotactic bacterium, designated strain BW-1 T , was isolated from a brackish spring in Death Valley National Park (California, USA) and cultivated in axenic culture. The Gram-negative cells of strain BW-1 T are relatively large and rod-shaped and possess a single polar flagellum (monotrichous). This strain is the first magnetotactic bacterium isolated in axenic culture capable of producing greigite and/or magnetite nanocrystals aligned in one or more chains per cell. Strain BW-1 T is an obligate anaerobe that grows chemoorganoheterotrophically while reducing sulfate as a terminal electron acceptor. Optimal growth occurred at pH 7.0 and 28°C with fumarate as electron donor and carbon source. Based on its genome sequence, the G+C content is 40.72mol %. Phylogenomic and phylogenetic analyses indicate that strain BW-1 T belongs to the Desulfobacteraceae family within the Deltaproteobacteria class. Based on average amino acid identity, strain BW-1 T can be considered as a novel species of a new genus, for which the name Desulfamplus magnetovallimortis is proposed. The type strain of D. magnetovallimortis is BW-1 T (JCM 18010 T -DSM 103535 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

Characterization of a Spontaneous Nonmagnetic Mutant of Magnetospirillum gryphiswaldense Reveals a Large Deletion Comprising a Putative Magnetosome Island

PubMed Central

Schübbe, Sabrina; Kube, Michael; Scheffel, André; Wawer, Cathrin; Heyen, Udo; Meyerdierks, Anke; Madkour, Mohamed H.; Mayer, Frank; Reinhardt, Richard; Schüler, Dirk

2003-01-01

Frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium Magnetospirillum gryphiswaldense MSR-1. A nonmagnetic mutant, designated strain MSR-1B, was isolated and characterized. The mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. The growth of strain MSR-1B was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iron-replete conditions. A large chromosomal deletion of approximately 80 kb was identified in strain MSR-1B, which comprised both the entire mamAB and mamDC clusters as well as further putative operons encoding a number of magnetosome-associated proteins. A bacterial artificial chromosome clone partially covering the deleted region was isolated from the genomic library of wild-type M. gryphiswaldense. Sequence analysis of this fragment revealed that all previously identified mam genes were closely linked with genes encoding other magnetosome-associated proteins within less than 35 kb. In addition, this region was remarkably rich in insertion elements and harbored a considerable number of unknown gene families which appeared to be specific for magnetotactic bacteria. Overall, these findings suggest the existence of a putative large magnetosome island in M. gryphiswaldense and other magnetotactic bacteria. PMID:13129949

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

PubMed Central

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

2014-01-01

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

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

DOE PAGES

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

2014-10-31

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

MamO Is a Repurposed Serine Protease that Promotes Magnetite Biomineralization through Direct Transition Metal Binding in Magnetotactic Bacteria

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

Hershey, David M.; Ren, Xuefeng; Melnyk, Ryan A.

2016-03-16

Many living organisms transform inorganic atoms into highly ordered crystalline materials. An elegant example of such biomineralization processes is the production of nano-scale magnetic crystals in magnetotactic bacteria. Previous studies have implicated the involvement of two putative serine proteases, MamE and MamO, during the early stages of magnetite formation in Magnetospirillum magneticum AMB-1. Here, using genetic analysis and X-ray crystallography, we show that MamO has a degenerate active site, rendering it incapable of protease activity. Instead, MamO promotes magnetosome formation through two genetically distinct, noncatalytic activities: activation of MamE-dependent proteolysis of biomineralization factors and direct binding to transition metal ions.more » By solving the structure of the protease domain bound to a metal ion, we identify a surface-exposed di-histidine motif in MamO that contributes to metal binding and show that it is required to initiate biomineralization in vivo. Finally, we find that pseudoproteases are widespread in magnetotactic bacteria and that they have evolved independently in three separate taxa. In conclusion, our results highlight the versatility of protein scaffolds in accommodating new biochemical activities and provide unprecedented insight into the earliest stages of biomineralization.« less

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

PubMed Central

Siqueira, José F.; Rôças, Isabela N.

2013-01-01

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

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil.

PubMed

Al-Sadi, Abdullah M; Al-Oweisi, Fatma A; Edwards, Simon G; Al-Nadabi, Hamed; Al-Fahdi, Ahmed M

2015-07-28

Trichoderma is one of the most common fungi in soil. However, little information is available concerning the diversity of Trichoderma in soil with no previous history of cultivation. This study was conducted to investigate the most common species and the level of genetic relatedness of Trichoderma species from uncultivated soil in relation to cultivated soil and potting media. A total of 24, 15 and 13 Trichoderma isolates were recovered from 84 potting media samples, 45 cultivated soil samples and 65 uncultivated soil samples, respectively. Analysis based on the internal transcribed spacer region of the ribosomal RNA (rRNA) and the translation elongation factor gene (EF1) indicated the presence of 9 Trichoderma species: T. harzianum (16 isolates), T. asperellum (13), T. citrinoviride (9), T. orientalis (3), T. ghanense (3), T. hamatum (3), T. longibrachiatum (2), T. atroviride (2), and T. viride (1). All species were found to occur in potting media samples, while five Trichoderma species were recovered from the cultivated soils and four from the uncultivated soils. AFLP analysis of the 52 Trichoderma isolates produced 52 genotypes and 993 polymorphic loci. Low to moderate levels of genetic diversity were found within populations of Trichoderma species (H = 0.0780 to 0.2208). Analysis of Molecular Variance indicated the presence of very low levels of genetic differentiation (Fst = 0.0002 to 0.0139) among populations of the same Trichoderma species obtained from the potting media, cultivated soil and uncultivated soil. The study provides evidence for occurrence of Trichoderma isolates in soil with no previous history of cultivation. The lack of genetic differentiation among Trichoderma populations from potting media, cultivated soil and uncultivated soil suggests that some factors could have been responsible for moving Trichoderma propagules among the three substrates. The study reports for the first time the presence of 4 Trichoderma species in Oman: T. asperellum, T. ghanense, T. longibrachiatum and T. orientalis.

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

PubMed Central

Knief, Claudia

2015-01-01

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

Axenic culture of a candidate division TM7 bacterium from the human oral cavity and biofilm interactions with other oral bacteria.

PubMed

Soro, Valeria; Dutton, Lindsay C; Sprague, Susan V; Nobbs, Angela H; Ireland, Anthony J; Sandy, Jonathan R; Jepson, Mark A; Micaroni, Massimo; Splatt, Peter R; Dymock, David; Jenkinson, Howard F

2014-10-01

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

NASA Technical Reports Server (NTRS)

Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

1994-01-01

When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

Changes in Soil Organic Carbon and Nitrogen as a Result of Cultivation

DOE Data Explorer

Post, Wilfred M [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mann, L. K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2005-01-01

We assembed and analyzed a data base of soil organic carbon and nitrogen information from over 1100 profiles in order to explore factors related to the changes in storage of soil organic matter resulting from land conversion. The relationship between cultivated and uncultivated organic carbon and nitrogen storage in soils can be described by regression lines with uncultivated storage on the abscissa, and cultivated storage on the ordinate. The slope of the regression lines is less than 1 indicating that the amount of carbon or nitrogen lost is an increasing fraction of the intial amount stored in the soil. Average carbon loss for soils with high initial carbon is 23% for 1-meter depth. Average nitrogen loss for the same depth is 6%. In addition, for soils with very low uncultivated carbon or nitrogen storage, cultivation results in increases in storage. In soils with the same uncultivated carbon contents, profiles with higher C:N ratios lost more carbon than those with low C:N ratios, suggesting that decomposition of organic matter may, in general, be more limited by microbial ability to break carbon bonds than by nitrogen deficiency.

[Anaerobic bacteria isolated from patients with suspected anaerobic infections].

PubMed

Ercis, Serpil; Tunçkanat, Ferda; Hasçelik, Gülşen

2005-10-01

The study involved 394 clinical samples sent to the Clinical Microbiology Laboratory of Hacettepe University Adult Hospital between January 1997 and May 2004 for anaerobic cultivation. Since multiple cultures from the same clinical samples of the same patient were excluded, the study was carried on 367 samples. The anaerobic cultures were performed in anaerobic jar using AnaeroGen kits (Oxoid, Basingstoke, U.K.) or GENbox (bioMérieux, Lyon, France). The isolates were identified by both classical methods and "BBL Crystal System" (Becton Dickinson, U.S.A.). While no growth was detected in 120 (32.7%) of the clinical samples studied, in 144 samples (39.2%) only aerobes, in 28 (7.6%) only anaerobes and in 75 (20.5%) of the samples both aerobes and anaerobes were isolated. The number of the anaerobic isolates was 217 from 103 samples with anaerobic growth. Of these 103 samples 15 showed single bacterial growth whereas in 88 samples multiple bacterial isolates were detected. Anaerobic isolates consisted of 92 Gram negative bacilli (Bacteroides spp. 50, Prevotella spp. 14, Porphyromonas spp. 10, Fusobacterium spp. 7, Tisierella spp. 2, unidentified 9), 57 Gram positive bacilli (Clostridium spp.17, Propionibacterium spp. 16, Lactobacillus spp. 8, Actinomyces spp. 5, Eubacterium spp. 2, Bifidobacterium adolescentis 1, Mobiluncus mulieris 1, unidentified nonspore forming rods 7), 61 Gram positive cocci (anaerobic cocci 44, microaerophilic cocci 17), and 7 Gram negative cocci (Veillonella spp.). In conclusion, in the samples studied with prediagnosis of anaerobic infection, Bacteroides spp. (23%) were the most common bacteria followed by anaerobic Gram positive cocci (20.3%) and Clostridium spp (7.8%).

Survival of gram positive anaerobic cocci on swabs and their isolation from the mouth and vagina.

PubMed Central

Smith, G L; Cumming, C G; Ross, P W

1986-01-01

The survival of Gram positive anaerobic cocci on plain cotton wool and albumin coated swabs held in various transport media was investigated. Results suggested that in most cases Amies', Stuart's and VMGII media do not offer any more protection to the bacteria than storing swabs dry in their containers. A technique was developed for the isolation and identification of Gram positive anaerobic cocci from the mouth and vagina, incorporating bicozamycin in the medium as a selective agent. Few strains were recovered from the oral cavity, but larger numbers were isolated from the vagina. Using a minimum number of antibiotic sensitivity and biochemical tests, including analysis of end products by gas-liquid chromatography, most isolates were identified to species level. PMID:3950035

Moderately halophilic gram-positive cocci from hypersaline environments.

PubMed

Ventosa, A; Ramos-Cormenzana, A; Kocur, M

1983-01-01

38 strains of moderately halophilic Gram-positive, catalase-positive cocci were isolated from saline soils and the ponds of a solar saltern in Alicante (Spain). They were divided into three biochemically distinct groups. On the basis of the characteristics investigated the 25 strains of group I corresponded to Planococcus halophilus; the ten strains of group II were morphologically and biochemically similar to the species Sporosarcina halophila; group III, comprising three strains, differed strikingly from the previous groups in certain biochemical tests. These strains differed from the planococci and micrococci so far described and were tentatively designated as Planococcus sp. The results have shown that moderately halophilic Gram-positive, motile cocci, are frequent inhabitants of hypersaline environments. Copyright © 1983 Gustav Fischer Verlag, Stuttgart/New York. Published by Elsevier GmbH.. All rights reserved.

In vitro activities of sitafloxacin (DU-6859a) and six other fluoroquinolones against 8,796 clinical bacterial isolates.

PubMed

Milatovic, D; Schmitz, F J; Brisse, S; Verhoef, J; Fluit, A C

2000-04-01

The in vitro activities of sitafloxacin, ciprofloxacin, trovafloxacin, levofloxacin, clinafloxacin, gatifloxacin, and moxifloxacin against 5,046 gram-negative bacteria, 3,344 gram-positive cocci, and 406 anaerobes were determined. Sitafloxacin was the most active agent against gram-positive cocci and anaerobes. Against Enterobacteriaceae and nonfermenters, its activity was either equivalent to or better than that of clinafloxacin.

“Altiarchaeales”: Uncultivated Archaea from the Subsurface

PubMed Central

Probst, Alexander J.; Moissl-Eichinger, Christine

2015-01-01

Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami”) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature. PMID:25984733

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.

PubMed

Nobu, Masaru K; Narihiro, Takashi; Rinke, Christian; Kamagata, Yoichi; Tringe, Susannah G; Woyke, Tanja; Liu, Wen-Tso

2015-08-01

Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.

Cultivation of a Synergistetes strain representing a previously uncultivated lineage

PubMed Central

Vartoukian, S R; Palmer, R M; Wade, W G

2010-01-01

Subgingival plaque samples obtained from human subjects with periodontitis, shown to include previously uncultivable members of the phylum Synergistetes, were used to inoculate Cooked Meat Medium (CMM). The presence of Cluster A (uncultivable) Synergistetes was monitored by fluorescent in situ hybridization (FISH) and quantitative PCR (Q-PCR). Cluster A Synergistetes were found to grow in CMM in co-culture with other plaque bacteria and growth was stimulated by the addition of mucin and serum. Plaque samples were also used to inoculate Blood Agar (BA) plates and growth of Cluster A Synergistetes was revealed after anaerobic incubation, by colony hybridization with specific probes. Surface growth on the plates in regions identified by colony hybridization was harvested and used to inoculate fresh plates, thus enriching for Cluster A Synergistetes. Cross-streaks of other plaque bacteria were also used to stimulate Synergistetes growth. In the early passages, no discrete Synergistetes colonies were seen, but after eight passages and the use of cross-streaks of other bacteria present in the enriched community, colonies arose, which consisted solely of Cluster A Synergistetes cells, as determined by 16S rRNA gene PCR and cloning. This is the first report of the successful culture of a member of the uncultivable branch of this phylum. PMID:20074237

Evaluation of the LightCycler Staphylococcus MGRADE Kits on Positive Blood Cultures That Contained Gram-Positive Cocci in Clusters

PubMed Central

Shrestha, Nabin K.; Tuohy, Marion J.; Padmanabhan, Ravindran A.; Hall, Gerri S.; Procop, Gary W.

2005-01-01

We evaluated the Roche LightCycler Staphylococcus MGRADE kits to differentiate between Staphylococcus aureus and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing S. aureus), the assay was 100% sensitive and 98.44% specific for S. aureus and 100% sensitive and specific for coagulase-negative staphylococci. PMID:16333115

Evaluation of the LightCycler Staphylococcus M GRADE kits on positive blood cultures that contained gram-positive cocci in clusters.

PubMed

Shrestha, Nabin K; Tuohy, Marion J; Padmanabhan, Ravindran A; Hall, Gerri S; Procop, Gary W

2005-12-01

We evaluated the Roche LightCycler Staphylococcus M(GRADE) kits to differentiate between Staphylococcus aureus and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing S. aureus), the assay was 100% sensitive and 98.44% specific for S. aureus and 100% sensitive and specific for coagulase-negative staphylococci.

[GEIPC-SEIMC (Study Group for Infections in the Critically Ill Patient of the Spanish Society for Infectious Diseases and Clinical Microbiology) and GTEI-SEMICYUC ( Working Group on Infectious Diseases of the Spanish Society of Intensive Medicine, Critical Care, and Coronary Units) recommendations for antibiotic treatment of gram-positive cocci infections in the critical patient].

PubMed

Astigarraga, P M Olaechea; Montero, J Garnacho; Cerrato, S Grau; Colomo, O Rodríguez; Martínez, M Palomar; Crespo, R Zaragoza; García-Paredes, P Muñoz; Cerdá, E Cerdá; Lerma, F Alvarez

2007-01-01

In recent years, an increment of infections caused by gram-positive cocci has been documented in nosocomial and hospital-acquired-infections. In diverse countries, a rapid development of resistance to common antibiotics against gram-positive cocci has been observed. This situation is exceptional in Spain but our country might be affected in the near future. New antimicrobials active against these multi-drug resistant pathogens are nowadays available. It is essential to improve our current knowledge about pharmacokinetic properties of traditional and new antimicrobials to maximize its effectiveness and to minimize toxicity. These issues are even more important in critically ill patients because inadequate empirical therapy is associated with therapeutic failure and a poor outcome. Experts representing two scientific societies (Grupo de estudio de Infecciones en el Paciente Crítico de la SEIMC and Grupo de trabajo de Enfermedades Infecciosas de la SEMICYUC) have elaborated a consensus document based on the current scientific evidence to summarize recommendations for the treatment of serious infections caused by gram-positive cocci in critically ill patients.

Rapid and reliable identification of Gram-negative bacteria and Gram-positive cocci by deposition of bacteria harvested from blood cultures onto the MALDI-TOF plate.

PubMed

Barnini, Simona; Ghelardi, Emilia; Brucculeri, Veronica; Morici, Paola; Lupetti, Antonella

2015-06-18

Rapid identification of the causative agent(s) of bloodstream infections using the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) methodology can lead to increased empirical antimicrobial therapy appropriateness. Herein, we aimed at establishing an easier and simpler method, further referred to as the direct method, using bacteria harvested by serum separator tubes from positive blood cultures and placed onto the polished steel target plate for rapid identification by MALDI-TOF. The results by the direct method were compared with those obtained by MALDI-TOF on bacteria isolated on solid media. Identification of Gram-negative bacilli was 100 % concordant using the direct method or MALDI-TOF on isolated bacteria (96 % with score > 2.0). These two methods were 90 % concordant on Gram-positive cocci (32 % with score > 2.0). Identification by the SepsiTyper method of Gram-positive cocci gave concordant results with MALDI-TOF on isolated bacteria in 87 % of cases (37 % with score > 2.0). The direct method herein developed allows rapid identification (within 30 min) of Gram-negative bacteria and Gram-positive cocci from positive blood cultures and can be used to rapidly report reliable and accurate results, without requiring skilled personnel or the use of expensive kits.

Regional dust storm modeling for health services: The case of valley fever

NASA Astrophysics Data System (ADS)

Sprigg, William A.; Nickovic, Slobodan; Galgiani, John N.; Pejanovic, Goran; Petkovic, Slavko; Vujadinovic, Mirjam; Vukovic, Ana; Dacic, Milan; DiBiase, Scott; Prasad, Anup; El-Askary, Hesham

2014-09-01

On 5 July 2011, a massive dust storm struck Phoenix, Arizona (USA), raising concerns for increased cases of valley fever (coccidioidomycosis, or, cocci). A quasi-operational experimental airborne dust forecast system predicted the event and provides model output for continuing analysis in collaboration with public health and air quality communities. An objective of this collaboration was to see if a signal in cases of valley fever in the region could be detected and traced to the storm - an American haboob. To better understand the atmospheric life cycle of cocci spores, the DREAM dust model (also herein, NMME-DREAM) was modified to simulate spore emission, transport and deposition. Inexact knowledge of where cocci-causing fungus grows, the low resolution of cocci surveillance and an overall active period for significant dust events complicate analysis of the effect of the 5 July 2011 storm. In the larger context of monthly to annual disease surveillance, valley fever statistics, when compared against PM10 observation networks and modeled airborne dust concentrations, may reveal a likely cause and effect. Details provided by models and satellites fill time and space voids in conventional approaches to air quality and disease surveillance, leading to land-atmosphere modeling and remote sensing that clearly mark a path to advance valley fever epidemiology, surveillance and risk avoidance.

Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium

NASA Astrophysics Data System (ADS)

Freeman, Michael F.; Helf, Maximilian J.; Bhushan, Agneya; Morinaka, Brandon I.; Piel, Jörn

2017-04-01

Uncultivated bacteria represent a massive resource of new enzymes and bioactive metabolites, but such bacteria remain functionally enigmatic. Polytheonamides are potent peptide cytotoxins produced by uncultivated bacteria that exist as symbionts in a marine sponge. Outside glycobiology, polytheonamides represent the most heavily post-translationally modified biomolecules that are derived from amino acids. The biosynthesis of polytheonamides involves up to 50 site-specific modifications to create a membrane-spanning β-helical structure. Here, we provide functional evidence that only seven enzymes are necessary for this process. They iteratively catalyse epimerization, methylation and hydroxylation of diverse amino acids. To reconstitute C-methylation, we employed the rarely used heterologous host Rhizobium leguminosarum to invoke the activities of two cobalamin-dependent C-methyltransferases. We observed 44 of the modifications to systematically unravel the biosynthesis of one of the most densely modified and metabolically obscure ribosome-derived molecules found in nature.

Magnetotactic bacteria form magnetite from a phosphate-rich ferric hydroxide via nanometric ferric (oxyhydr)oxide intermediates.

PubMed

Baumgartner, Jens; Morin, Guillaume; Menguy, Nicolas; Perez Gonzalez, Teresa; Widdrat, Marc; Cosmidis, Julie; Faivre, Damien

2013-09-10

The iron oxide mineral magnetite (Fe3O4) is produced by various organisms to exploit magnetic and mechanical properties. Magnetotactic bacteria have become one of the best model organisms for studying magnetite biomineralization, as their genomes are sequenced and tools are available for their genetic manipulation. However, the chemical route by which magnetite is formed intracellularly within the so-called magnetosomes has remained a matter of debate. Here we used X-ray absorption spectroscopy at cryogenic temperatures and transmission electron microscopic imaging techniques to chemically characterize and spatially resolve the mechanism of biomineralization in those microorganisms. We show that magnetite forms through phase transformation from a highly disordered phosphate-rich ferric hydroxide phase, consistent with prokaryotic ferritins, via transient nanometric ferric (oxyhydr)oxide intermediates within the magnetosome organelle. This pathway remarkably resembles recent results on synthetic magnetite formation and bears a high similarity to suggested mineralization mechanisms in higher organisms.

Oxygen and iron isotope studies of magnetite produced by magnetotactic bacteria

USGS Publications Warehouse

Mandernack, K.W.; Bazylinski, D.A.; Shanks, Wayne C.; Bullen, T.D.

1999-01-01

A series of carefully controlled laboratory studies was carried out to investigate oxygen and iron isotope fractionation during the intracellular production of magnetite (Fe3O4) by two different species of magnetotactic bacteria at temperatures between 4??and 35??C under microaerobic and anaerobic conditions. No detectable fractionation of iron isotopes in the bacterial magnetites was observed. However, oxygen isotope measurements indicated a temperature-dependent fractionation for Fe3O4 and water that is consistent with that observed for Fe3O4 produced extracellularly by thermophilic Fe3+-reducing bacteria. These results contrast with established fractionation curves estimated from either high-temperature experiments or theoretical calculations. With the fractionation curve established in this report, oxygen-18 isotope values of bacterial Fe3O4 may be useful in paleoenvironmental studies for determining the oxygen-18 isotope values of formation waters and for inferring paleotemperatures.

Flagellated Magnetotactic Bacteria as Controlled MRI-trackable Propulsion and Steering Systems for Medical Nanorobots Operating in the Human Microvasculature.

PubMed

Martel, Sylvain; Mohammadi, Mahmood; Felfoul, Ouajdi; Lu, Zhao; Pouponneau, Pierre

2009-04-01

Although nanorobots may play critical roles for many applications in the human body such as targeting tumoral lesions for therapeutic purposes, miniaturization of the power source with an effective onboard controllable propulsion and steering system have prevented the implementation of such mobile robots. Here, we show that the flagellated nanomotors combined with the nanometer-sized magnetosomes of a single Magnetotactic Bacterium (MTB) can be used as an effective integrated propulsion and steering system for devices such as nanorobots designed for targeting locations only accessible through the smallest capillaries in humans while being visible for tracking and monitoring purposes using modern medical imaging modalities such as Magnetic Resonance Imaging (MRI). Through directional and magnetic field intensities, the displacement speeds, directions, and behaviors of swarms of these bacterial actuators can be controlled from an external computer.

Instabilities, rheology and spontaneous flows in magnetotactic bacterial suspensions

NASA Astrophysics Data System (ADS)

Alonso-Matilla, Roberto; Saintillan, David

2017-11-01

Magnetotactic bacteria are motile prokaryotes, mostly present in marine habitats, that synthesize intracellular magnetic membrane-bounded crystals known as magnetosomes. They behave as self-propelled permanent magnetic dipoles that orient and migrate along the geomagnetic field lines of the Earth. In this work, we analyze the macroscopic transport properties of suspensions of such bacteria in microfluidic devices. When placed in an external magnetic field, these microorganisms feel a net magnetic torque which is transmitted to the surrounding fluid, and can give rise to a net unidirectional fluid flow in a planar channel, with a flow rate and direction that can be controlled by adjusting both the magnitude and orientation of the external field. Using a continuum kinetic model, we provide a physical explanation for the onset of these spontaneous flows. We also study the rheological properties and stability of these suspensions in both an applied shear flow and a pressure-driven flow.

Cobalt ferrite nanocrystals: out-performing magnetotactic bacteria.

PubMed

Prozorov, Tanya; Palo, Pierre; Wang, Lijun; Nilsen-Hamilton, Marit; Jones, DeAnna; Orr, Daniel; Mallapragada, Surya K; Narasimhan, Balaji; Canfield, Paul C; Prozorov, Ruslan

2007-10-01

Magnetotactic bacteria produce exquisitely ordered chains of uniform magnetite (Fe(3)O(4)) nanocrystals, and the use of the bacterial mms6 protein allows for the shape-selective synthesis of Fe(3)O(4) nanocrystals. Cobalt ferrite (CoFe(2)O(4)) nanoparticles, on the other hand, are not known to occur in living organisms. Here we report on the use of the recombinant mms6 protein in a templated synthesis of CoFe(2)O(4) nanocrystals in vitro. We have covalently attached the full-length mms6 protein and a synthetic C-terminal domain of mms6 protein to self-assembling polymers in order to template hierarchical CoFe(2)O(4) nanostructures. This new synthesis pathway enables facile room-temperature shape-specific synthesis of complex magnetic crystalline nanomaterials with particle sizes in the range of 40-100 nm that are difficult to produce using conventional techniques.

Functional metagenomic selection of RubisCOs from uncultivated bacteria

USGS Publications Warehouse

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

2016-01-01

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

In Vitro Cultivation of 'Unculturable' Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores.

PubMed

Vartoukian, Sonia R; Adamowska, Aleksandra; Lawlor, Megan; Moazzez, Rebecca; Dewhirst, Floyd E; Wade, William G

2016-01-01

Over a third of oral bacteria are as-yet-uncultivated in-vitro. Siderophores have been previously shown to enable in-vitro growth of previously uncultivated bacteria. The objective of this study was to cultivate novel oral bacteria in siderophore-supplemented culture media. Various compounds with siderophore activity, including pyoverdines-Fe-complex, desferricoprogen and salicylic acid, were found to stimulate the growth of difficult-to-culture strains Prevotella sp. HOT-376 and Fretibacterium fastidiosum. Furthermore, pyrosequencing analysis demonstrated increased proportions of the as-yet-uncultivated phylotypes Dialister sp. HOT-119 and Megasphaera sp. HOT-123 on mixed culture plates supplemented with siderophores. Therefore a culture model was developed, which incorporated 15 μg siderophore (pyoverdines-Fe-complex or desferricoprogen) or 150 μl neat subgingival-plaque suspension into a central well on agar plates that were inoculated with heavily-diluted subgingival-plaque samples from subjects with periodontitis. Colonies showing satellitism were passaged onto fresh plates in co-culture with selected helper strains. Five novel strains, representatives of three previously-uncultivated taxa (Anaerolineae bacterium HOT-439, the first oral taxon from the Chloroflexi phylum to have been cultivated; Bacteroidetes bacterium HOT-365; and Peptostreptococcaceae bacterium HOT-091) were successfully isolated. All novel isolates required helper strains for growth, implying dependence on a biofilm lifestyle. Their characterisation will further our understanding of the human oral microbiome.

Gram-positive rods prevailing in teeth with apical periodontitis undergoing root canal treatment.

PubMed

Chávez de Paz, L E; Molander, A; Dahlén, G

2004-09-01

To identify Gram-positive rods from root canals of teeth with apical periodontitis and to examine their associations with other species. Consecutive root canal samples (RCSs) from 139 teeth undergoing root canal treatment were analyzed prospectively for cultivable microbes. Gram-positive rods in the first RCS submitted after chemo-mechanical preparation were categorised to genus level by selective media and gas-liquid chromatography (GLC), and identified to species level by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Associations between organisms were measured by odds ratios (OR). In the first samples submitted a total of 158 Gram-positive rods, 115 Gram-positive cocci, 26 Gram-negative rods and 9 Gram-negative cocci, were identified. At genus levels Gram-positive rods were classified into: Lactobacillus spp. (38%), Olsenella spp. (18%), Propionibacterium spp. (13%), Actinomyces spp. (12%), Bifidobacterium spp. (13%) and Eubacterium spp. (6%). The most frequent species were Olsenella uli, Lactobacillus paracasei and Propionibacterium propionicum. In subsequent samples taken during treatment, Gram-positive rods were also identified, although the number of strains was considerably reduced. Positive associations were observed between members of the genus lactobacilli and Gram-positive cocci (OR>2). Olsenella uli and Lactobacillus spp. predominated over other Gram-positive rods. A possible association exists between Lactobacillus spp. and Gram-positive cocci in root canals of teeth with apical periodontitis receiving treatment.

Title: Biogenic Magnetite Prevails in Oxic Pelagic Red Clay Core in the South Pacific Gyre

NASA Astrophysics Data System (ADS)

Shimono, T.; Yamazaki, T.

2012-12-01

Magnetotactic bacteria have been observed in wide variety of environments, including soils, freshwater lakes, and marine sediments, since Blakemore (1975) first described in 1975. Magnetotactic bacteria, which most commonly live within the oxic-anoxic transition zone (OATZ) of aquatic environments, produce intracellular crystals of magnetic minerals, specifically magnetite or greigite. It is considered that the magnetite/greigite crystals facilitate the bacteria's search for optimal conditions within the sharp chemical gradients of the OATZ. Petermann and Bleil (1993) reported living magnetotactic bacteria in pelagic and hemipelagic sediments near OATZ in the eastern South Atlantic at water depths to about 3,000 m, but they couldn't find actively swimming magnetotactic bacteria in sediments of deeper water depths. The South Pacific Gyre (SPG) is far from continents and the lowest productivity region on Earth. IODP site U1365 (water depth ~5,700 m) cored pelagic red clay of 75.5 m thick above ~100 Ma basement (except for the chart layer from ~42 to 63.5 m) in the western edge of the SPG. The core mainly consists of iron rich clay. The color is dark reddish and/or dark brown throughout the core. We conducted a paleomagnetic and environmental rock magnetic study of the pelagic clay core. The magnetostratigraphy revealed the top 5 m sediments cover the last 5 My, and sedimentation rate decreases downward from 1.7 to 0.6 m/m.y. Geochemical measurements of pore water indicate that dissolved oxygen was present throughout the core (>50 μM). Thus oxygen penetrates through the entire sediment column to the sediment/basalt interface, and there is no OATZ. Magnetic mineral assemblage of this core is dominated by biogenic magnetite despite no OATZ. First-order reversal curve (FORC) diagrams of all specimens have a narrow central ridge along the Hc axis with very small vertical spread. This indicates very weak magnetostatic interaction (Roberts et al., 2000), and is the characteristic of biogenic magnetite (Egli et al., 2010; Roberts et al., 2011). Presence of biogenic magnetite was confirmed by TEM observation. Occurrence of biogenic magnetite was reported also in pelagic red clay of the North Pacific with TEM observations (Yamazaki and Ioka, 1997), and these samples also display the characteristic FORC diagrams. These observations suggest that biogenic magnetites commonly occur in oxic pelagic red clay without OATZ.

Gram-positive, motile, cluster-forming cocci as a cause of urinary infection

PubMed Central

Virtanen, S.

1974-01-01

One hundred and thirteen strains of motile, Gram-positive, catalase-positive, cluster-forming cocci were isolated from patients with urinary infection attending a private surgery. They constituted 1% of the total 11 302 positive cultures. The biochemical characteristics and the drug sensitivities of the strains are described. The significance of motility for organisms which cause urinary infections is pointed out. At the present time the organisms isolated are orphans in the controversial classification of staphylococci and micrococci. Images PMID:4852184

Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells.

PubMed

Chang, Ho-Won; Sung, Youlboong; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Kim, Min-Soo; Jeon, Che Ok; Bae, Jin-Woo

2008-08-15

A crucial problem in the use of previously developed genome-probing microarrays (GPM) has been the inability to use uncultivated bacterial genomes to take advantage of the high sensitivity and specificity of GPM in microbial detection and monitoring. We show here a method, digital multiple displacement amplification (MDA), to amplify and analyze various genomes obtained from single uncultivated bacterial cells. We used 15 genomes from key microbes involved in dichloromethane (DCM)-dechlorinating enrichment as microarray probes to uncover the bacterial population dynamics of samples without PCR amplification. Genomic DNA amplified from single cells originating from uncultured bacteria with 80.3-99.4% similarity to 16S rRNA genes of cultivated bacteria. The digital MDA-GPM method successfully monitored the dynamics of DCM-dechlorinating communities from different phases of enrichment status. Without a priori knowledge of microbial diversity, the digital MDA-GPM method could be designed to monitor most microbial populations in a given environmental sample.

Estimating growth rates of uncultivated clades of archaea and bacteria in marine sediments

NASA Astrophysics Data System (ADS)

Lloyd, K. G.

2016-12-01

The vast majority of microbes present in marine sediments have never been cultivated in laboratory conditions. It is therefore difficult to estimate the growth rates of these organisms in situ. Quantitative PCR (qPCR) and 16S rRNA gene libraries from sediments below 10 cm show very little change in abundance of these organisms with depth or with redox conditions. Therefore, we hypothesized that uncultivated clades of bacteria and archaea that are ubiquitous in marine sediments, actually grow in the upper 10 cm of marine sediments. We collected sediment cores from the White Oak River estuary, sectioned them in 1 cm intervals, and examined the changes in abundance of uncultivated microbes with depth using 16S rRNA gene libraries and qPCR. We found that some of the key clades associated with the deep subsurface microbiome, such as Bathyarchaeota and MBG-D, increase in abundance with depth, demonstrating extremely slow growth in these shallow subsurface sediments.

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

Detection of the free-living forms of sulfide-oxidizing gill endosymbionts in the lucinid habitat (Thalassia testudinum environment).

PubMed

Gros, Olivier; Liberge, Martine; Heddi, Abdelaziz; Khatchadourian, Chaqué; Felbeck, Horst

2003-10-01

Target DNA from the uncultivable Codakia orbicularis endosymbiont was PCR amplified from sea-grass sediment. To confirm that such amplifications originated from intact bacterial cells rather than free DNA, whole-cell hybridization (fluorescence in situ hybridization technique) with the specific probe Symco2 was performed along with experimental infection of aposymbiotic juveniles placed in contact with the same sediment. Taken together, the data demonstrate that the sulfide-oxidizing gill endosymbiont of Codakia orbicularis is present in the environment as a free-living uncultivable form.

Differential staining of bacteria: gram stain.

PubMed

Moyes, Rita B; Reynolds, Jackie; Breakwell, Donald P

2009-11-01

In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram-positive cocci, Gram-negative cocci, Gram-positive rods, and Gram-negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures. (c) 2009 by John Wiley & Sons, Inc.

Chains of magnetite crystals in the meteorite ALH84001: Evidence of biological origin

PubMed Central

Friedmann, E. Imre; Wierzchos, Jacek; Ascaso, Carmen; Winklhofer, Michael

2001-01-01

The presence of magnetite crystal chains, considered missing evidence for the biological origin of magnetite in ALH84001 [Thomas-Keprta, K. L., Bazylinski, D. A., Kirschvink, J. L., Clemett, S. J., McKay, D. S., Wentworth, S. J., Vali, H., Gibson, E. K., Jr., & Romanek, C. S. (2000) Geochim. Cosmochim. Acta 64, 4049–4081], is demonstrated by high-power stereo backscattered scanning electron microscopy. Five characteristics of such chains (uniform crystal size and shape within chains, gaps between crystals, orientation of elongated crystals along the chain axis, flexibility of chains, and a halo that is a possible remnant of a membrane around chains), observed or inferred to be present in magnetotactic bacteria but incompatible with a nonbiological origin, are shown to be present. Although it is unlikely that magnetotactic bacteria were ever alive in ALH84001, decomposed remains of such organisms could have been deposited in cracks in the rock while it was still on the surface on Mars. PMID:11226212

Gram-positive, catalase-positive cocci from dry cured Iberian ham and their enterotoxigenic potential.

PubMed Central

Rodríguez, M; Núñez, F; Córdoba, J J; Bermúdez, E; Asensio, M A

1996-01-01

Iberian ham is an uncooked, cured meat product ripened under natural uncontrolled conditions for 18 to 24 months. Gram-positive, catalase-positive cocci are the main microbial population in Iberian ham for most of the ripening time. Since some of these organisms are able to produce enterotoxins, adequate characterization and toxicological study are needed. For this, 1,327 gram-positive, catalase-positive cocci, isolated from Iberian hams at different stages and locations, were characterized by physiological and biochemical tests. Selected isolates were further characterized by guanine-cytosine (G+C) content and restriction enzyme analysis of genes coding for 16S rRNA. The toxigenic potential of these organisms was tested with specific DNA gene probes for staphylococcal enterotoxins A, B, C, and D and confirmed by semiquantitative sandwich enzyme immunoassay. The majority of the isolates were identified as Staphylococcus spp. and Micrococcus spp. Non-identified gram-positive, catalase-positive cocci which were moderately halophilic and showed a 42 to 52% G+C content were detected. A great variety of staphylococcal strains were found within the different species at any sampling time. Two strains of Staphylococcus xylosus, one Staphylococcus cohnii strain, and four of the non-identified organisms with 42 to 52% G+C contents hybridized with some of the DNA probes for C and D staphylococcal enterotoxin genes. S. xylosus hybridizing with C-enterotoxin probe reacted with both C and D enterotoxins in the immunological test. In addition, enterotoxin D was confirmed in the nonidentified strains. Some toxigenic organisms were isolated from the final product, posing a health hazard for the consumer. PMID:8787389

Agreement Between Deoxyribonucleic Acid Base Composition and Taxometric Classification of Gram-Positive Cocci1

PubMed Central

Silvestri, L. G.; Hill, L. R.

1965-01-01

Silvestri, L. G. (Università Statale, Milan, Italy), and L. R. Hill. Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci. J. Bacteriol. 90:136–140. 1965.—It had been previously proposed, from taxometric analyses, that gram-positive, catalase-positive cocci be divided into two subgroups. Thirteen strains, representative of both subgroups, were examined for deoxyribonucleic acid (DNA) base composition, determined from melting temperatures. Per cent GC (guanine + cytosine/total bases) values fell into two groups: 30.8 to 36.5% GC and 69 to 75% GC. Strains with low per cent GC values belonged to the Staphylococcus aureus–S. saprophyticus–S. lactis taxometric subgroups, and those with high per cent GC values belonged to the S. roseus–S. afermentans subgroup. The hypothetical nature of any classification is emphasized, and, in the present work, the hypothesis derived from taxometric analyses of division into two subgroups is confirmed by the study of DNA base ratios. The two subgroups correspond, respectively, to the genera Staphylococcus and Micrococcus. PMID:16562008

Detection of the Free-Living Forms of Sulfide-Oxidizing Gill Endosymbionts in the Lucinid Habitat (Thalassia testudinum Environment)

PubMed Central

Gros, Olivier; Liberge, Martine; Heddi, Abdelaziz; Khatchadourian, Chaqué; Felbeck, Horst

2003-01-01

Target DNA from the uncultivable Codakia orbicularis endosymbiont was PCR amplified from sea-grass sediment. To confirm that such amplifications originated from intact bacterial cells rather than free DNA, whole-cell hybridization (fluorescence in situ hybridization technique) with the specific probe Symco2 was performed along with experimental infection of aposymbiotic juveniles placed in contact with the same sediment. Taken together, the data demonstrate that the sulfide-oxidizing gill endosymbiont of Codakia orbicularis is present in the environment as a free-living uncultivable form. PMID:14532089

Efficacy of direct Gram stain in differentiating staphylococci from streptococci in blood cultures positive for gram-positive cocci.

PubMed Central

Agger, W A; Maki, D G

1978-01-01

A preponderance of clusters seen on direct Gram stain of blood cultures positive for gram-positive cocci was 98% sensitive and 100% specific for identification of staphylococcal species or of Peptococcus. A preponderance of chains, pairs, or both was 100% sensitive and 98% specific for identifying streptococci. Further presumptive identification of either staphylococci or streptococci based on microscopic morphology was unreliable. The direct Gram stain is highly reliable for differentiating staphylococci from streptococci and should be of considerable value to clinicians selecting initial antimicrobial therapy. PMID:75888

Adsorption-desorption reactions of selenium (VI) in tropical cultivated and uncultivated soils under Cerrado biome.

PubMed

Lessa, J H L; Araujo, A M; Silva, G N T; Guilherme, L R G; Lopes, G

2016-12-01

Soil management may affect selenium (Se) adsorption capacity. This study investigated adsorption and desorption of Se (VI) in selected Brazilian soils from the Cerrado biome, an area of ever increasing importance for agriculture expansion in Brazil. Soil samples were collected from cultivated and uncultivated soils, comprising clayed and sandy soils. Following chemical and mineralogical characterization, soil samples were subjected to Se adsorption and desorption tests. Adsorption was evaluated after a 72-h reaction with increasing concentrations of Se (0-2000 μg L -1 ) added as Na 2 SeO 4 in a NaCl electrolyte solution (pH 5.5; ionic strength 15 mmol L -1 ). Desorption, as well as distribution coefficients (K d ) for selenate were also assessed. Soil management affected Se adsorption capacity, i.e., Se adsorbed amounts were higher for uncultivated soils, when compared to cultivated ones. Such results were also supported by data of K d and maximum adsorption capacity of Se. This fact was attributed mainly to the presence of greater amounts of competing anions, especially phosphate, in cultivated soils, due to fertilizer application. Phosphate may compete with selenate for adsorption sites, decreasing Se retention. For the same group of soils (cultivated and uncultivated), Se adsorption was greater in the clayed soils compared to sandy ones. Our results support the idea that adding Se (VI) to the soil is a good strategy to increase Se levels in food crops (agronomic biofortification), especially when crops are grown in soils that have been cultivated over the time due to their low Se adsorption capacity (high Se availability). Copyright © 2016 Elsevier Ltd. All rights reserved.

Micrometric periodic assembly of magnetotactic bacteria and magnetic nanoparticles using audio tapes

NASA Astrophysics Data System (ADS)

Godoy, M.; Moreno, A. J.; Jorge, G. A.; Ferrari, H. J.; Antonel, P. S.; Mietta, J. L.; Ruiz, M.; Negri, R. M.; Pettinari, M. J.; Bekeris, V.

2012-02-01

We report micrometric periodic assembly of live and dead magnetotactic bacteria, Magnetospirillum magneticum AMB-1, which synthesize chains of magnetic nanoparticles inside their bodies, and of superparamagnetic Fe3O4 and ferromagnetic CoFe2O4 nanoparticles in aqueous suspensions using periodically magnetized audio tapes. The distribution of the stray magnetic field at the surface of the tapes was determined analytically and experimentally by magneto-optic imaging. Calculations showed that the magnetic field close to the tape surface was of the order of 100 mT, and the magnetic field gradient was larger than 1 T mm-1. Drops of aqueous solutions were deposited on the tapes, and bacteria and particles were trapped at locations where magnetic energy is minimized, as observed using conventional optical microscopy. Suspensions of M. magneticum AMB-1 treated with formaldehyde and kanamycin were studied, and patterns of trapped dead bacteria indicated that magnetic forces dominate over self-propelling forces in these experiments, in accordance with calculated values. The behavior of the different types of samples is discussed.

Alterations in soil microbial community composition and biomass following agricultural land use change.

PubMed

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-04

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Alterations in soil microbial community composition and biomass following agricultural land use change

NASA Astrophysics Data System (ADS)

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-01

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Phenotypic and genotypic diversity of dominant lactic acid bacteria isolated from traditional yoghurts produced by tribes of Iran

PubMed Central

RoushanZadeh, S; Eskandari, M. H.; Shekarforoush, S. S.; Hosseini, A

2014-01-01

Morphological, biochemical and molecular characteristics were studied to identify dominant lactic acid bacteria (LAB), isolated from traditional yoghurts produced by tribes of Iran. From 60 yoghurt samples, a total of 137 LAB isolates were determined, in which 66 and 71 were identified as lactic acid cocci and bacilli, respectively. Biochemical tests showed the occurrence of 9.76% mesophilic homofermentative, 10.98% mesophilic hetrofermentative, 26.83% thermophilic homofermentative and 47.56% mesophilic homofermentative cocci. As for lactic acid bacilli, mesophilic facultative hetrofermentative (26%); thermophilic obligate homofermentative (56%); mesophilic obligate hetrofermentative (18%) were found. Genetically the presence of the following species were verified: E. faecium; E. faecalis; E. durans; L. lactis subsp. lactis; St. thermophilus; Lb. delbruecki subsp. bulgaricus; Lb. brevis; Lb. diolivorans; Lb. helveticus; Lb. jensenii; Lb. plantarum. 9% of the Lactobacillus isolates showed incompatible results between phenotypic and genotypic characteristics. From the cocci isolates, 38.46% showed identical results between phylogenetic characteristics. The current study constitutes the first step in the designing process of LAB starter cultures, to protect the typical organoleptic characteristics of traditional yoghurt. The results could also be used to introduce new starter cultures for commercial use. PMID:27175129

Bacteria and fungi on the surface and within noninflamed hair follicles of skin biopsy specimens from horses with healthy skin or inflammatory dermatoses.

PubMed

Cook, Christopher P; Scott, Danny W; Erb, Hollis N; Miller, William H

2005-02-01

A retrospective study using light microscopy was performed to assess the prevalence of surface and follicular bacteria and fungi in skin biopsy specimens from 247 horses with inflammatory dermatoses and from 27 horses with healthy skin. Cocci were found on the surface of specimens from 23% (95% confidence interval 18%, 29%) and 7% (95% confidence interval, 0%, 19%), respectively, of horses with skin disease and horses with healthy skin. Of the nine dermatoses with at least 10 cases in our series of horses, bacterial folliculitis had a higher prevalence of surface bacteria (57%; 95% confidence interval 34%, 81%) than the other eight (which all had a prevalence < 30%). There was a significant association between the prevalence of surface cocci and the extent of epidermal hyperkeratosis. Cocci were found in the keratin of noninflamed hair follicles in only 2% of the horses with skin disease, and in none of the horses with healthy skin. Fungal poroconidia were found on the surface of 4% of the horses with skin disease, and on none of the horses with healthy skin. Yeasts were not found.

Mass-dependent and -independent fractionation of Fe isotopes in magnetotactic bacteria

NASA Astrophysics Data System (ADS)

Amor, M.; Busigny, V.; Louvat, P.; Gelabert, A.; Cartigny, P.; Durand-Dubief, M.; Ona-Nguema, G.; Alphandéry, E.; Chebbi, I.; Guyot, F. J.

2016-12-01

Magnetotactic bacteria (MTB) perform biomineralization of intracellular magnetite (Fe3O4) nanoparticles. Although they may be among the oldest microorganisms capable of biomineralization on Earth, identification of their activity in the geological record remains poorly resolved because of the lack of reliable signatures. Here, we determined Fe isotope fractionation by the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1 to better understand Fe cycling in MTB and provide new signatures of the contribution of MTB to iron geochemistry. AMB-1 strain was cultivated with either Fe(III)-quinate or Fe(II)-ascorbate as Fe sources. Iron isotope composition of Fe sources, bacterial growth media after AMB-1 cultures, bacterial lysates (corresponding to AMB-1 cells devoid of magnetite) and magnetite samples were analyzed by MC-ICP-MS after column chromatography. In the two culture conditions, growth media after AMB-1 cultures were enriched in light Fe isotopes relative to Fe sources. Two distinct bacterial Fe reservoirs were characterized in AMB-1: (1) magnetite enriched in the light Fe isotopes by 1.5 to 2.5‰ in δ56Fe relative to Fe sources, and (2) lysate enriched in the heavy Fe isotopes by 0.3 to 0.8‰ relative to Fe sources. More importantly, mass-independent fractionations in odd (57Fe) but not in even isotopes (54Fe, 56Fe and 58Fe) were observed for the first time, highlighting a magnetic isotope effect. Magnetite samples were significantly enriched in 57Fe by 0.23‰ relative to 54Fe, 56Fe and 58Fe. Based on our results, we propose a model for Fe cycling and magnetite biomineralization in AMB-1, and propose to use this specific mass-independent signature of Fe isotopes to evaluate the contribution of MTB to the iron biogeochemistry of recent and ancient environmental samples.

Evidence for Biogenic Iron in Ediacaran Limestones of the Yenisei Ridge Vorogovka Series (South-Western Framing of the Siberian Craton).

NASA Astrophysics Data System (ADS)

Vinogradov, E.; Kosareva, L.; Metelkin, D. V.; Vishnevskaya, I.

2017-12-01

The composition and origin of magnetic minerals are used for reconstructing paleogeography and changes in paleoenvironments. Ediacaran limestones of the Vorogovka Series were studied in the Yenisei Ridge. Rock magnetism of the upper part of the Vorogovka Series completely depends on terrigenous admixture of iron. Non-carbonate residue consists of quartz, plagioclase, muscovite, Fe-Mg chlorite, smectite and pyrite. A prominent positive correlation is observed between the Fe content (1550…9350 ppm) and the amount of insoluble residue. Magnetization of the lower part of Vorogovka Series is due to authigenic iron. There are several indirect indications of the presence of magnetotactic bacteria and seaweed remains in these limestones. While Fe content is high (1200…8330 ppm), Fe-hydroxides, pyrite and other minerals indicating secondary transformations were not detected. Thus, iron was included in the carbonate material during sedimentation. There is no correlation between iron content and the amount of insoluble residue, which indicates that iron could not have been taken from terrigenous admixture. Study of the dependence of magnetic susceptibility from temperature in inert atmosphere (argon) revealed magnetic minerals with demagnetization temperatures of 320°C and 580°C. The former may correspond to greigite (Curie Temperature 307°C) or hexagonal pyrrhotine (325°C). The latter indicates magnetite (Curie Temperature 586°C) which may be authigenic or newly formed during the experiment. Both magnetite and greigite, are major biogenic minerals produced by magnetotactic bacteria. The main environment of modern magnetotactic bacteria is microaerophilic habitat. Therefore, their abundant presence in the Ediacaran sediments is quite natural. All of these are preliminary conclusions until bacteria can be visualized by electron microscopy, which is an ongoing. The work was supported by the Ministry of Education and Science of Russia 5.2324.2017/4.6 and the RFBR 15-05-01428.

Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle

PubMed Central

Kato, Shingo; Sakai, Sanae; Hirai, Miho; Tasumi, Eiji; Nishizawa, Manabu; Suzuki, Katsuhiko; Takai, Ken

2018-01-01

Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment. PMID:29459499

[Production of antibacterial substances by resident corynebacteria isolated from human skin].

PubMed

Kwaszewska, Anna; Szewczyk, Eligia M

2007-01-01

Coryneform bacteria, especially lipophilic species, form stable but not dominant population on a human skin. This position is probably controlled by secretion of bacteriocin-like substances, which act directly on coexisting bacteria. Among 118 investigated corynebacteria belonging to seven species/taxa and isolated from human skin, 90% possessed an ability to produce such substances. The spectrum of their activity was restricted to killing gram-positive bacteria, but along with corynebacteria it also covered cocci, with Staphylococcus aureus in this group. This feature was revealed better on low pH media (pH 5.6) and media with 1.5% NaCl for cocci, but on pH 7,4 for corynebacteria.

Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

PubMed

Nunoura, Takuro; Hirayama, Hisako; Takami, Hideto; Oida, Hanako; Nishi, Shinro; Shimamura, Shigeru; Suzuki, Yohey; Inagaki, Fumio; Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

2005-12-01

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

Use of Enzyme Tests in Characterization and Identification of Aerobic and Facultatively Anaerobic Gram-Positive Cocci

PubMed Central

Bascomb, Shoshana; Manafi, Mammad

1998-01-01

The contribution of enzyme tests to the accurate and rapid routine identification of gram-positive cocci is introduced. The current taxonomy of the genera of aerobic and facultatively anaerobic cocci based on genotypic and phenotypic characterization is reviewed. The clinical and economic importance of members of these taxa is briefly summarized. Tables summarizing test schemes and kits available for the identification of staphylococci, enterococci, and streptococci on the basis of general requirements, number of tests, number of taxa, test classes, and completion times are discussed. Enzyme tests included in each scheme are compared on the basis of their synthetic moiety. The current understanding of the activity of enzymes important for classification and identification of the major groups, methods of testing, and relevance to the ease and speed of identification are reviewed. Publications describing the use of different identification kits are listed, and overall identification successes and problems are discussed. The relationships between the results of conventional biochemical and rapid enzyme tests are described and considered. The use of synthetic substrates for the detection of glycosidases and peptidases is reviewed, and the advantages of fluorogenic synthetic moieties are discussed. The relevance of enzyme tests to accurate and meaningful rapid routine identification is discussed. PMID:9564566

Antibiogram pattern of oral microflora in periodontic children of age group 6 to 12 years: a clinicomicrobiological study.

PubMed

Fysal, N; Jose, Santhosh; Kulshrestha, Reena; Arora, Dimple; Hafiz, Ka Abdul; Vasudevan, Sanjay

2013-07-01

The study was carried out to see the diversity of oral microflora and its antibiotic sensitivity test in children of age group 6 to 12 years was carried. Total 50 patients of age group 6 to 12 years were analyzed for their oral microflora and then checked for the antibiotic susceptibility test. The samples that were collected were incubated at 37°C for 48 hours. Once dispersed samples were taken and Gram staining was done, also they were spread on to a number of freshly prepared agar plates and incubated to allow cells to form microbial colony. The result showed microflora common in all types, Gram-positive facultative anaerobic rods and cocci. In normal children Gram-positive facultative anaerobic and fermenting cocci were predominant where as in children with caries growth of microbiota that were Gram-negative and positive, capnophilic, motile and anaerobic rods and cocci belonging to members of genera S. mutans and A. actinomycetemcomitans was seen. By the present study it has been concluded that the number of bacteria determined by microscopic counts was twice as high in caries patients as in healthy sites, and also recommended that amoxicillin, ampicillin and amikacin are the most effective antibacterial drugs for the treatment of dental caries.

Automated Interpretation of Blood Culture Gram Stains by Use of a Deep Convolutional Neural Network.

PubMed

Smith, Kenneth P; Kang, Anthony D; Kirby, James E

2018-03-01

Microscopic interpretation of stained smears is one of the most operator-dependent and time-intensive activities in the clinical microbiology laboratory. Here, we investigated application of an automated image acquisition and convolutional neural network (CNN)-based approach for automated Gram stain classification. Using an automated microscopy platform, uncoverslipped slides were scanned with a 40× dry objective, generating images of sufficient resolution for interpretation. We collected 25,488 images from positive blood culture Gram stains prepared during routine clinical workup. These images were used to generate 100,213 crops containing Gram-positive cocci in clusters, Gram-positive cocci in chains/pairs, Gram-negative rods, or background (no cells). These categories were targeted for proof-of-concept development as they are associated with the majority of bloodstream infections. Our CNN model achieved a classification accuracy of 94.9% on a test set of image crops. Receiver operating characteristic (ROC) curve analysis indicated a robust ability to differentiate between categories with an area under the curve of >0.98 for each. After training and validation, we applied the classification algorithm to new images collected from 189 whole slides without human intervention. Sensitivity and specificity were 98.4% and 75.0% for Gram-positive cocci in chains and pairs, 93.2% and 97.2% for Gram-positive cocci in clusters, and 96.3% and 98.1% for Gram-negative rods. Taken together, our data support a proof of concept for a fully automated classification methodology for blood-culture Gram stains. Importantly, the algorithm was highly adept at identifying image crops with organisms and could be used to present prescreened, classified crops to technologists to accelerate smear review. This concept could potentially be extended to all Gram stain interpretive activities in the clinical laboratory. Copyright © 2018 American Society for Microbiology.

A new rapid method for direct antimicrobial susceptibility testing of bacteria from positive blood cultures.

PubMed

Barnini, Simona; Brucculeri, Veronica; Morici, Paola; Ghelardi, Emilia; Florio, Walter; Lupetti, Antonella

2016-08-12

Rapid identification and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections can lead to prompt appropriate antimicrobial therapy. To shorten species identification, in this study bacteria were recovered from monomicrobial blood cultures by serum separator tubes and spotted onto the target plate for direct MALDI-TOF MS identification. Proper antibiotics were selected for direct AST based on species identification. In order to obtain rapid AST results, bacteria were recovered from positive blood cultures by two different protocols: by serum separator tubes (further referred to as PR1), or after a short-term subculture in liquid medium (further referred to as PR2). The results were compared with those obtained by the method currently used in our laboratory consisting in identification by MALDI-TOF and AST by Vitek 2 or Sensititre on isolated colonies. The direct MALDI-TOF method concordantly identified with the current method 97.5 % of the Gram-negative bacteria and 96.1 % of the Gram-positive cocci contained in monomicrobial blood cultures. The direct AST by PR1 and PR2 for all isolate/antimicrobial agent combinations was concordant/correct with the current method for 87.8 and 90.5 % of Gram-negative bacteria and for 93.1 and 93.8 % of Gram-positive cocci, respectively. In particular, 100 % categorical agreement was found with levofloxacin for Enterobacteriaceae by both PR1 and PR2, and 99.0 and 100 % categorical agreement was observed with linezolid for Gram-positive cocci by PR1 and PR2, respectively. There was no significant difference in accuracy between PR1 and PR2 for Gram-negative bacteria and Gram-positive cocci. This newly described method seems promising for providing accurate AST results. Most importantly, these results would be available in a few hours from blood culture positivity, which would help clinicians to promptly confirm or streamline an effective antibiotic therapy in patients with bloodstream infections.

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

PubMed

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

2007-03-20

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

Rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism.

PubMed

Staniland, Sarah; Ward, Bruce; Harrison, Andrew; van der Laan, Gerrit; Telling, Neil

2007-12-04

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-time in vivo study of Magnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process.

Covalent binding of nanoliposomes to the surface of magnetotactic bacteria for the synthesis of self-propelled therapeutic agents.

PubMed

Taherkhani, Samira; Mohammadi, Mahmood; Daoud, Jamal; Martel, Sylvain; Tabrizian, Maryam

2014-05-27

The targeted and effective delivery of therapeutic agents remains an unmet goal in the field of controlled release systems. Magnetococcus marinus MC-1 magnetotactic bacteria (MTB) are investigated as potential therapeutic carriers. By combining directional magnetotaxis-microaerophilic control of these self-propelled agents, a larger amount of therapeutics can be delivered surpassing the diffusion limits of large drug molecules toward hard-to-treat hypoxic regions in solid tumors. The potential benefits of these carriers emphasize the need to develop an adequate method to attach therapeutic cargos, such as drug-loaded nanoliposomes, without substantially affecting the cell's ability to act as delivery agents. In this study, we report on a strategy for the attachment of liposomes to MTB (MTB-LP) through carbodiimide chemistry. The attachment efficacy, motility, and magnetic response of the MTB-LP were investigated. Results confirm that a substantial number of nanoliposomes (∼70) are efficiently linked with MTB without compromising functionality and motility. Cytotoxicity assays using three different cell types (J774, NIH/3T3, and Colo205) reveal that liposomal attachments to MTB formulation improve the biocompatibility of MTB, whereas attachment does not interfere with liposomal uptake.

Yield cultivation of magnetotactic bacteria and magnetosomes: A review.

PubMed

Ali, Imran; Peng, Changsheng; Khan, Zahid M; Naz, Iffat

2017-08-01

Magnetotactic bacteria (MTB) have started to be employed for the biosynthesis of magnetic nanoparticles, due to the rapidly increasing demand for nanoparticles in biomedical, biotechnology and environmental protection. MBT are the group of prokaryotes that have the ability to produce bio-magnetic minerals or bio-magnetic crystals of either magnetite (Fe 3 O 4 ) or greigite (Fe 3 S 4 ) in numerous shapes and size ranges, known as magnetosomes (MS). MS compel MTB to respond to the applied external magnetic field. However, it is extremely difficult to grow MTB and produce high yield of MS under artificial environmental conditions, thus creating a major hurdle to relocate MTB technology from laboratory scale to industrial or commercial level. Therefore, to best of our knowledge this review is the first attempt to highlight existing research developments about the laboratory scale and mass production of MS by MTB. Moreover, the optimum culture media and environmental conditions used for the cultivation of MTB were also considered. Finally, future research is encouraged for the improvement of MS yield which will result in the development of advanced nanotechnology/magnetotechnology. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-cell analysis of uncultured magnetotactic bacteria via fluorescence-coupled electron microscopy approach

NASA Astrophysics Data System (ADS)

LI, J.; Zhang, H.; Liu, P.; Menguy, N.; Pan, Y.

2017-12-01

Magnetotactic bacteria (MTB) are phylogenetically diverse and can biomineralize magnetic nanocrystals of magnetite or greigite in intracellular structures termed magnetosomes. Their remains within sediments or sedimentary rocks, i.e. magnetofossils, have been used to retrieve paleomagnetic and paleoenvironmental information of deposition time, as well as to trace the origin and evolution of life on Earth and even perhaps Mars. A precise identification of magnetofossils heavily depends on our knowledge of phylogenetic diversity and magnetosomal biomineralization within natural MTB. In this paper, we will present a novel method which can rapidly characterize both the phylogenetic and biomineralogical properties of uncultured MTB at the single-cell level by coupling fluorescence and electron microscopy. Using this method, we have successfully identified several uncultured MTB strains from natural environments in China. These MTB are phylogenetically affiliated with the Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria and Nitrospirae phylum, and form octahedral, cuboctahedral, prismatic, tooth-like and bullet-shaped magnetite magnetosomes. A corresponding analysis of magnetosome morphology and bacterial phylogenetics on each MTB strain has shown a species/strain-specific magnetosome biomineralization. The new method is not only promising for better understanding the correlation between magnetosome mineral habits and MTB phylogenies, but also crucial for unambiguously identifying magnetofossils.

Seasonal changes in the vertical distribution of two types of multicellular magnetotactic prokaryotes in the sediment of Lake Yuehu, China.

PubMed

Liu, Jia; Zhang, Wenyan; Du, Haijian; Leng, Xiaoyun; Li, Jin-Hua; Pan, Hongmiao; Xu, Jianhong; Wu, Long-Fei; Xiao, Tian

2018-04-24

There are two genetically distinct morphological types of multicellular magnetotactic prokaryotes (MMPs) in the intertidal zone of Lake Yuehu (China): ellipsoidal MMPs (eMMPs) and spherical MMPs (sMMPs). We studied the vertical distribution of both types of MMPs in the sediment at Lake Yuehu during 1 year. Both types of MMPs were observed at sediment depths ranging from 1 to 34 cm, depending on the seasons. The eMMPs distributed at depths of 2-34 cm during spring, 1-11 cm during summer, 2-21 cm during autumn and 9-32 cm during winter. The eMMP species Candidatus Magnetananas rongchenensis, with magnetite magnetosomes, dominated at all distribution depths. These results suggested that Ca. M. rongchenensis migrated vertically during four seasons. The vertical profiles of oxidation-reduction potential (ORP) in Lake Yuehu changed seasonally, and these changes coincided with the seasonal distribution of MMPs, suggesting that the ORP affected the vertical distribution of MMPs. In addition, high concentrations of ammonium and silicate were associated with low abundances of MMPs. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Magnetotactic bacteria on Earth and on Mars.

PubMed

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

2003-01-01

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

Magnetotactic bacteria on Earth and on Mars

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Cytotoxicity and genotoxicity of bacterial magnetosomes against human retinal pigment epithelium cells

NASA Astrophysics Data System (ADS)

Qi, Lei; Lv, Xiujuan; Zhang, Tongwei; Jia, Peina; Yan, Ruiying; Li, Shuli; Zou, Ruitao; Xue, Yuhua; Dai, Liming

2016-06-01

A variety of nanomaterials have been developed for ocular diseases. The ability of these nanomaterials to pass through the blood-ocular barrier and their biocompatibility are essential characteristics that must be considered. Bacterial magnetosomes (BMs) are a type of biogenic magnetic nanomaterials synthesized by magnetotactic bacteria. Due to their unique biomolecular membrane shell and narrow size distribution of approximately 30 nm, BMs can pass through the blood-brain barrier. The similarity of the blood-ocular barrier to the blood-brain barrier suggests that BMs have great potential as treatments for ocular diseases. In this work, BMs were isolated from magnetotactic bacteria and evaluated in various cytotoxicity and genotoxicity studies in human retinal pigment epithelium (ARPE-19) cells. The BMs entered ARPE-19 cells by endocytosis after a 6-h incubation and displayed much lower cytotoxicity than chemically synthesized magnetic nanoparticles (MNPs). MNPs exhibited significantly higher genotoxicity than BMs and promoted the expression of Bax (the programmed cell death acceleration protein) and the induction of greater cell necrosis. In BM-treated cells, apoptosis tended to be suppressed via increased expression of the Bcl-2 protein. In conclusion, BMs display excellent biocompatibility and potential for use in the treatment of ocular diseases.

Light effects on the multicellular magnetotactic prokaryote 'Candidatus Magnetoglobus multicellularis' are cancelled by radiofrequency fields: the involvement of radical pair mechanisms.

PubMed

de Melo, Roger Duarte; Acosta-Avalos, Daniel

2017-02-01

'Candidatus Magnetoglobus multicellularis' is the most studied multicellular magnetotactic prokaryote. It presents a light-dependent photokinesis: green light decreases the translation velocity whereas red light increases it, in comparison to blue and white light. The present article shows that radio-frequency electromagnetic fields cancel the light effect on photokinesis. The frequency to cancel the light effect corresponds to the Zeeman resonance frequency (DC magnetic field of 4 Oe and radio-frequency of 11.5 MHz), indicating the involvement of a radical pair mechanism. An analysis of the orientation angle relative to the magnetic field direction shows that radio-frequency electromagnetic fields disturb the swimming orientation when the microorganisms are illuminated with red light. The analysis also shows that at low magnetic fields (1.6 Oe) the swimming orientation angles are well scattered around the magnetic field direction, showing that magnetotaxis is not efficiently in the swimming orientation to the geomagnetic field. The results do not support cryptochrome as being the responsible chromophore for the radical pair mechanism and perhaps two different chromophores are necessary to explain the radio-frequency effects.

Aspects of eukaryotic-like signaling in Gram-positive cocci: a focus on virulence

PubMed Central

Burnside, Kellie; Rajagopal, Lakshmi

2011-01-01

Living organisms adapt to the dynamic external environment for their survival. Environmental adaptation in prokaryotes is thought to be primarily accomplished by signaling events mediated by two-component systems, consisting of histidine kinases and response regulators. However, eukaryotic-like serine/threonine kinases (STKs) have recently been described to regulate growth, antibiotic resistance and virulence of pathogenic bacteria. This article summarizes the role of STKs and their cognate phosphatases (STPs) in Gram-positive cocci that cause invasive infections in humans. Given that a large number of inhibitors to eukaryotic STKs are approved for use in humans, understanding how serine/threonine phosphorylation regulates virulence and antibiotic resistance will be beneficial for the development of novel therapeutic strategies against bacterial infections. PMID:21797690

Prevalence of new candidate pathogens Prevotella baroniae, Prevotella multisaccharivorax and as-yet-uncultivated Bacteroidetes clone X083 in primary endodontic infections.

PubMed

Rôças, Isabela N; Siqueira, José F

2009-10-01

Culture-independent studies have revealed a broad spectrum of oral bacterial taxa that may be associated with disease. This study investigated the prevalence of three new candidate oral pathogens: Prevotella baroniae, Prevotella multisaccharivorax, and as-yet-uncultivated Bacteroidetes oral clone X083 in primary endodontic infections using a devised culture-independent approach. Genomic DNA was isolated from samples taken from 52 teeth with different forms of apical periodontitis and used as template in a taxon-specific 16S rRNA gene-based nested polymerase chain reaction assay to determine the prevalence of the 3 target taxa. Bacteroidetes clone X083, P. baroniae, and P. multisaccharivorax were respectively detected in 81%, 43%, and 38% of the root canals of teeth associated with chronic apical periodontitis, in 60%, 40% and 40% of the canals of teeth with acute apical periodontitis, and in 14%, 24%, and 5% of the pus aspirates from acute apical abscesses. No targeted taxon was positively associated with abscesses or clinical symptoms. Overall, Bacteroidetes clone X083, P. baroniae, and P. multisaccharivorax were found in 50%, 35%, and 25% of the samples taken from primary endodontic infections, respectively. Findings confirmed that the two newly named species and the uncultivated phylotype targeted in this study are associated with different forms of apical periodontitis, and a pathogenetic or at least an ecologic role is suspected.

Subsurface metagenomes uncover a vast repertoire of hypervariable proteins encoded by genetic elements in uncultivated organisms and viruses

NASA Astrophysics Data System (ADS)

Paul, B. G.; Burstein, D.; Castelle, C. J.; Banfield, J. F.; Valentine, D. L.; Miller, J. F.; Ghosh, P.; Handa, S.; Arambula, D.; Czornyj, E.; Thomas, B. C.

2016-12-01

Uncultivated microorganisms primarily account for the remarkable diversity harbored in subsurface environments and represent an expansive subset of the current Tree of Life. Recent metagenomic efforts to investigate subsurface biomes have unveiled an array of bacterial and archaeal candidate phyla, whose members have minimal genomes and an apparent host-dependent existence. Still, little is known about the adaptive strategies that mediate host interactions in these organisms or their viruses. Genomic features known as diversity-generating retroelements (DGRs), which guide variability into targeted genes, were recently discovered in two single-cell genomes of uncultivated nanoarchaea, and independently in the genome of a marine virus from methane seep sediments. These prodigious drivers of protein hypervariability were first identified as the key force behind phage tail fiber diversification for binding different host receptors. Since their discovery, approximately 500 new DGRs have been found across a wide range of bacterial genomes representing various niches. We identified an unexpected 1136 distinct diversifiers from a single groundwater environment in reconstructed microbial genomes and genome fragments. The newly detected DGRs - predominantly linked to members of the candidate phyla radiation (CPR) - appear to target genes associated with cell-cell attachment, signaling, and transcription regulation. These findings suggest that targeted protein diversification may have an important role in regulating symbiotic or parasitic associations in groundwater microbiomes.

Urine flow cytometry can rule out urinary tract infection, but cannot identify bacterial morphologies correctly.

PubMed

Geerts, N; Jansz, A R; Boonen, K J M; Wijn, R P W F; Koldewijn, E L; Boer, A K; Scharnhorst, V

2015-08-25

The diagnosis of urinary tract infection (UTI) by urine culture is a time-consuming and costly procedure. Usage of a screening method, to identify negative samples, would therefore affect time-to-diagnosis and laboratory cost positively. Urine flow cytometers are able to identify particles in urine. Together with the introduction of a cut-off value, which determines if a urine sample is subsequently cultured or not, the number of cultures can be reduced, while maintaining a low level of false negatives and a high negative predictive value. Recently, Sysmex developed additional software for their urine flow cytometers. Besides measuring the number of bacteria present in urine, information is given on bacterial morphology, which may guide the physician in the choice of antibiotic. In this study, we evaluated this software update. The UF1000i classifies bacteria into two categories: 'rods' and 'cocci/mixed'. Compared to the actual morphology of the bacterial pathogen found, the 'rods' category scores reasonably well with 91% chance of classifying rod-shaped bacteria correctly. The 'cocci/mixed' category underperforms, with only 29% of spherical-shaped bacteria (cocci) classified as such. In its current version, the bacterial morphology software does not classify bacteria, according to their morphology, well enough to be of clinical use in this study population. Copyright © 2015 Elsevier B.V. All rights reserved.

Phage-inducible islands in the Gram-positive cocci.

PubMed

Martínez-Rubio, Roser; Quiles-Puchalt, Nuria; Martí, Miguel; Humphrey, Suzanne; Ram, Geeta; Smyth, Davida; Chen, John; Novick, Richard P; Penadés, José R

2017-04-01

The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we found that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful lifestyle. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci.

Investigating Cell-Material Interactions of Magnetospirillum magneticum as an Approach for Probing Submerged Surface Structural Integrity

DTIC Science & Technology

2012-07-01

developed a microscope- based , offset Helmholtz coil system with a custom-designed microcontroller. We have developed a microfabrication approach for...implemented an experimental model system using ferromagnetic beads. We have applied direct and frequency based magnetic fields for controlling magnetotactic...fields. Expanded Accomplishments We have developed a microscope- based , offset Helmholtz coil system with a custom- designed microcontroller. To be

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

PubMed

Ji, Boyang; Zhang, Sheng-Da; Zhang, Wei-Jia; Rouy, Zoe; Alberto, François; Santini, Claire-Lise; Mangenot, Sophie; Gagnot, Séverine; Philippe, Nadège; Pradel, Nathalie; Zhang, Lichen; Tempel, Sébastien; Li, Ying; Médigue, Claudine; Henrissat, Bernard; Coutinho, Pedro M; Barbe, Valérie; Talla, Emmanuel; Wu, Long-Fei

2017-03-01

Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Novel MRI Contrast Agent from Magnetotactic Bacteria Enables In Vivo Tracking of iPSC-derived Cardiomyocytes.

PubMed

Mahmoudi, Morteza; Tachibana, Atsushi; Goldstone, Andrew B; Woo, Y Joseph; Chakraborty, Papia; Lee, Kayla R; Foote, Chandler S; Piecewicz, Stephanie; Barrozo, Joyce C; Wakeel, Abdul; Rice, Bradley W; Bell Iii, Caleb B; Yang, Phillip C

2016-06-06

Therapeutic delivery of human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs) represents a novel clinical approach to regenerate the injured myocardium. However, methods for robust and accurate in vivo monitoring of the iCMs are still lacking. Although superparamagnetic iron oxide nanoparticles (SPIOs) are recognized as a promising tool for in vivo tracking of stem cells using magnetic resonance imaging (MRI), their signal persists in the heart even weeks after the disappearance of the injected cells. This limitation highlights the inability of SPIOs to distinguish stem cell viability. In order to overcome this shortcoming, we demonstrate the use of a living contrast agent, magneto-endosymbionts (MEs) derived from magnetotactic bacteria for the labeling of iCMs. The ME-labeled iCMs were injected into the infarcted area of murine heart and probed by MRI and bioluminescence imaging (BLI). Our findings demonstrate that the MEs are robust and effective biological contrast agents to track iCMs in an in vivo murine model. We show that the MEs clear within one week of cell death whereas the SPIOs remain over 2 weeks after cell death. These findings will accelerate the clinical translation of in vivo MRI monitoring of transplanted stem cell at high spatial resolution and sensitivity.

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

NASA Astrophysics Data System (ADS)

Egli, Ramon; Mao, Xuegang

2015-04-01

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

Ecology, Diversity, and Evolution of Magnetotactic Bacteria

PubMed Central

Bazylinski, Dennis A.

2013-01-01

SUMMARY Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation. PMID:24006473

Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.

PubMed

Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V; Aglyamova, Galina V; Bulman, Simon; Fiers, Mark; Keeling, Patrick J; Pawlowski, Jan

2010-12-02

Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a. Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.

Spatial Variation of Soil Organic Carbon and Total Nitrogen in the Coastal Area of Mid-Eastern China.

PubMed

Xu, Yan; Pu, Lijie; Liao, Qilin; Zhu, Ming; Yu, Xue; Mao, Tianying; Xu, Chenxing

2017-07-14

Soils play an important role in sequestrating atmospheric CO₂. Coastal tidal flats have been intensively reclaimed for food security and living spaces worldwide. We aimed to identify the changes of soil organic carbon (SOC) and total nitrogen (TN) following coastal reclamation and their spatial variation in the coastal area of mid-Eastern China to provide information for coastal cropland management. We measured SOC and TN of 463 soil samples in the coastal plain of mid-Eastern China. The results showed that SOC and TN increased highly from the uncultivated coastal tidal flat (2.49 g·kg -1 and 0.21 g·kg -1 , respectively) to the cropland (10.73 g·kg -1 and 1.3 g·kg -1 , respectively). After long-term cultivation, SOC and TN in the old farmland (12.98 g·kg -1 and 1.49 g·kg -1 , respectively) were greater than those in the young farmland (5.76 g·kg -1 and 0.86 g·kg -1 , respectively). The density of SOC in the uncultivated coastal tidal flat, young farmland, and old farmland were 0.68 kg·C·m -2 , 1.52 kg·C·m -2 , and 3.31 kg·C·m -2 , respectively. The density of TN in the uncultivated coastal tidal flat, young farmland and old farmland were 0.05 kg·N·m -2 , 0.23 kg·N·m -2 , and 0.38 kg·N·m -2 , respectively. The C/N (11.17) in the uncultivated coastal tidal flat was highest comparing to that in the young and old farmland due to lower nitrogen. The C/N increased from 6.78 to 8.71 following cultivation. Reclaimed coastal tidal flats had high carbon and nitrogen sequestration potential that not only mitigated the threat of global warming, but also improved soil fertility for crop production. Coastal management of cropland should consider the spatial distribution of SOC and TN to improve ecosystem services of coastal soils.

Spatial Variation of Soil Organic Carbon and Total Nitrogen in the Coastal Area of Mid-Eastern China

PubMed Central

Pu, Lijie; Liao, Qilin; Zhu, Ming; Yu, Xue; Mao, Tianying; Xu, Chenxing

2017-01-01

Soils play an important role in sequestrating atmospheric CO2. Coastal tidal flats have been intensively reclaimed for food security and living spaces worldwide. We aimed to identify the changes of soil organic carbon (SOC) and total nitrogen (TN) following coastal reclamation and their spatial variation in the coastal area of mid-Eastern China to provide information for coastal cropland management. We measured SOC and TN of 463 soil samples in the coastal plain of mid-Eastern China. The results showed that SOC and TN increased highly from the uncultivated coastal tidal flat (2.49 g·kg−1 and 0.21 g·kg−1, respectively) to the cropland (10.73 g·kg−1 and 1.3 g·kg−1, respectively). After long-term cultivation, SOC and TN in the old farmland (12.98 g·kg−1 and 1.49 g·kg−1, respectively) were greater than those in the young farmland (5.76 g·kg−1 and 0.86 g·kg−1, respectively). The density of SOC in the uncultivated coastal tidal flat, young farmland, and old farmland were 0.68 kg·C·m−2, 1.52 kg·C·m−2, and 3.31 kg·C·m−2, respectively. The density of TN in the uncultivated coastal tidal flat, young farmland and old farmland were 0.05 kg·N·m−2, 0.23 kg·N·m−2, and 0.38 kg·N·m−2, respectively. The C/N (11.17) in the uncultivated coastal tidal flat was highest comparing to that in the young and old farmland due to lower nitrogen. The C/N increased from 6.78 to 8.71 following cultivation. Reclaimed coastal tidal flats had high carbon and nitrogen sequestration potential that not only mitigated the threat of global warming, but also improved soil fertility for crop production. Coastal management of cropland should consider the spatial distribution of SOC and TN to improve ecosystem services of coastal soils. PMID:28708078

Sediment composition for the assessment of water erosion and nonpoint source pollution in natural and fire-affected landscapes.

PubMed

Carkovic, Athena B; Pastén, Pablo A; Bonilla, Carlos A

2015-04-15

Water erosion is a leading cause of soil degradation and a major nonpoint source pollution problem. Many efforts have been undertaken to estimate the amount and size distribution of the sediment leaving the field. Multi-size class water erosion models subdivide eroded soil into different sizes and estimate the aggregate's composition based on empirical equations derived from agricultural soils. The objective of this study was to evaluate these equations on soil samples collected from natural landscapes (uncultivated) and fire-affected soils. Chemical, physical, and soil fractions and aggregate composition analyses were performed on samples collected in the Chilean Patagonia and later compared with the equations' estimates. The results showed that the empirical equations were not suitable for predicting the sediment fractions. Fine particles, including primary clay, primary silt, and small aggregates (<53 μm) were over-estimated, and large aggregates (>53 μm) and primary sand were under-estimated. The uncultivated and fire-affected soils showed a reduced fraction of fine particles in the sediment, as clay and silt were mostly in the form of large aggregates. Thus, a new set of equations was developed for these soils, where small aggregates were defined as particles with sizes between 53 μm and 250 μm and large aggregates as particles>250 μm. With r(2) values between 0.47 and 0.98, the new equations provided better estimates for primary sand and large aggregates. The aggregate's composition was also well predicted, especially the silt and clay fractions in the large aggregates from uncultivated soils (r(2)=0.63 and 0.83, respectively) and the fractions of silt in the small aggregates (r(2)=0.84) and clay in the large aggregates (r(2)=0.78) from fire-affected soils. Overall, these new equations proved to be better predictors for the sediment and aggregate's composition in uncultivated and fire-affected soils, and they reduce the error when estimating soil loss in natural landscapes. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of the VITEK 2 System for Identification and Antimicrobial Susceptibility Testing of Medically Relevant Gram-Positive Cocci

PubMed Central

Ligozzi, Marco; Bernini, Cinzia; Bonora, Maria Grazia; de Fatima, Maria; Zuliani, Jessica; Fontana, Roberta

2002-01-01

A study was conducted to evaluate the new VITEK 2 system (bioMérieux) for identification and antibiotic susceptibility testing of gram-positive cocci. Clinical isolates of Staphylococcus aureus (n = 100), coagulase-negative staphylococci (CNS) (n = 100), Enterococcus spp. (n = 89), Streptococcus agalactiae (n = 29), and Streptococcus pneumoniae (n = 66) were examined with the ID-GPC identification card and with the AST-P515 (for staphylococci), AST-P516 (for enterococci and S. agalactiae) and AST-P506 (for pneumococci) susceptibility cards. The identification comparison methods were the API Staph for staphylococci and the API 20 Strep for streptococci and enterococci; for antimicrobial susceptibility testing, the agar dilution method according to the procedure of the National Committee for Clinical Laboratory Standards (NCCLS) was used. The VITEK 2 system correctly identified to the species level (only one choice or after simple supplementary tests) 99% of S. aureus, 96.5% of S. agalactiae, 96.9% of S. pneumoniae, 92.7% of Enterococcus faecalis, 91.3% of Staphylococcus haemolyticus, and 88% of Staphylococcus epidermidis but was least able to identify Enterococcus faecium (71.4% correct). More than 90% of gram-positive cocci were identified within 3 h. According to the NCCLS breakpoints, antimicrobial susceptibility testing with the VITEK 2 system gave 96% correct category agreement, 0.82% very major errors, 0.17% major errors, and 2.7% minor errors. Antimicrobial susceptibility testing showed category agreement from 94 to 100% for S. aureus, from 90 to 100% for CNS, from 91 to 100% for enterococci, from 96 to 100% for S. agalactiae, and from 91 to 100% for S. pneumoniae. Microorganism-antibiotic combinations that gave very major errors were CNS-erythromycin, CNS-oxacillin, enterococci-teicoplanin, and enterococci-high-concentration gentamicin. Major errors were observed for CNS-oxacillin and S. agalactiae-tetracycline combinations. In conclusion the results of this study indicate that the VITEK 2 system represents an accurate and acceptable means for performing identification and antibiotic susceptibility tests with medically relevant gram-positive cocci. PMID:11980942

Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

PubMed Central

Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M.; Lösekann, Tina; Ivanova, Natalia; Martin, Hector Garcia; Szeto, Ernest; Platt, Darren; Hugenholtz, Philip; Relman, David A.; Quake, Stephen R.

2007-01-01

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community. PMID:17620602

The future is now: single-cell genomics of bacteria and archaea

PubMed Central

Blainey, Paul C.

2013-01-01

Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology. PMID:23298390

Stomach Fermentation in East African Colobus Monkeys in Their Natural State

PubMed Central

Ohwaki, Kyoko; Hungate, R. E.; Lotter, Leonard; Hofmann, R. R.; Maloiy, Geoffrey

1974-01-01

The microbial fermentation in the stomachs of two monkeys, Colobus polykomos, collected in Kenya, was studied. The gas accumulated within the stomach contained H2 but no CH4. Volatile fatty acid concentrations were high, but accumulated acid prevented determination of the fermentation rate in untreated, incubated stomach contents. Upon addition of bicarbonate, a very rapid rate could be demonstrated. Some D- and L-lactate were in the stomach contents. Starchy seeds or fruits rather than leaves appeared to have been consumed. Microscopically, the most prominent microorganisms seen were large, very refringent cocci, possibly Sarcina ventriculi, and various smaller cocci and rods. The 28 cultured strains of bacteria included 14 Staphylococcus, 2 Streptococcus, 10 Propionibacterium, and 2 Peptostreptococcus. The culture count constituted 10 to 20% of the direct count. No protozoa or cellulolytic bacteria were found. Images PMID:4207763

Does negative-pressure wound therapy influence subjacent bacterial growth? A systematic review.

PubMed

Glass, Graeme E; Murphy, George R F; Nanchahal, Jagdeep

2017-08-01

Negative-pressure wound therapy is a ubiquitous wound management resource. The influence of NPWT on the bacterial bioburden of the subjacent wound remains unclear. We sought to examine the evidence. MEDLINE, Embase, PubMed, the Cochrane Database of Systematic Reviews and the Cochrane Controlled Trials Register were searched for articles quantitatively evaluating bacterial load under NPWT. Twenty-four studies met the inclusion criteria including 4 randomised controlled trials, 8 clinical series and 12 experimental studies. Twenty studies evaluated conventional NPWT, while 4 evaluated infiltration-based NPWT. While 8 studies using conventional NPWT failed to demonstrate an observable effect on bacterial load, 7 studies reported that NPWT was inherently bacteriostatic and 5 others reported species selectivity with suppression of non-fermentative gram-negative bacilli (NFGNB), including Pseudomonas spp. Simultaneously, there was some evidence of enhanced proliferation of gram-positive cocci where the niche was cleared of NFGNB. Two of the 4 studies using infiltration-based NPWT also reported selectively impaired proliferation of Pseudomonas spp. The assumption that NPWT suppresses bacterial proliferation is oversimplified. There is evidence that NPWT exhibits species selectivity, suppressing the proliferation of NFGNB. However, this may depopulate the niche for exploitation by gram-positive cocci. This, in turn, has implications for the use of NPWT where highly virulent strains of gram-positive cocci have been isolated and the duration of NPWT therapy and frequency of dressing changes. Copyright © 2017 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Geobiology of Marine Magnetotactic Bacteria

DTIC Science & Technology

2006-06-01

acids (e.g. lactate, acetate, oxalate , succinate, fumarate, malate, and citrate) which are continually transported into the soil, in part due to the...microbial mats, and hydrothermal vent waters. J Environ Monit 3: 61-66. 177 Lyons TW (1997) Sulfur isotopic trends and pathways of iron sulfide formation in...case in sediments, microbial mats, and hydrothermal vent waters. J Environ Monit 3: 61-66. 200 O’Sullivan DW, Hanson Jr AK, Kester DR (1997) The

Magnetite Biomineralization: Fifty years of progress, from beach-combing to the SQUID microscope

NASA Astrophysics Data System (ADS)

Kirschvink, J. L.; Dixson, A. D.; Raub, T.

2012-12-01

Magnetite biomineralization was first discovered 50 years ago as a hardening agent in the teeth of the Polyplacophoran molluscs (chitons) by the late Prof. Heinz A. Lowenstam of Caltech, when he noticed unusual erosional effects produced by their grazing in the intertidal zones of Palau (Lowenstam, 1962). Since then, biogenic magnetite has been detected in a broad range of organisms, including magnetotactic bacteria, protists, insects, fish, amphibians, reptiles, birds, and mammals including humans. In many species, the role of ferromagnetic material as a neurophysiological transducer is demonstrated clearly through the effects of pulse-remagnetization on behavior. A brief (1 uS), properly configured magnetic discharge from a rectified LC circuit, tailored to exceed the coercivity of the magnetite, will often abolish a magnetic behavioral response, or in some cases make the organism go the wrong way. This is a unique ferromagnetic effect. The genes controlling magnetite biomineralization are well characterized in several species of bacteria, and the ability of some of these bacterial genes to initiate magnetite precipitation in mammalian cell lines argues for a common descent, probably via a magnetotactic mitochondrial ancestor. Previous studies in fish reported the presence of single-domain magnetite crystals in cells near projections of the trigeminal nerve, co-located in the olfactory epithelium. Although the cells are rare, the recent development of a spinning magnetic field technique allows easy identification and isolation of these cells for individual study (Eder et al., 2012). The cells are surprisingly magnetic, with moments hundreds of times larger than typical magnetotactic bacteria. Subsequent efforts to identify the anatomical seat of magnetoreceptors have focused on the same locations in new organisms, excluding other areas. Using SQUID moment magnetometry and SQUID scanning microscopy, we report here the unexpected presence of biogenic magnetite in the lateral line region of the zebrafish, Danio rerio. We suspect that the magnetic field receptor cells of the trigeminal system in animals may be co-located within a variety of other sensory tissues (olfaction, lateral line, vision, hearing, taste, etc.) as a means of spatially dispersing cells with large magnetic moments to prevent magnetostatic interactions between them. References: Eder et al., Magnetic characterization of isolated candidate vertebrate magnetoreceptor cells. Proc. Natl. Acad. Sci. USA 2012; 109:12022-12027. Lowenstam, H.A., 1962. Magnetite in denticle capping in recent chitons (Polyplacophora). Bulletin of the Geological Society of America 73, 435-438.

Iron uptake and magnetite biomineralization in the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1: An iron isotope study

NASA Astrophysics Data System (ADS)

Amor, Matthieu; Busigny, Vincent; Louvat, Pascale; Tharaud, Mickaël; Gélabert, Alexandre; Cartigny, Pierre; Carlut, Julie; Isambert, Aude; Durand-Dubief, Mickaël; Ona-Nguema, Georges; Alphandéry, Edouard; Chebbi, Imène; Guyot, François

2018-07-01

Magnetotactic bacteria (MTB) produce intracellular, membrane-bounded magnetite [Fe(II)Fe(III)2O4] crystals in a genetically controlled way. They are ubiquitous in aquatic environments, and have been proposed to represent some of the most ancient biomineralizing organisms on Earth. Although tremendous advances have been made in constraining the mechanisms of magnetite formation in MTB, the precise biomineralization pathways are still a matter of debate. To further constrain the processes of Fe uptake and magnetite precipitation in MTB, Fe stable isotope measurements were carried out with the magnetotactic strain AMB-1 cultivated with Fe(III), Fe(II) or mixed Fe(III)/Fe(II) species in the growth media. The Fe isotope compositions of growth media before and after AMB-1 cultures, bacterial lysates (i.e. cells devoid of magnetite) and magnetite samples were measured. Single valence Fe(III) or Fe(II) growth media after AMB-1 cultures showed depletion in heavy Fe isotopes by 0.2 to 1.5‰ (δ56Fe), relative to the initial Fe source. Contrastingly, heavy Fe isotopes accumulated in the growth media supplemented with mixed Fe(III)/Fe(II) sources, with enrichment up to 0.25‰. These results support a preferential bacterial uptake of Fe(II) when both Fe(III) and Fe(II) are bioavailable. Bacterial lysates contained at least 50% of the total cellular Fe; thus, magnetite was not the main Fe reservoir in AMB-1 under the experimental conditions investigated in this study. In all cultures, bacterial lysates δ56Fe were 0.4 to 0.8‰ higher than the initial Fe sources, while magnetite δ56Fe were 1.2 to 2.5‰ lower. This depletion in heavy Fe isotopes of magnetite can be explained by partial reduction of Fe(III) to Fe(II) within the cell and subsequent magnetite precipitation. The data also show mass-independent fractionations (MIF) in odd (57Fe) but not in even (54Fe, 56Fe, 58Fe) isotopes, expressed mainly in magnetite crystals, and supporting a magnetic isotope effect on 57Fe. Bacterial Fe uptake and MIF patterns suggest that Fe(II) species can freely exchange between the intracellular and external media. Based on these observations, an integrative biogeochemical model for Fe uptake, cellular trafficking, and magnetite precipitation in AMB-1 is presented.

The microbiota of acute apical abscesses.

PubMed

Siqueira, J F; Rôças, I N

2009-01-01

As the breadth of bacterial diversity in the oral cavity has been deciphered by molecular studies, several newly identified species/phylotypes have emerged as potential pathogens. We hypothesized that many of these species/phylotypes could also be involved with the etiology of endodontic abscesses. Abscess aspirates from 42 persons were analyzed for the presence of 81 species/phylotypes by means of a reverse-capture checkerboard hybridization assay. Associations between the most frequently detected taxa were calculated. The most prevalent taxa were Fusobacterium nucleatum, Parvimonas micra, and Porphyromonas endodontalis. Other frequently found taxa included Olsenella uli, streptococci, Eikenella corrodens, some as-yet-uncultivated phylotypes (Bacteroidetes clone X083 and Synergistes clone BA121), and newly named species (Prevotella baroniae and Dialister invisus). Several positive bacterial associations were disclosed. Findings not only strengthen the association of many cultivable species with abscesses, but also include some newly named species and uncultivated phylotypes in the set of candidate pathogens associated with this disease.

Cutaneous Granulomas in Dolphins Caused by Novel Uncultivated Paracoccidioides brasiliensis

PubMed Central

Vilela, Raquel; Bossart, Gregory D.; St. Leger, Judy A.; Dalton, Leslie M.; Reif, John S.; Schaefer, Adam M.; McCarthy, Peter J.; Fair, Patricia A.

2016-01-01

Cutaneous granulomas in dolphins were believed to be caused by Lacazia loboi, which also causes a similar disease in humans. This hypothesis was recently challenged by reports that fungal DNA sequences from dolphins grouped this pathogen with Paracoccidioides brasiliensis. We conducted phylogenetic analysis of fungi from 6 bottlenose dolphins (Tursiops truncatus) with cutaneous granulomas and chains of yeast cells in infected tissues. Kex gene sequences of P. brasiliensis from dolphins showed 100% homology with sequences from cultivated P. brasiliensis, 73% with those of L. loboi, and 93% with those of P. lutzii. Parsimony analysis placed DNA sequences from dolphins within a cluster with human P. brasiliensis strains. This cluster was the sister taxon to P. lutzii and L. loboi. Our molecular data support previous findings and suggest that a novel uncultivated strain of P. brasiliensis restricted to cutaneous lesions in dolphins is probably the cause of lacaziosis/lobomycosis, herein referred to as paracoccidioidomycosis ceti. PMID:27869614

Cutaneous Granulomas in Dolphins Caused by Novel Uncultivated Paracoccidioides brasiliensis.

PubMed

Vilela, Raquel; Bossart, Gregory D; St Leger, Judy A; Dalton, Leslie M; Reif, John S; Schaefer, Adam M; McCarthy, Peter J; Fair, Patricia A; Mendoza, Leonel

2016-12-01

Cutaneous granulomas in dolphins were believed to be caused by Lacazia loboi, which also causes a similar disease in humans. This hypothesis was recently challenged by reports that fungal DNA sequences from dolphins grouped this pathogen with Paracoccidioides brasiliensis. We conducted phylogenetic analysis of fungi from 6 bottlenose dolphins (Tursiops truncatus) with cutaneous granulomas and chains of yeast cells in infected tissues. Kex gene sequences of P. brasiliensis from dolphins showed 100% homology with sequences from cultivated P. brasiliensis, 73% with those of L. loboi, and 93% with those of P. lutzii. Parsimony analysis placed DNA sequences from dolphins within a cluster with human P. brasiliensis strains. This cluster was the sister taxon to P. lutzii and L. loboi. Our molecular data support previous findings and suggest that a novel uncultivated strain of P. brasiliensis restricted to cutaneous lesions in dolphins is probably the cause of lacaziosis/lobomycosis, herein referred to as paracoccidioidomycosis ceti.

Vancomycin-Resistant Gram-Positive Cocci Isolated from the Saliva of Wild Songbirds

PubMed Central

Ishihara, Shingo; Bitner, Jessica J.; Farley, Greg H.

2014-01-01

We analyzed highly vancomycin-resistant Gram-positive bacteria isolated from the saliva of migratory songbirds captured, sampled, and released from a birdbanding station in western Kansas. Individual bacterial isolates were identified by partial 16S rRNA sequencing. Most of the bacteria in this study were shown to be Staphylococcus succinus with the majority being isolated from the American Robin. Some of these bacteria were shown to carry vanA, vanB, and vanC vancomycin-resistance genes and have the ability to form biofilms. One of the van gene-carrying isolates is also coagulase positive, which is normally considered a virulence factor. Other organisms isolated included Staphylococcus saprophyticus as well as Enterococcus gallinarum. Given the wide range of the American Robin and ease of horizontal gene transfer between Gram-positive cocci, we postulate that these organisms could serve as a reservoir of vancomycin-resistance genes capable of transferring to human pathogens. PMID:23224296

Vancomycin-resistant gram-positive cocci isolated from the saliva of wild songbirds.

PubMed

Ishihara, Shingo; Bitner, Jessica J; Farley, Greg H; Gillock, Eric T

2013-04-01

We analyzed highly vancomycin-resistant Gram-positive bacteria isolated from the saliva of migratory songbirds captured, sampled, and released from a bird-banding station in western Kansas. Individual bacterial isolates were identified by partial 16S rRNA sequencing. Most of the bacteria in this study were shown to be Staphylococcus succinus with the majority being isolated from the American Robin. Some of these bacteria were shown to carry vanA, vanB, and vanC vancomycin-resistance genes and have the ability to form biofilms. One of the van gene-carrying isolates is also coagulase positive, which is normally considered a virulence factor. Other organisms isolated included Staphylococcus saprophyticus as well as Enterococcus gallinarum. Given the wide range of the American Robin and ease of horizontal gene transfer between Gram-positive cocci, we postulate that these organisms could serve as a reservoir of vancomycin-resistance genes capable of transferring to human pathogens.

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe.

PubMed

Fillol-Salom, Alfred; Martínez-Rubio, Roser; Abdulrahman, Rezheen F; Chen, John; Davies, Robert; Penadés, José R

2018-06-06

Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.

Biomagnetic Imaging Applications using NV Centers in Diamond

NASA Astrophysics Data System (ADS)

Glenn, David; Lesage, David; Connolly, Colin; Walsworth, Ronald

2015-05-01

We present new measurements of magnetic fields produced by a range of biological specimens using a wide-field magnetic imaging system based on NV centers in diamond. In particular, we show (i) the first magnetic images of a previously unstudied strain of magnetotactic bacteria, and (ii) a general platform for magnetic imaging of immunomagnetically labeled cells, which provides a useful alternative to traditional immunofluorescence techniques in the presence of strong autofluorescence and/or optically scattering media.

Photosynthetic microorganism-mediated synthesis of akaganeite (beta-FeOOH) nanorods.

PubMed

Brayner, Roberta; Yéprémian, Claude; Djediat, Chakib; Coradin, Thibaud; Herbst, Fréderic; Livage, Jacques; Fiévet, Fernand; Couté, Alain

2009-09-01

Common Anabaena and Calothrix cyanobacteria and Klebsormidium green algae are shown to form intracellularly akaganeite beta-FeOOH nanorods of well-controlled size and unusual morphology at room temperature. X-ray diffraction (XRD), transmission electron microscopy (TEM), and scanning electron microscopy X-ray energy dispersive spectrometry (SEM-EDS) analyses are used to investigate particle structure, size, and morphology. A mechanism involving iron-siderophore complex formation is proposed and compared with iron biomineralization in magnetotactic bacteria.

Presumed magnetic biosignatures observed in magnetite derived from abiotic reductive alteration of nanogoethite

NASA Astrophysics Data System (ADS)

Till, Jessica L.; Guyodo, Yohan; Lagroix, France; Morin, Guillaume; Menguy, Nicolas; Ona-Nguema, Georges

2017-03-01

The oriented chains of nanoscale Fe-oxide particles produced by magnetotactic bacteria are a striking example of biomineralization. Several distinguishing features of magnetite particles that comprise bacterial magnetosomes have been proposed to collectively constitute a biosignature of magnetotactic bacteria (Thomas-Keprta et al., 2001). These features include high crystallinity, chemical purity, a single-domain magnetic structure, well-defined crystal morphology, and arrangement of particles in chain structures. Here, we show that magnetite derived from the inorganic breakdown of nanocrystalline goethite exhibits magnetic properties and morphologies remarkably similar to those of biogenic magnetite from magnetosomes. During heating in reducing conditions, oriented nanogoethite aggregates undergo dehydroxylation and transform into stoichiometric magnetite. We demonstrate that highly crystalline single-domain magnetite with euhedral grain morphologies produced abiogenically from goethite meets several of the biogenicity criteria commonly used for the identification of magnetofossils. Furthermore, the suboxic conditions necessary for magnetofossil preservation in sediments are conducive to the reductive alteration of nanogoethite, as well as the preservation of detrital magnetite originally formed from goethite. The findings of this study have potential implications for the identification of biogenic magnetite, particularly in older sediments where diagenesis commonly disrupts the chain structure of magnetosomes. Our results indicate that isolated magnetofossils cannot be positively distinguished from inorganic magnetite on the basis of their magnetic properties and morphology, and that intact chain structures remain the only reliable distinguishing feature of fossil magnetosomes.

Characteristics and optimized fermentation of a novel magnetotactic bacterium, Magnetospirillum sp. ME-1.

PubMed

Ke, Linfeng; Chen, Yajun; Liu, Pengming; Liu, Shan; Wu, Dandan; Yuan, Yihui; Wu, Yan; Gao, Meiying

2018-03-04

Magnetotactic bacteria (MTB) can biosynthesize magnetosomes, which have great potential for applications. A new MTB strain, Magnetospirillum sp. ME-1, was isolated and cultivated from freshwater sediments of East Lake (Wuhan, China) using the limiting dilution method. ME-1 had a chain of 17 ± 4 magnetosomes in the form of cubooctahedral crystals with a shape factor of 0.89. ME-1 was closest to Magnetospirillum sp. XM-1 according to 16S rRNA gene sequence similarity. Compared with XM-1, ME-1 possessed additional copy of mamPA and a larger mamO in magnetosome-specific genes. ME-1 had an intact citric acid cycle, and complete pathway models of ammonium assimilation and dissimilatory nitrate reduction. Potential carbon and nitrogen sources in these pathways were confirmed to be used in ME-1. Adipate was determined to be used in the fermentation medium as a new kind of dicarboxylic acid. The optimized fermentation medium was determined by orthogonal tests. The large-scale production of magnetosomes was achieved and the magnetosome yield (wet weight) reached 120 mg/L by fed-batch cultivation of ME-1 at 49 h in a 10-L fermenter with the optimized fermentation medium. This study may provide insights into the isolation and cultivation of other new MTB strains and the production of magnetosomes.

Light irradiation helps magnetotactic bacteria eliminate intracellular reactive oxygen species.

PubMed

Li, Kefeng; Wang, Pingping; Chen, Chuanfang; Chen, Changyou; Li, Lulu; Song, Tao

2017-09-01

Magnetotactic bacteria (MTB) demonstrate photoresponse. However, little is known about the biological significance of this behaviour. Magnetosomes exhibit peroxidase-like activity and can scavenge reactive oxygen species (ROS). Magnetosomes extracted from the Magnetospirillum magneticum strain AMB-1 show enhanced peroxidase-like activity under illumination. The present study investigated the effects of light irradiation on nonmagnetic (without magnetosomes) and magnetic (with magnetosomes) AMB-1 cells. Results showed that light irradiation did not affect the growth of nonmagnetic and magnetic cells but significantly increased magnetosome synthesis and reduced intracellular ROS level in magnetic cells. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to analyse the expression level of magnetosome formation-associated genes (mamA, mms6, mms13 and mmsF) and stress-related genes (recA, oxyR, SOD, amb0664 and amb2684). Results showed that light irradiation upregulated the expression of mms6, mms13 and mmsF. Furthermore, light irradiation upregulated the expression of stress-related genes in nonmagnetic cells but downregulated them in magnetic cells. Additionally, magnetic cells exhibited stronger phototactic behaviour than nonmagnetic ones. These results suggested that light irradiation could heighten the ability of MTB to eliminate intracellular ROS and help them adapt to lighted environments. This phenomenon may be related to the enhanced peroxidase-like activity of magnetosomes under light irradiation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium.

PubMed

Lefèvre, Christopher T; Howse, Paul A; Schmidt, Marian L; Sabaty, Monique; Menguy, Nicolas; Luther, George W; Bazylinski, Dennis A

2016-12-01

Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O 2 . For example, SRB remain viable in many aerobic environments while some even reduce O 2 to H 2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O 2 concentration gradient formed, or under O 2 -free N 2 gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O 2 as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Calculation of ferromagnetic resonance spectra for chains of magnetic particles

NASA Astrophysics Data System (ADS)

Newell, A. J.

2010-12-01

Magnetotactic bacteria are a taxonomically diverse group of bacteria that have chains of ferromagnetic crystals inside. These bacteria mostly live in the oxic-anoxic interface (OAI) of aquatic environments. The magnetic chains orient the bacteria parallel to the Earth's magnetic field and help them to maintain their position near the OAI. These chains show the fingerprint of natural selection acting to optimize the magnetic moment per unit iron. This is achieved in a number of ways: the alignment in chains, a narrow size range, crystallographic perfection and chemical purity. Because of these distinctive characteristics, the particles can still be identified after the bacteria have died. Such magnetofossils are useful both as records of bacterial evolution and environmental markers. They can most reliably be identified by microscopy, but that is very labor-intensive. A number of magnetic measurements have been developed to identify magnetofossils quickly and non-invasively. However, the only test that can specifically identify the chain structure is ferromagnetic resonance (FMR), which measures the response to a magnetic field oscillating at microwave frequencies. Although the experimental side of ferromagnetic resonance is well developed, the theoretical models for interpreting them have been limited. A new method is presented for calculating resonance frequencies as well as complete power spectra for chains of interacting magnetic particles. Spectra are calculated and compared with data for magnetotactic bacteria.

Soil redistribution model for undisturbed and cultivated sites based on Chernobyl-derived cesium-137 fallout.

PubMed

Hrachowitz, Markus; Maringer, Franz-Josef; Steineder, Christian; Gerzabek, Martin H

2005-01-01

Measurements of 137Cs fallout have been used in combination with a range of conversion models for the investigation of soil relocation mechanisms and sediment budgets in many countries for more than 20 yr. The objective of this paper is to develop a conversion model for quantifying soil redistribution, based on Chernobyl-derived 137Cs. The model is applicable on uncultivated as well as on cultivated sites, taking into account temporal changes in the 137Cs depth distribution pattern as well as tillage-induced 137Cs dilution effects. The main idea of the new model is the combination of a modified exponential model describing uncultivated soil with a Chapman distribution based model describing cultivated soil. The compound model subsequently allows a dynamic description of the Chernobyl derived 137Cs situation in the soil and its change, specifically migration and soil transport processes over the course of time. Using the suggested model at the sampling site in Pettenbach, in the Austrian province of Oberösterreich 137Cs depth distributions were simulated with a correlation coefficient of 0.97 compared with the measured 137Cs depth profile. The simulated rates of soil distribution at different positions at the sampling site were found to be between 27 and 60 Mg ha(-1) yr(-1). It was shown that the model can be used to describe the temporal changes of 137Cs depth distributions in cultivated as well as uncultivated soils. Additionally, the model allows to quantify soil redistribution in good correspondence with already existing models.

Leuconostoc garlicum: an unusual pathogen in the era of vancomycin therapy.

PubMed

Kumar, Anil; Augustine, Deepthi; Mehta, Asmita; Dinesh, Kavitha R; Viswam, Darsana; Philip, Rosamma

2012-01-01

Leuconostoc garlicum, belonging to the family of Leuconostocaceae, is a catalase-negative, Gram-positive ovoid cocci, intrinsically resistant to vancomycin. Clinical infection by Leuconostoc garlicum is rare. We report a case of respiratory tract infection subsequent to vancomycin therapy.

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”

PubMed Central

Seitz, Kiley W.; Temperton, Ben; Gillies, Lauren E.; Rabalais, Nancy N.; Henrissat, Bernard; Mason, Olivia U.

2017-01-01

ABSTRACT Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called “dead zones,” are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments—Parcubacteria (OD1) and Peregrinibacteria. Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter. PMID:28900024

Stop Codon Reassignment in the Wild

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

Ivanova, Natalia; Schwientek, Patrick; Tripp, H. James

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hostsmore » must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences« less

Use of Positive Blood Cultures for Direct Identification and Susceptibility Testing with the Vitek 2 System

PubMed Central

de Cueto, Marina; Ceballos, Esther; Martinez-Martinez, Luis; Perea, Evelio J.; Pascual, Alvaro

2004-01-01

In order to further decrease the time lapse between initial inoculation of blood culture media and the reporting of results of identification and antimicrobial susceptibility tests for microorganisms causing bacteremia, we performed a prospective study in which specially processed fluid from positive blood culture bottles from Bactec 9240 (Becton Dickinson, Cockeysville, Md.) containing aerobic media were directly inoculated into Vitek 2 system cards (bio-Mérieux, France). Organism identification and susceptibility results were compared with those obtained from cards inoculated with a standardized bacterial suspension obtained following subculture to agar; 100 consecutive positive monomicrobic blood cultures, consisting of 50 gram-negative rods and 50 gram-positive cocci, were included in the study. For gram-negative organisms, 31 of the 50 (62%) showed complete agreement with the standard method for species identification, while none of the 50 gram-positive cocci were correctly identified by the direct method. For gram-negative rods, there were 50% categorical agreements between the direct and standard methods for all drugs tested. The very major error rate was 2.4%, and the major error rate was 0.6%. The overall error rate for gram-negatives was 6.6%. Complete agreement in clinical categories of all antimicrobial agents evaluated was obtained for 19 of 50 (38%) gram-positive cocci evaluated; the overall error rate was 8.4%, with 2.8% minor errors, 2.4% major errors, and 3.2% very major errors. These findings suggest that the Vitek 2 cards inoculated directly from positive Bactec 9240 bottles do not provide acceptable bacterial identification or susceptibility testing in comparison with corresponding cards tested by a standard method. PMID:15297523

Antimicrobial-Resistance Genetic Markers in Potentially Pathogenic Gram Positive Cocci Isolated from Brazilian Soft Cheese.

PubMed

Resende, Juliana Alves; Fontes, Cláudia Oliveira; Ferreira-Machado, Alessandra Barbosa; Nascimento, Thiago César; Silva, Vânia Lúcia; Diniz, Cláudio Galuppo

2018-02-01

Although most Brazilian dairy products meet high technological standards, there are quality issues regarding milk production, which may reduce the final product quality. Several microbial species may contaminate milk during manufacture and handling. If antimicrobial usage remains uncontrolled in dairy cattle, the horizontal transfer of antimicrobial resistance genes in foodstuffs may be of particular concern for both food producers and dairy industry. This study focused on the evaluation of putative Gram positive cocci in Minas cheese and of antimicrobial and biocide resistance genes among the isolated bacteria. Representative samples of 7 different industrially trademarked Minas cheeses (n = 35) were processed for selective culture and isolation of Gram positive cocci. All isolated bacteria were identified by DNA sequencing of the 16S rRNA gene. Antimicrobial resistance genes were screened by PCR. Overall, 208 strains were isolated and identified as follows: Enterococcus faecalis (47.6%), Macrococcus caseolyticus (18.3%), Enterococcus faecium (11.5%), Enterococcus caseliflavus (7.7%), Staphylococcus haemolyticus (7.2%), Staphylococcus aureus (4.3%), Staphylococcus epidermidis (2.9%), and Enterococcus hirae (0.5%). The genetic markers mecA (78.0%) and smr (71.4%) were the most prevalent, but others were also detected, such as blaZ (65.2%), msrA (60.9%), msrB (46.6%), linA (54.7%), and aacA-aphD (47.6%). The occurrence of opportunist pathogenic bacteria harboring antimicrobial resistance markers in the cheese samples are of special concern, since these bacteria are not considered harmful contaminating agents according to the Brazilian sanitary regulations. However, they are potentially pathogenic bacteria and the cheese may be considered a reservoir for antimicrobial resistance genes available for horizontal transfer through the food chain, manufacturing personnel and consumers. © 2018 Institute of Food Technologists®.

Evaluation of the in vitro activity of levornidazole, its metabolites and comparators against clinical anaerobic bacteria.

PubMed

Hu, Jiali; Zhang, Jing; Wu, Shi; Zhu, Demei; Huang, Haihui; Chen, Yuancheng; Yang, Yang; Zhang, Yingyuan

2014-12-01

This study evaluated the in vitro anti-anaerobic activity and spectrum of levornidazole, its metabolites and comparators against 375 clinical isolates of anaerobic bacteria, including Gram-negative bacilli (181 strains), Gram-negative cocci (11 strains), Gram-positive bacilli (139 strains) and Gram-positive cocci (44 strains), covering 34 species. Minimum inhibitory concentrations (MICs) of levornidazole, its five metabolites and three comparators against these anaerobic isolates were determined by the agar dilution method. Minimum bactericidal concentrations (MBCs) of levornidazole and metronidazole were measured against 22 strains of Bacteroides fragilis. Levornidazole showed good activity against B. fragilis, other Bacteroides spp., Clostridium difficile, Clostridium perfringens and Peptostreptococcus magnus, evidenced by MIC90 values of 0.5, 1, 0.25, 2 and 1mg/L, respectively. The activity of levornidazole and the comparators was poor for Veillonella spp. Generally, levornidazole displayed activity similar to or slightly higher than that of metronidazole, ornidazole and dextrornidazole against anaerobic Gram-negative bacilli, Gram-positive bacilli and Gram-positive cocci, especially B. fragilis. Favourable anti-anaerobic activity was also seen with levornidazole metabolites M1 and M4 but not M2, M3 or M5. For the 22 clinical B. fragilis strains, MBC50 and MBC90 values of levornidazole were 2mg/L and 4mg/L, respectively. Both MBC50/MIC50 and MBC90/MIC90 ratios of levornidazole were 4, similar to those of metronidazole. Levornidazole is an important anti-anaerobic option in clinical settings in terms of its potent and broad-spectrum in vitro activity, bactericidal property, and the anti-anaerobic activity of its metabolites M1 and M4. Copyright © 2014 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Infective Endocarditis: Identification of Catalase-Negative, Gram-Positive Cocci from Blood Cultures by Partial 16S rRNA Gene Analysis and by Vitek 2 Examination.

PubMed

Abdul-Redha, Rawaa Jalil; Kemp, Michael; Bangsborg, Jette M; Arpi, Magnus; Christensen, Jens Jørgen

2010-01-01

Streptococci, enterococci and Streptococcus-like bacteria are frequent etiologic agents of infective endocarditis and correct species identification can be a laboratory challenge. Viridans streptococci (VS) not seldomly cause contamination of blood cultures. Vitek 2 and partial sequencing of the 16S rRNA gene were applied in order to compare the results of both methods. STRAINS ORIGINATED FROM TWO GROUPS OF PATIENTS: 149 strains from patients with infective endocarditis and 181 strains assessed as blood culture contaminants. Of the 330 strains, based on partial 16S rRNA gene sequencing results, 251 (76%) were VS strains, 10 (3%) were pyogenic streptococcal strains, 54 (16%) were E. faecalis strains and 15 (5%) strains belonged to a group of miscellaneous catalase-negative, Gram-positive cocci. Among VS strains, respectively, 220 (87,6%) and 31 (12,3%) obtained agreeing and non-agreeing identifications with the two methods with respect to allocation to the same VS group. Non-agreeing species identification mostly occurred among strains in the contaminant group, while for endocarditis strains notably fewer disagreeing results were observed.Only 67 of 150 strains in the mitis group strains obtained identical species identifications by the two methods. Most VS strains belonging to the groups of salivarius, anginosus, and mutans obtained agreeing species identifications with the two methods, while this only was the case for 13 of the 21 bovis strains. Pyogenic strains (n=10), Enterococcus faecalis strains (n=54) and a miscellaneous group of catalase-negative, Gram-positive cocci (n=15) seemed well identified by both methods, except that disagreements in identifications in the miscellaneous group of strains occurred for 6 of 15 strains.

New bacterial species associated with chronic periodontitis.

PubMed

Kumar, P S; Griffen, A L; Barton, J A; Paster, B J; Moeschberger, M L; Leys, E J

2003-05-01

Recent investigations of the human subgingival oral flora based on ribosomal 16S cloning and sequencing have shown many of the bacterial species present to be novel species or phylotypes. The purpose of the present investigation was to identify potential periodontal pathogens among these newly identified species and phylotypes. Species-specific ribosomal 16S primers for PCR amplification were developed for detection of new species. Associations with chronic periodontitis were observed for several new species or phylotypes, including uncultivated clones D084 and BH017 from the Deferribacteres phylum, AU126 from the Bacteroidetes phylum, Megasphaera clone BB166, clone X112 from the OP11 phylum, and clone I025 from the TM7 phylum, and the named species Eubacterium saphenum, Porphyromonas endodontalis, Prevotella denticola, and Cryptobacterium curtum. Species or phylotypes more prevalent in periodontal health included two uncultivated phylotypes, clone W090 from the Deferribacteres phylum and clone BU063 from the Bacteroidetes, and named species Atopobium rimae and Atopobium parvulum.

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

PubMed

Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

2008-03-01

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

Are Uncultivated Bacteria Really Uncultivable?

PubMed Central

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

2012-01-01

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

Biogenic magnetite as a primary remanence carrier in limestone deposits

NASA Astrophysics Data System (ADS)

Chang, Shih-Bin R.; Kirschvink, Joseph L.; Stolz, John F.

1987-06-01

Studies on the microbial communities and magnetic phases of samples collected from carbonate oozes at Sugarloaf Key, FL, U.S.A. and calcareous laminated sediments from Laguna Figueroa, Baja California, Mexico have revealed the existence of magnetotactic bacteria and ultrafine-grained single domain magnetite in both environments. Magnetotactic bacteria were identified by light and electron microscopy. The single domain magnetite was detected by coercivity spectra analysis with a SQUID magnetometer and examined under the transmission electron microscope. The similarity, in terms of size and shape, between the single domain magnetite found in these sediments and the magnetite observed in the bacterial magnetosome from enriched cultures indicates the ultrafine-grained magnetite in these two marine environments was biologically formed. These results, combined with the common occurrences of ultrafine-grained magnetite in limestone deposits detected rock magnetically, suggest biogenic magnetite may be present and contribute to the magnetic remanence in these rocks. Several Cambrian limestone samples, separately collected from Siberia, China, and Kazakhstan, were examined for the presence of bacterial magnetite. Samples from the Lower Cambrian Sinskian Formation at Siberia Platform were found to contain both a large amount of apparently bacterial magnetite particles and a very stable primary magnetic component. Post-Cambrian diagenesis does not seem to affect the microgranulometry of these apparently bacterial magnetite crystals or the magnetic remanence carried by them. Assessing the potential role of biogenic magnetite as a primary remanence carrier in other Phanerozoic limestone deposits ought to be further pursued.

Interventional procedure based on nanorobots propelled and steered by flagellated magnetotactic bacteria for direct targeting of tumors in the human body.

PubMed

Martel, Sylvain; Felfoul, Ouajdi; Mohammadi, Mahmood; Mathieu, Jean-Baptiste

2008-01-01

Flagellated bacteria used as bio-actuators may prove to be efficient propulsion mechanisms for future hybrid medical nanorobots when operating in the microvasculature. Here, we briefly describe a medical interventional procedure where flagellated bacteria and more specifically MC-1 Magnetotactic Bacteria (MTB) can be used to propel and steer micro-devices and nanorobots under computer control to reach remote locations in the human body. In particular, we show through experimental results the potential of using MTB-tagged robots to deliver therapeutic agents to tumors even the ones located in deep regions of the human body. We also show that such bacterial nanorobots can be tracked inside the human body for enhanced targeting under computer guidance using MRI as imaging modality. MTB can not only be guided and controlled directly towards a specific target, but we also show experimentally that these flagellated bacterial nanorobots can be propelled and steered in vivo deeply through the interstitial region of a tumor. The targeting efficacy is increased when combined with larger ferromagnetic micro-carriers being propelled by magnetic gradients generated by a MRI platform to carry and release nanorobots propelled by a single flagellated bacterium near the arteriocapillar entry. Based on the experimental data obtained and the experience gathered during several experiments conducted in vivo with this new approach, a general medical interventional procedure is briefly described here in a biomedical engineering context.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Functional Analysis of the Magnetosome Island in Magnetospirillum gryphiswaldense: The mamAB Operon Is Sufficient for Magnetite Biomineralization

PubMed Central

Lohße, Anna; Ullrich, Susanne; Katzmann, Emanuel; Borg, Sarah; Wanner, Gerd; Richter, Michael; Voigt, Birgit; Schweder, Thomas; Schüler, Dirk

2011-01-01

Bacterial magnetosomes are membrane-enveloped, nanometer-sized crystals of magnetite, which serve for magnetotactic navigation. All genes implicated in the synthesis of these organelles are located in a conserved genomic magnetosome island (MAI). We performed a comprehensive bioinformatic, proteomic and genetic analysis of the MAI in Magnetospirillum gryphiswaldense. By the construction of large deletion mutants we demonstrate that the entire region is dispensable for growth, and the majority of MAI genes have no detectable function in magnetosome formation and could be eliminated without any effect. Only <25% of the region comprising four major operons could be associated with magnetite biomineralization, which correlated with high expression of these genes and their conservation among magnetotactic bacteria. Whereas only deletion of the mamAB operon resulted in the complete loss of magnetic particles, deletion of the conserved mms6, mamGFDC, and mamXY operons led to severe defects in morphology, size and organization of magnetite crystals. However, strains in which these operons were eliminated together retained the ability to synthesize small irregular crystallites, and weakly aligned in magnetic fields. This demonstrates that whereas the mamGFDC, mms6 and mamXY operons have crucial and partially overlapping functions for the formation of functional magnetosomes, the mamAB operon is the only region of the MAI, which is necessary and sufficient for magnetite biomineralization. Our data further reduce the known minimal gene set required for magnetosome formation and will be useful for future genome engineering approaches. PMID:22043287

Experimental mixtures of superparamagnetic and single-domain magnetite with respect to Day-Dunlop plots

NASA Astrophysics Data System (ADS)

Kumari, Monika; Hirt, Ann M.; Uebe, Rene; Schüler, Dirk; Tompa, Éva; Pósfai, Mihály; Lorenz, Wolfram; Ahrentorp, Fredrik; Jonasson, Christian; Johansson, Christer

2015-06-01

Day-Dunlop plots are widely used in paleomagnetic and environmental studies as a tool to determine the magnetic domain state of magnetite, i.e., superparamagnetic (SP), stable single-domain (SD), pseudosingle-domain (PSD), multidomain (MD), and their mixtures. The few experimental studies that have examined hysteresis properties of SD-SP mixtures of magnetite found that the ratios of saturation remanent magnetization to saturation magnetization and the coercivity of remanence to coercivity are low, when compared to expected theoretical mixing trends based on Langevin theory. This study reexamines Day-Dunlop plots using experimentally controlled mixtures of SD and SP magnetite grains. End-members include magnetotactic bacteria (MSR-1) as the SD source, and a commercial ferrofluid or magnetotactic bacteria (ΔA12) as the SP source. Each SP-component was added incrementally to a SD sample. Experimental results from these mixing series show that the magnetization and coercivity ratios are lower than the theoretical prediction for bulk SP magnetic size. Although steric repulsion was present between the particles, we cannot rule out interaction in the ferrofluid for higher concentrations. The SP bacteria are noninteracting as the magnetite was enclosed by an organic bilipid membrane. Our results demonstrate that the magnetization and coercivity ratios of SD-SP mixtures can lie in the PSD range, and that an unambiguous interpretation of particle size can only be made with information about the magnetic properties of the end-members.

Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs

PubMed Central

Katzmann, E.; Eibauer, M.; Lin, W.; Pan, Y.; Plitzko, J. M.

2013-01-01

Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale. PMID:24096429

Magnetotactic Bacteria as Potential Sources of Bioproducts

PubMed Central

Araujo, Ana Carolina V.; Abreu, Fernanda; Silva, Karen Tavares; Bazylinski, Dennis A.; Lins, Ulysses

2015-01-01

Magnetotactic bacteria (MTB) produce intracellular organelles called magnetosomes which are magnetic nanoparticles composed of magnetite (Fe3O4) or greigite (Fe3S4) enveloped by a lipid bilayer. The synthesis of a magnetosome is through a genetically controlled process in which the bacterium has control over the composition, direction of crystal growth, and the size and shape of the mineral crystal. As a result of this control, magnetosomes have narrow and uniform size ranges, relatively specific magnetic and crystalline properties, and an enveloping biological membrane. These features are not observed in magnetic particles produced abiotically and thus magnetosomes are of great interest in biotechnology. Most currently described MTB have been isolated from saline or brackish environments and the availability of their genomes has contributed to a better understanding and culturing of these fastidious microorganisms. Moreover, genome sequences have allowed researchers to study genes related to magnetosome production for the synthesis of magnetic particles for use in future commercial and medical applications. Here, we review the current information on the biology of MTB and apply, for the first time, a genome mining strategy on these microorganisms to search for secondary metabolite synthesis genes. More specifically, we discovered that the genome of the cultured MTB Magnetovibrio blakemorei, among other MTB, contains several metabolic pathways for the synthesis of secondary metabolites and other compounds, thereby raising the possibility of the co-production of new bioactive molecules along with magnetosomes by this species. PMID:25603340

A microsensor for the detection of a single pathogenic bacterium using magnetotactic bacteria-based bio-carriers: simulations and preliminary experiments.

PubMed

Denomme, Ryan C; Lu, Zhao; Martel, Sylvain

2007-01-01

The proposed Magnetotactic Bacteria (MTB) based bio-carrier has the potential to greatly improve pathogenic bacteria detection time, specificity, and sensitivity. Microbeads are attached to the MTB and are modified with a coating of an antibody or phage that is specific to the target pathogenic bacteria. Using magnetic fields, the modified MTB are swept through a solution and the target bacteria present become attached to the microbeads (due to the coating). Then, the MTB are brought to the detection region and the number of pathogenic bacteria is determined. The high swimming speed and controllability of the MTB make this method ideal for the fast detection of small concentrations of specific bacteria. This paper focuses on an impedimetric detection system that will be used to identify if a target bacterium is attached to the microbead. The proposed detection system measures changes in electrical impedance as objects (MTB, microbeads, and pathogenic bacteria) pass through a set of microelectrodes embedded in a microfluidic device. FEM simulation is used to acquire the optimized parameters for the design of such a system. Specifically, factors such as electrode/detection channel geometry, object size and position, which have direct effects on the detection sensitivity for a single bacterium or microparticle, are investigated. Polymer microbeads and the MTB system with an E. coli bacterium are considered to investigate their impedance variations. Furthermore, preliminary experimental data using a microfabricated microfluidic device connected to an impedance analyzer are presented.

[Significance of the bacterial flora in the etiology of apical periodontitis. Qualitative, quantitative and topographical aspects].

PubMed

Accorsi, S; Lavagnoli, G; Frigeri, S; Fiamminghi, L

1990-01-01

In the international literature it is shown the central role of root canal infection in the etiology of periapical lesions. As a matter of fact it has been proved (13) that sterile necrotic pulp tissue is completely unable to cause inflammatory reactions at the periapex. Infection of endodontic origin extends to the supporting tissues of the tooth only in the case of their acute inflammation (e.g. acute apical periodontitis, acute alveolar abscess, phoenix abscess). On the other hand in chronic inflammation bacteria remain confined in the endodontic space. Only few exceptions to this general rule have been experimentally proved. In endodontics we deal with a mixed infection which is composed by obligate anaerobes and by facultative anaerobes. The most frequently found obligate anaerobes are Bacteroides sp. and Fusobacterium sp. (Gram- rods) Anaerobic Diphtheroides (Gram+ rods) Peptostreptococcus sp. (Gram+ cocci) and Veilonella sp. (Gram- cocci). Actinomyces sp., Lactobacillus sp., Streptococcus sp., and Staphilococcus sp. are the facultative anaerobes most frequently found.

A scoring scheme for evaluating magnetofossil identifications

NASA Astrophysics Data System (ADS)

Kopp, R. E.; Kirschvink, J. L.

2007-12-01

In many Quaternary lacustrine and marine settings, fossil magnetotactic bacteria are a major contributor to sedimentary magnetization [1]. Magnetite particles produced by magnetotactic bacteria have traits, shaped by natural selection, that increase the efficiency with which the bacteria utilize iron and also facilitate the recognition of the particles' biological origin. In particular, magnetotactic bacteria generally produce particles with characteristic shapes and narrow size and shape distributions that lie within the single domain stability field. The particles have effective positive magnetic anisotropy, produced by alignment in chains and frequently by particle elongation. In addition, the crystals are often nearly stochiometric and have few crystallographic defects. Yet, despite these distinctive traits, there are few identified magnetofossils that predate the Quaternary, and many putative identifications are highly controversial. We propose a six-criteria scoring scheme for evaluating identifications based on the quality of the geological, magnetic, and electron microscopic evidence. Our criteria are: (1) whether the geological context is well-constrained stratigraphically, and whether paleomagnetic evidence suggests a primary magnetization; (2) whether magnetic or microscopic evidence support the presence of significant single-domain magnetite; (3) whether magnetic or ferromagnetic resonance evidence indicates narrow size and shape distributions, and whether microscopic evidence reveals single-domain particles with truncated edges, elongate single-domain particles, and/or narrow size and shape distributions; (4) whether ferromagnetic resonance, low-temperature magnetic, or electron microscopic evidence reveals the presence of chains; (5) whether low-temperature magnetometry, energy dispersive X-ray spectroscopy, or other techniques demonstrate the near-stochiometry of the particles; and (6) whether high-resolution TEM indicates the near- absence of crystallographic defects. We use criterion 1 to set the threshold for determining whether a magnetofossil identification is robust. Criteria 3 and 4 are assigned numerical scores that range from 0 to 4, while criteria 2, 5, and 6 are evaluated based on presence or absence. Based on this scheme, the oldest robust magnetofossils yet found come from the Cretaceous chalk beds of southern England [2], though Lower Cambrian limestones of the Pestrotsvet Formation, Siberia Platform, only marginally fail to meet our robust criteria [3]. Although magnetofossils have also been reported from Proterozoic, Archean, and Martian rocks, none of these identifications are robust. References: [1] R. E. Kopp and J. L. Kirschvink (2007). Earth Sci. Rev. doi:10.1016/j.earscirev.2007.08.001. [2] P. Montgomery et al. (1998). Earth Planet. Sci. Lett. 156: 209-224. [3] S. B. R. Chang et al. (1987). Phys. Earth Planet. Int. 46: 289-303.

Genetic variability of Spodoptera frugiperda (Lepidoptera: Noctuidae) in the Western Hemisphere

USDA-ARS?s Scientific Manuscript database

The fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith) is a migratory and polyphagous pest of both cultivated and uncultivated plant species in the Western Hemisphere. We investigated the genetic diversity of FAW by collecting 31 representative samples from the United States, Argentina, Panama...

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".

PubMed

Thrash, J Cameron; Seitz, Kiley W; Baker, Brett J; Temperton, Ben; Gillies, Lauren E; Rabalais, Nancy N; Henrissat, Bernard; Mason, Olivia U

2017-09-12

Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota , SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments- Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter. IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia. Copyright © 2017 Thrash et al.

Applications of Bacterial Magnetic Nanoparticles in Nanobiotechnology.

PubMed

Chen, Chuanfang; Wang, Pingping; Li, Linlin

2016-03-01

The bacterial magnetic nanoparticle (BMP) has been well researched in nanobiotechnology as a new magnetic crystal. The BMPs are extracted from magnetotactic bacteria and under precise biological control. Compared with engineered magnetic nanoparticles synthesized by chemical approaches, BMPs have the properties of large production, monodispersity, high crystallinity, and close-to-bulk magnetization, which enable BMPs to be the highly promising magnetic nanoparticles for nanobiotechnology. In this paper, we review the biomedical applications of BMPs in magnetic hyperthermia, drug treatment with tumour and bioseparation. In addition, the biodistribution and toxicity are also reviewed.

Final Environmental Assessment Demolition of Alpha Ramp, Grand Forks Air Force Base, North Dakota

DTIC Science & Technology

2007-01-01

including spring wheat, barley, sunflowers, potatoes, and sugar beets. Uncultivated lands are generally used for pasture and hay, urban...Forks, ND 58203 Jack HOURS; Adul* Mon.-Sat. 12 noon - 6pm Main www.gfpets.com (next to Dairy Queen) Emerado, ND 58228 * Competitive prices & Monthly

Environmental Assessment, Demolition of Alpha Ramp Grand Forks Air Force Base, North Dakota

DTIC Science & Technology

2007-01-01

potatoes, and sugar beets. Uncultivated lands are generally used for pasture and hay, urban development, recreation, and wildlife habitat. The main area...6pm Main www.gfpets.com (next to Dairy Queen) Emerado, ND 58228 * Competitive prices & Monthly specials * Military discounts * Homebound licensed

Ultra high-throughput nucleic acid sequencing as a tool for virus discovery in the turkey gut.

USDA-ARS?s Scientific Manuscript database

Recently, the use of the next generation of nucleic acid sequencing technology (i.e., 454 pyrosequencing, as developed by Roche/454 Life Sciences) has allowed an in-depth look at the uncultivated microorganisms present in complex environmental samples, including samples with agricultural importance....

Antibacterial properties of propolis (bee glue).

PubMed Central

Grange, J M; Davey, R W

1990-01-01

Propolis (bee glue) was found to have antibacterial activity against a range of commonly encountered cocci and Gram-positive rods, including the human tubercle bacillus, but only limited activity against Gram-negative bacilli. These findings confirm previous reports of antimicrobial properties of this material, possibly attributable to its high flavonoid content. PMID:2182860

The Bacterial Actin MamK

PubMed Central

Ozyamak, Ertan; Kollman, Justin; Agard, David A.; Komeili, Arash

2013-01-01

It is now recognized that actin-like proteins are widespread in bacteria and, in contrast to eukaryotic actins, are highly diverse in sequence and function. The bacterial actin, MamK, represents a clade, primarily found in magnetotactic bacteria, that is involved in the proper organization of subcellular organelles, termed magnetosomes. We have previously shown that MamK from Magnetospirillum magneticum AMB-1 (AMB-1) forms dynamic filaments in vivo. To gain further insights into the molecular mechanisms that underlie MamK dynamics and function, we have now studied the in vitro properties of MamK. We demonstrate that MamK is an ATPase that, in the presence of ATP, assembles rapidly into filaments that disassemble once ATP is depleted. The mutation of a conserved active site residue (E143A) abolishes ATPase activity of MamK but not its ability to form filaments. Filament disassembly depends on both ATPase activity and potassium levels, the latter of which results in the organization of MamK filaments into bundles. These data are consistent with observations indicating that accessory factors are required to promote filament disassembly and for spatial organization of filaments in vivo. We also used cryo-electron microscopy to obtain a high resolution structure of MamK filaments. MamK adopts a two-stranded helical filament architecture, but unlike eukaryotic actin and other actin-like filaments, subunits in MamK strands are unstaggered giving rise to a unique filament architecture. Beyond extending our knowledge of the properties and function of MamK in magnetotactic bacteria, this study emphasizes the functional and structural diversity of bacterial actins in general. PMID:23204522

Novel magnetite-producing magnetotactic bacteria belonging to the Gammaproteobacteria.

PubMed

Lefèvre, Christopher T; Viloria, Nathan; Schmidt, Marian L; Pósfai, Mihály; Frankel, Richard B; Bazylinski, Dennis A

2012-02-01

Two novel magnetotactic bacteria (MTB) were isolated from sediment and water collected from the Badwater Basin, Death Valley National Park and southeastern shore of the Salton Sea, respectively, and were designated as strains BW-2 and SS-5, respectively. Both organisms are rod-shaped, biomineralize magnetite, and are motile by means of flagella. The strains grow chemolithoautotrophically oxidizing thiosulfate and sulfide microaerobically as electron donors, with thiosulfate oxidized stoichiometrically to sulfate. They appear to utilize the Calvin-Benson-Bassham cycle for autotrophy based on ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity and the presence of partial sequences of RubisCO genes. Strains BW-2 and SS-5 biomineralize chains of octahedral magnetite crystals, although the crystals of SS-5 are elongated. Based on 16S rRNA gene sequences, both strains are phylogenetically affiliated with the Gammaproteobacteria class. Strain SS-5 belongs to the order Chromatiales; the cultured bacterium with the highest 16S rRNA gene sequence identity to SS-5 is Thiohalocapsa marina (93.0%). Strain BW-2 clearly belongs to the Thiotrichales; interestingly, the organism with the highest 16S rRNA gene sequence identity to this strain is Thiohalospira alkaliphila (90.2%), which belongs to the Chromatiales. Each strain represents a new genus. This is the first report of magnetite-producing MTB phylogenetically associated with the Gammaproteobacteria. This finding is important in that it significantly expands the phylogenetic diversity of the MTB. Physiology of these strains is similar to other MTB and continues to demonstrate their potential in nitrogen, iron, carbon and sulfur cycling in natural environments.

Electron cryotomography of vitrified cells with a Volta phase plate.

PubMed

Fukuda, Yoshiyuki; Laugks, Ulrike; Lučić, Vladan; Baumeister, Wolfgang; Danev, Radostin

2015-05-01

Electron cryotomography provides a means of studying the three dimensional structure of pleomorphic objects, such as organelles or cells, with a resolution of 1-3nm. A limitation in the study of radiation sensitive biological samples is the low signal-to-noise ratio of the tomograms which may obscure fine details. To overcome this limitation, the recently developed Volta phase plate (VPP) was applied in electron cryotomographic studies of a wide range of cellular structures, from magnetotactic bacteria to primary cultured neurons. The results show that the VPP improves contrast significantly and consequently the signal-to-noise ratio of the tomograms, moreover it avoids disturbing fringing artifacts typical for Zernike phase plates. The contrast improvement provided by the VPP was also confirmed in projection images of relatively thick (∼400nm) samples. In order to investigate the respective contributions of the VPP and the energy filter, images acquired with different combinations of the two were compared. Zero-loss energy filtering reduced the background noise in thicker areas of the sample and improved the contrast of features such as poly-β-hydroxybutyrate granules in magnetotactic bacteria, whereas the VPP provided an overall contrast improvement for all sample areas. After 3D reconstruction, tomograms acquired with the combination of a VPP and an energy filter showed structural features in neuronal processes with outstanding clarity. We also show that the VPP can be combined with focused ion beam milling to examine structures embedded deeply inside cells. Thus, we expect that VPP will become a standard element of the electron cryotomography workflow. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of temperate agriculture on neotropical migrant landbirds

Treesearch

Nicholas L. Rodenhouse; Louis B. Best; Raymond J. O' Connor; Eric K. Bollinger

1993-01-01

The ecology of Neotropical migrant landbirds in temperate farmland is reviewed to develop management recommendations for the conservation of migrants. Migrants constitute about 71% of bird species using farmland and 86% of bird species nesting there. The number and abundances of Neotropical migrants using farmland are greatest in uncultivated edges with trees and...

Spatial genetic variation among Spodoptera frugiperda (Lepidoptera: Noctuidae) sampled from the United States, Puerto Rico, Panama, and Argentina

USDA-ARS?s Scientific Manuscript database

The fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), is a migratory and polyphagous pest of both cultivated and uncultivated plant species in the Western Hemisphere. Understanding the genetic diversity and gene flow of this economically important pest can help to de...

Diversity of spirochetes in endodontic infections.

PubMed

Sakamoto, Mitsuo; Siqueira, José F; Rôças, Isabela N; Benno, Yoshimi

2009-05-01

The diversity of spirochetes in primary endodontic infections of teeth with chronic apical periodontitis or acute apical abscesses was investigated using 16S rRNA gene clone library analysis. The prevalences of three common cultivable oral Treponema species were also determined using species-specific nested PCR. All detected spirochetes belonged to the genus Treponema. Overall, 28 different taxa were identified from the 431 clones sequenced: 9 cultivable and validly named species, 1 cultivable as-yet-uncharacterized strain, and 18 as-yet-uncultivated phylotypes, 17 of which were novel. The large majority of clones (94%) were from cultivable named species. The numbers of Treponema species/phylotypes per selected positive sample ranged from 2 to 12. Species-specific nested PCR detected T. denticola, T. socranskii, and T. maltophilum in 59 (66%), 33 (37%), and 26 (29%) of the 90 cases of primary endodontic infections, respectively. Clone library analysis revealed diverse Treponema species/phylotypes as part of the microbiota associated with asymptomatic and symptomatic (abscess) endodontic infections. Although several as-yet-uncultivated Treponema phylotypes were disclosed, including novel taxa, cultivable named species were more abundant and frequently detected.

HEx: A heterologous expression platform for the discovery of fungal natural products

PubMed Central

Schlecht, Ulrich; Horecka, Joe; Lin, Hsiao-Ching; Naughton, Brian; Miranda, Molly; Li, Yong Fuga; Hennessy, James R.; Vandova, Gergana A.; Steinmetz, Lars M.; Sattely, Elizabeth; Khosla, Chaitan; Hillenmeyer, Maureen E.

2018-01-01

For decades, fungi have been a source of U.S. Food and Drug Administration–approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products. PMID:29651464

Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques

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

McLean, Jeffrey S.; Fansler, Sarah J.; Majors, Paul D.

Many human microbial infectious diseases including dental caries are polymicrobial in nature and how these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral microbes have been characterized in vitro, their physiology in vivo in the presence of the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these oral species remain uncultivated to date and little is known except their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated microorganisms will remain enigmatic despite their apparent disease correlation.more » To start addressing these knowledge gaps, we applied a novel combination of in vivo Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for temporal monitoring of carbohydrate utilization, organic acid production and identification of metabolically active and inactive bacterial species.« less

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

NASA Astrophysics Data System (ADS)

Jahn, Martin T.; Markert, Sebastian M.; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas

2016-10-01

Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

DOE PAGES

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica; ...

2014-08-29

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

Isolation of anaerobes from bubo associated with chancroid.

PubMed Central

Kumar, B; Sharma, V K; Bakaya, V; Ayyagiri, A

1991-01-01

Ten men with bubo associated with chancroid were studied for bacterial flora especially anaerobes. Anaerobes were isolated from all 10 buboes and eight out of 10 ulcers of chancroid. Anaerobic cocci, B melaninogenicus and B fragilis were the most common isolates. anaerobes probably play a role in the pathogenesis of bubo in chancroid. PMID:1680792

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa)

USDA-ARS?s Scientific Manuscript database

Strain NRRL B-41902 and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, gram-negative rods that formed cocci in late stationary phase. Subsequent to sequencing the 16S ribosomal RNA gene, it was found that strain NRRL B-41902 was...

Virulence arsenal of the most pathogenic species among the Gram-positive anaerobic cocci, Finegoldia magna.

PubMed

Boyanova, Lyudmila; Markovska, Rumyana; Mitov, Ivan

2016-12-01

This review focuses on the virulence arsenal of the most pathogenic species among Gram positive anaerobic cocci, Finegoldia magna according to recently published data from 2012 to 2016. Virulence factors like sortase dependent pili and F. magna adhesion factor (FAF) facilitate the start of the infection. Albumin binding protein (PAB) enhances F. magna survival. FAF, subtilisin-like extracellular serine protease (SufA) and superantigen protein L protect the bacteria from factors of innate defense system. SufA, capsule and tissue-destroying enzymes provide a deep penetration or spread of the infections and the protein L is associated with infection severity. Biofilm production results in infection chronification and complicated treatment as well as to persistence of multi-species biofilms. Resistance rates to quinolones (13.0->70%) and clindamycin (0-40.0%) are important, and resistance to penicillins (<4%), chloramphenicol (7.0%) and metronidazole (<7%) has been reported. F. magna should not be overlooked when present in monoinfections or mixed infections in humans. Copyright © 2016 Elsevier Ltd. All rights reserved.

The affect of low-coherent light on microbial colony forming ability and morphology of some gram-positive and gram-negative bacteria

NASA Astrophysics Data System (ADS)

Popov, Denis E.; Tuchina, Elena S.; Chernova, Julia A.; Podshibyakin, Dmitry; Rudik, Dmitry V.; Samsonova, Maria; Gromov, Igor; Tuchin, Valery V.

2005-06-01

Gram-negative E. coli, gram-positive facultative anaerobe cocci Staphylococcus lugdensis, Micrococcus halobius, and Stomatococcus mucilaginosus as subjects of study were chosen. LEDs with spectrum maxima at 405 nm (without any exogenous sensitizer) and 660 nm (in conjunction with methylene blue) and power densities of 23 mW/cm2 and 5.7 mW/cm2 accordingly as continuous light sources were chosen. Photosensitized light's affect by methylene blue was studied on E. coli only. The original scheme of experiment set up was developed. It permits one to increase expositions quantity in each experiment for more certain trend's construction over dose curves and decrease parasite flora sowing. As a result of accomplished studies it was established that blue low-coherent light have unalike weak light's dose depending suppressing effect on cocci whereas red low-coherent light have a moderate dose-depended suppressing effect at low irradiation doses and a moderate dose-depended stimulating effect at high irradiation doses on sensitized by MeBlue E. coli. For all ofthis, but Staphylococcus morphology changes were observed.

Genomics approach to the environmental community of microorganisms

NASA Astrophysics Data System (ADS)

Kawarabayasi, Y.; Maruyama, A.

2004-12-01

It was indicated by microscopic observation or comparison of 16S rDNA sequence that many extremophiles were surviving in many hydrothermal environments. But it is generally said that over 99% of total microbes are now uncultivable. Thus, we planned to identify uncultivable microbes through direct sequencing of environmental DNA. At first, shotgun plasmid libraries were directly constructed with the DNA molecules prepared from mixed microbes collected from low-temperature hydrothermal water at RM24 in the Southern East Pacific Rise (S-EPR). It was shown that the sequences of some number of clones indicated the similar feature to the intron in eukaryote or tandem repetitive sequence identified in some human familiar diseases. The results indicated that many microorganisms with eukaryotic feature were dominant in low temperature water of S-EPR. Secondly, shotgun plasmid libraries were constructed from the environmental DNA prepared from Beppu hot springs. The ORFs were easily identified all clones determined entire sequence. Thus it can be said that hot springs is good resources for searching novel genes. At last, the mixed microbes isolated from Suiyo seamount were used for construction of shotgun library. The clones in this library contained the ORFs. From some clones in hot spring and Suiyo sample, aminoacyl-tRNA synthatase, which is generally present in all organisms, was isolated by similarity. The phylogenetic analysis of aminoacyl-tRNA synthetase identified indicated that novel and unidentified microorganisms should be present in hot spring or Suiyo seamount. The novel genes identified from Suiyo seamount were also utilized for expression in E. coli. Some gene products were successfully obtained from the E. coli cells as soluble proteins. Some protein indicated the thermostability up to 70_E#8249;C, meaning that the original host cell of this gene should be stable up to the same temperature. Our work indicates that environmental genomics, including the direct cloning, sequencing of environmental DNA and expression of gene identified, is powerful approach to collect novel uncultivable microbes or novel active genes.

Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.

PubMed

McLean, Jeffrey S; Fansler, Sarah J; Majors, Paul D; McAteer, Kathleen; Allen, Lisa Z; Shirtliff, Mark E; Lux, Renate; Shi, Wenyuan

2012-01-01

Many human microbial infectious diseases including dental caries are polymicrobial in nature. How these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. Supragingival plaque samples from caries-free children incubated with (13)C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that are active at low pH can lead to a better understanding of oral caries onset and generate appropriate targets for preventative measures in the early stages.

Improved Method for Direct Detection of Environmental Microorganisms Using an Amplification of 16S rDNA Region

NASA Astrophysics Data System (ADS)

Tsujimura, M.; Akutsu, J.; Zhang, Z.; Sasaki, M.; Tajima, H.; Kawarabayasi, Y.

2004-12-01

The thermostable proteins or enzymes were expected to be capable to be utilized in many areas of industries. Many thermophilic microorganisms, which possess the thermostable proteins or enzymes, were identified from the extreme environment. However, many unidentified and uncultivable microorganisms are still remaining in the environment on the earth. It is generally said that the cultivable microorganisms are less than 1% of entire microorganisms living in the earth, remaining over 99% are still uncultivable. As an approach to the uncultivable microorganisms, the PCR amplification of 16S rDNA region using primer sets designed from the conserved region has been generally utilized for detection and community analysis of microorganism in the environment. However, the facts, that PCR amplification introduces the mutation in the amplified DNA fragment and efficiency of PCR amplification is depend on the sequences of primer sets, indicated that the improving of PCR analysis was necessary for more correct detection of microorganisms. As the result of evaluation for the quality of DNA polymerases, sequences of primers used for amplification and conditions of PCR amplification, the DNA polymerase, the primer set and the conditions for amplification, which did not amplify the DNA fragment from the DNA contaminated within the DNA polymerase itself, were successfully selected. Also the rate of mutation in the DNA fragment amplified was evaluated using this conditions and the genomic DNA from cultivable microbes as a template. The result indicated the rate of mutation introduced by PCR was approximately 0.1% to 0.125%. The improved method using these conditions and error rate calculated was applied for the analysis of microorganisms in the geothermal environment. The result indicated that four kinds of dominant microorganisms, including both of bacteria and archaea, were alive within soil in the hot spring in Tohoku Area. We would like to apply this improved method to detection of microorganisms with important genes from more other environments.

In vitro activity of monoclonal and recombinant yeast killer toxin-like antibodies against antibiotic-resistant gram-positive cocci.

PubMed Central

Conti, S.; Magliani, W.; Arseni, S.; Dieci, E.; Frazzi, R.; Salati, A.; Varaldo, P. E.; Polonelli, L.

2000-01-01

BACKGROUND: Monoclonal (mAbKT) and recombinant single-chain (scFvKT) anti-idiotypic antibodies were produced to represent the internal image of a yeast killer toxin (KT) characterized by a wide spectrum of antimicrobial activity, including gram-positive cocci. Pathogenic eukaryotic and prokaryotic microorganisms, such as Candida albicans, Pneumocystis carinii, and a multidrug-resistant strain of Mycobacterium tuberculosis, presenting specific, although yet undefined, KT-cell wall receptors (KTR), have proven to be killed in vitro by mAbKT and scFvKT. mAbKT and scFvKT exert a therapeutic effect in vivo in experimental models of candidiasis and pneumocystosis by mimicking the functional activity of protective antibodies naturally produced in humans against KTR of infecting microorganisms. The swelling tide of concern over increasing bacterial resistance to antibiotic drugs gives the impetus to develop new therapeutic compounds against microbial threat. Thus, the in vitro bactericidal activity of mAbKT and scFvKT against gram-positive, drug-resistant cocci of major epidemiological interest was investigated. MATERIALS AND METHODS: mAbKT and scFvKT generated by hybridoma and DNA recombinant technology from the spleen lymphocytes of mice immunized with a KT-neutralizing monoclonal antibody (mAb KT4) were used in a conventional colony forming unit (CFU) assay to determine, from a qualitative point of view, their bactericidal activity against Staphylococcus aureus, S. haemolyticus, Enterococcus faecalis, E. faecium, and Streptococcus pneumoniae strains. These bacterial strains are characterized by different patterns of resistance to antibiotics, including methicillin, vancomycin, and penicillin. RESULTS: According to the experimental conditions adopted, no bacterial isolate proved to be resistant to the activity of mAbKT and scFvKT. CONCLUSIONS: scFvKT exerted a microbicidal activity against multidrug resistant bacteria, which may represent the basis for the drug modeling of new antibiotics with broad antibacterial spectra to tackle the emergence of microbial resistance. PMID:10997342

Bacterial Magnetosome: A Novel Biogenetic Magnetic Targeted Drug Carrier with Potential Multifunctions

PubMed Central

Sun, Jianbo; Li, Ying; Liang, Xing-Jie; Wang, Paul C.

2012-01-01

Bacterial magnetosomes (BMs) synthesized by magnetotactic bacteria have recently drawn great interest due to their unique features. BMs are used experimentally as carriers for antibodies, enzymes, ligands, nucleic acids, and chemotherapeutic drugs. In addition to the common attractive properties of magnetic carriers, BMs also show superiority as targeting nanoscale drug carriers, which is hardly matched by artificial magnetic particles. We are presenting the potential applications of BMs as drug carriers by introducing the drug-loading methods and strategies and the recent research progress of BMs which has contributed to the application of BMs as drug carriers. PMID:22448162

Application of duplex droplet digital PCR for detection of “Candidatus Liberibacter asiaticus” using 16S rRNA and ribonucleotide reductase genes

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) is the most destructive disease of citrus and has been detected in over 250 urban citrus trees in southern California. HLB is associated with the uncultivable bacterium “Candidatus Liberibacter asiaticus” (CLas) and is transmitted by the Asian citrus psyllid. Quarantines in Calif...

Single-cell genomics for the masses

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

Tringe, Susannah G.

In this issue of Nature Biotechnology, Lan et al. describe a new tool in the toolkit for studying uncultivated microbial communities, enabling orders of magnitude higher single cell genome throughput than previous methods. This is achieved by a complex droplet microfluidics workflow encompassing steps from physical cell isolation through genome sequencing, producing tens of thousands of lowcoverage genomes from individual cells.

Single-cell genomics for the masses

DOE PAGES

Tringe, Susannah G.

2017-07-12

In this issue of Nature Biotechnology, Lan et al. describe a new tool in the toolkit for studying uncultivated microbial communities, enabling orders of magnitude higher single cell genome throughput than previous methods. This is achieved by a complex droplet microfluidics workflow encompassing steps from physical cell isolation through genome sequencing, producing tens of thousands of lowcoverage genomes from individual cells.

Politics of aviation fields

NASA Technical Reports Server (NTRS)

Vivent, Jacques

1922-01-01

In short, the "politics of aviation" lies in a few propositions: the need of having as large a number of fields as possible and of sufficient area; the utilization of the larger part of the existing military fields; the selection of uncultivated or unproductive fields, whenever technical conditions permit; ability to disregard (save in exceptional cases) objections of an agricultural nature.

Bacteremia Caused by Kocuria kristinae from Egypt: Are There More? A Case Report and Review of the Literature.

PubMed

Hassan, Reem M; Bassiouny, Dina M; Matar, Yomna

2016-01-01

Kocuria kristinae is opportunistic Gram-positive cocci from the family Micrococcaceae. It is usually considered part of the normal flora that rarely is isolated from clinical specimens. Here, we report a case of Kocuria kristinae bacteremia; to the best of our knowledge, this is the first report from Egypt.

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro

USDA-ARS?s Scientific Manuscript database

Aims: The goal was to determine the effect of starch source (corn, oats and wheat) and concentration on: 1) total amylolytic bacteria, Group D Gram-positive cocci (GPC), lactobacilli, and lactate-utilizing bacteria, and 2) fermentation by equine microflora. Methods and Results: When fecal washed cel...

Occurrence of gigantic biogenic magnetite during the Paleocene-Eocene Thermal Maximum

NASA Astrophysics Data System (ADS)

Schumann, D.; Raub, T. D.; Kopp, R. E.; Guerquin-Kern, J. L.; Wu, T. D.; Rouiller, I.; Smirnov, A. V.; Sears, S. K.; Lücken, U.; Tikoo, S. M.; Hesse, R.; Kirschvink, J. L.; Vali, H.

2009-04-01

The Paleocene-Eocene Thermal Maximum (PETM) is one of the most severe climatic events of the Cenozoic Era. A massive injection of light carbon into the oceans and atmosphere over a few thousand of years triggered drastic perturbation of Earth's climate resulting in abrupt global warming of ~5-9oC [Sluijs et al., 2007] that persisted for ~180,000 years. This episode is marked by the diversification and radiation of terrestrial plants and mammals while in the marine realm numerous deep-sea benthic foraminifera species disappeared and new forms evolved. Sediments deposited during the PETM are clay-rich and contain distinct evidence of these climatic changes. Kopp et al., (2007) and Lippert & Zachos (2007) report an extraordinary magnetofossil ‘Lagerstätte' in lowermost Eocene kaolinite-rich clay sediments deposited at subtropical paleolatitude in the Atlantic Coastal Plain of New Jersey, USA. Magnetofossils are magnetic particles produced most abundantly by magnetotactic bacteria. Kopp et al. (2007) and Lippert & Zachos (2007) used ferromagnetic resonance (FMR) spectroscopy, other rock magnetic methods, and transmission electron microscopy (TEM) of magnetic separates to characterize sediments from boreholes at Ancora (ODP Leg 174AX) and Wilson Lake, NJ, respectively. These sediments contain abundant ~40- to 300-nm cuboidal, elongate-prismatic and bullet-shaped magnetofossils, sometimes arranged in short chains, resembling crystals in living magnetotactic bacteria. Despite the scarcity of intact magnetofossil chains, the asymmetry ratios of the FMR spectra reflects a profusion of elongate single domain (SD) crystals and/or chains. Here we address both conundrums by reporting the discovery from these same sediments of exceptionally large and novel biogenic magnetite crystals unlike any previously reported from living organisms or from sediments. Aside from abundant bacterial magnetofossils, electron microscopy reveals novel spearhead-like and spindle-like magnetite crystals up to 4 μm long (eight times larger than magnetite produced by magnetotactic bacteria) and elongated hexaoctahedra up to 1.4 μm long. Similar to magnetite produced by magnetotactic bacteria, these single-crystal particles exhibit chemical composition and lattice perfection consistent with a biogenic origin. The oxygen isotopic composition of indiviual particles supports a low temperature aquatic origin. Electron holography indicates single-domain magnetization despite the large crystal size. In a few cases, we observed apparently intact, tip-outward spherical assemblages of spearhead-like particles that possibly represent the preserved original biological arrangement of these crystals in a hitherto unknown magnetite producing organism. The discovery of these exceptionally large biogenic magnetite crystals that possibly represent the remains of a new microorganism that appeared and disappeared with the PETM sheds some light upon the ecological response to biogeochemical changes that occurred during this warming event. The abundance of fossil magnetotactic bacteria on the Atlantic Coastal Plain during the PETM could be explained by enhanced production, enhanced preservation, or both. The presence of novel magnetofossils, however, argues that changes in growth conditions are a major part of the explanation. Considering that other bacterial magnetofossils are present (although less abundant) and well-preserved in sediments below and above the PETM clay, as well as in a sand lens within the PETM clay [Kopp et al., 2007], suggests that the new magnetofossils are unlikely to be a preservation artefact. We conclude, therefore, that the development of a thick suboxic zone with high iron bioavailability - a product of dramatic changes in weathering and sedimentation patterns driven by severe global warming - resulted in diversification of magnetite-forming organisms, likely including eukaryotes. In this study we extended the search for these new magnetofossils [Schumann et al. 2008] to other PETM locations of the Atlantic margin and to a possible modern analog environment. High surface productivity with low-organic carbon density sediments and meter-scale sedimentary suboxic zones are provided by tropical shelves fed by energetic river systems, such as the Amazon. We inverstigated several magnetic extracts of samples taken from the meter-scale suboxic zones of the Amazone delta system. Sluijs A, Brinkhuis H, Schouten S, Bohaty SM, John CM, Zachos JC, Reichart GJ, Damste JSS, Crouch EM, Dickens GR. 2007. Environmental precursors to rapid light carbon injection at the Palaeocene/Eocene boundary. Nature 450:1218-1221. Kopp RE, Raub TD, Schumann D, Vali H, Smirnov AV, Kirschvink JL 2007. Magnetofossil spike during the Paleocene-Eocene thermal maximum: Ferromagnetic resonance, rock magnetic, and electron microscopy evidence from Ancora, New Jersey, United States. Paleoceanography, doi:10.1029/2007pa001473. Lipper PC, Zachos JC 2007. A biogenic origin for anomalous fine-grained magnetic material at the Paleocone-Eocene booundary at Wilson Lake, New Jesery. Paleoceanography, doi:10.1029/2007pa001471. Schumann D, Raub TD, Kopp RE, Guerquin-Kern JL, Wu TD, Rouiller I, Smirnov AV, Sears K, Lücken U, Tikoo SM, Hesse R, Kirschvink JL, Vali H 2008. Gigantism in unique biogenic magnetite at the Paleocene-Eocene Thermal Maximum. PNAS, 105:17648-17653.

From Magnetotactic Bacteria to Sediment Magnetizations: new insights

NASA Astrophysics Data System (ADS)

Egli, R.; Mao, X.; Zhao, X.

2015-12-01

Magnetotactic bacteria (MTB) represent one of the most intriguing examples of iron biomineralization and magnetic navigation in nature. MTB synthesize magnetic nanocrystals, called magnetosomes, which act as an incorporated compass for navigation purposes (magnetotaxis). MTB are ubiquitous organisms living in chemically stratified freshwater and marine environments, where they contribute significantly to the Fe cycle. Magnetosomes accumulate as fossil MTB remains in sediment (magnetofossils). The recent development of magnetic measurement protocols enabling to detect small magnetosome concentrations among complex iron mineral mixtures led to the discovery that magnetofossil preservation over geological times is not uncommon. Therefore, magnetofossils can play an important role in sedimentary records of the Earth's magnetic field, as well as conveying selective information about past environmental conditions (e.g. redox conditions and nutrient concentration). Paleomagnetic and environmental applications require us to understand the processes that control MTB occurrence, magnetofossil formation and preservation, and the final alignment with the Earth's magnetic field. Our current knowledge relies mostly on experiments performed with cultured MTB in aqueous solutions, under physical and chemical conditions that do not necessarily reproduce those encountered in sediment. These experiments have been pivotal for understanding magnetosome growth and the fundaments of magnetotaxis. On the other hand, recent investigations of living MTB populations in sediment with specially developed observation techniques led to unexpected findings, with important implications for magnetotaxis models, MTB ecology, and, indirectly, for modeling the acquisition of natural magnetizations in bioturbated sediments. Ludwig, P. et al. (2013), Global Planet. Change 110, 321-339. Mao, X. et al. (2014), Geochem. Geophys. Geosys. 15, doi:10.1002/2013GC005034. Mao, X. et al. (2014). PLoS ONE 9, doi:10.1371/journal.pone.0102810. Roberts, A. et al. (2012). J. Geophys. Res. 117, B08104.

Effect of surface hydrophobicity on the function of the immobilized biomineralization protein Mms6

DOE PAGES

Liu, Xunpei; Zhang, Honghu; Nayak, Srikanth; ...

2015-08-13

Magnetotactic bacteria produce magnetic nanocrystals with uniform shapes and sizes in nature, which has inspired in vitro synthesis of uniformly sized magnetite nanocrystals under mild conditions. Mms6, a biomineralization protein from magnetotactic bacteria with a hydrophobic N-terminal domain and a hydrophilic C-terminal domain, can promote formation of magnetite nanocrystals in vitro with well-defined shape and size in gels under mild conditions. Here we investigate the role of surface hydrophobicity on the ability of Mms6 to template magnetite nanoparticle formation on surfaces. Our results confirmed that Mms6 can form a protein network structure on a monolayer of hydrophobic octadecanethiol (ODT)-coated goldmore » surfaces and facilitate magnetite nanocrystal formation with uniform sizes close to those seen in nature, in contrast to its behavior on more hydrophilic surfaces. We propose that this hydrophobicity effect might be due to the amphiphilic nature of the Mms6 protein and its tendency to incorporate the hydrophobic N-terminal domain into the hydrophobic lipid bilayer environment of the magnetosome membrane, exposing the hydrophilic C-terminal domain that promotes biomineralization. Supporting this hypothesis, the larger and well-formed magnetite nanoparticles were found to be preferentially located on ODT surfaces covered with Mms6 as compared to control samples, as characterized by scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and atomic force microscopy studies. A C-terminal domain mutant of this protein did not form the same network structure as wild-type Mms6, suggesting that the network structure is important for the magnetite nanocrystal formation. This article provides valuable insights into the role of surface hydrophilicity on the action of the biomineralization protein Mms6 to synthesize magnetic nanocrystals and provides a facile route to controlling bioinspired nanocrystal synthesis in vitro.« less

Tracking heterotrophic and autotrophic carbon cycling by magnetotactic bacteria in freshwater sediments using DNA stable isotope probing

NASA Astrophysics Data System (ADS)

Kürşat Coşkun, Ömer; Roud, Sophie; He, Kuang; Petersen, Nikolai; Gilder, Stuart; Orsi, William D.

2017-04-01

Magnetotactic bacteria (MTB) are diverse, widespread, motile prokaryotes which biomineralize nanosize magnetic minerals, either magnetite or gregite, under highly conserved genetic control and have magnetotaxis to align their position in aquatic environment according to Earth's magnetic field. They play important roles on some geobiological cycle of important minerals such as iron, sulphur, nitrogen and carbon. Yet, to date, their importance in carbon cycle and carbon source in their natural environment have not been previously studied. In this study, we focused on freshwater benthic carbon cycling of MTB and total bacteria using DNA stable isotope probing (DNA-SIP) technique coupled with quantitative PCR (qPCR). Pond sediments from Unterlippach (Germany) were amended with 13C-labelled sodium bicarbonate and 13C-labelled organic matter, and incubated in the dark over a two week time period. Applying separate qPCR assays specific for total bacteria and MTB, respectively, allowed us to estimate the contribution of MTB to total heterotrophic and autotrophic carbon cycling via DNA-SIP. After one week, there was a slight degree of autotrophic activity which increased markedly after two weeks. Comparing total DNA to the qPCR data revealed that changes in the buoyant density of DNA was due mainly to autotrophic bacterial production. DNA-SIP also identified heterotrophic utilization of 13C-labelled organic matter by MTB after 1 week. The qPCR data also allowed us to estimate uptake rates based on the incubation times for heterotrophic and autotrophic MTB. High-throughput DNA sequencing of 16S rRNA genes showed that most of the MTB involved in carbon cycling were related to the Magnetococcus genus. This study sheds light on the carbon sources for MTB in a natural environment and helps unravel their ecological role in the carbon cycle.

Characterization of host plant resistance to zebra chip disease from species-derived potato genotypes and the identification of new sources of zebra chip resistance

USDA-ARS?s Scientific Manuscript database

‘Candidatus Liberibacter solanacearum’ (Lso), an uncultivable phloem-limited phytopathogenic bacterium, is known to be associated with Zebra Chip disease (ZC), which represents a major threat to potato production in the US and elsewhere. This pathogen is transmitted by the phloem-feeding potato psyl...

Occurrence of the western flower thrips, Franklliniella occidentalis, and potential predators on host plants in near-orchard habitats of Washington and Oregon (Thysanoptera: Thripidae)

USDA-ARS?s Scientific Manuscript database

One hundred thirty species of native and introduced plants growing in uncultivated land adjacent to apple and pear orchards of central Washington and northern Oregon were sampled for the presence of the western flower thrips (WFT) Frankliniella occidentalis (Pergande), 1895 and potential thrips pred...

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

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

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

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

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

PubMed Central

Roux, Simon; Hawley, Alyse K; Torres Beltran, Monica; Scofield, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J; Sullivan, Matthew B

2014-01-01

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs. DOI: http://dx.doi.org/10.7554/eLife.03125.001 PMID:25171894

Bacteremia Caused by Kocuria kristinae from Egypt: Are There More? A Case Report and Review of the Literature

PubMed Central

Bassiouny, Dina M.; Matar, Yomna

2016-01-01

Kocuria kristinae is opportunistic Gram-positive cocci from the family Micrococcaceae. It is usually considered part of the normal flora that rarely is isolated from clinical specimens. Here, we report a case of Kocuria kristinae bacteremia; to the best of our knowledge, this is the first report from Egypt. PMID:27872773

Disubstituted thiourea derivatives and their activity on CNS: synthesis and biological evaluation.

PubMed

Stefanska, Joanna; Szulczyk, Daniel; Koziol, Anna E; Miroslaw, Barbara; Kedzierska, Ewa; Fidecka, Sylwia; Busonera, Bernardetta; Sanna, Giuseppina; Giliberti, Gabriele; La Colla, Paolo; Struga, Marta

2012-09-01

A series of new thiourea derivatives of 1,2,4-triazole have been synthesized. The difference in structures of obtained compounds are directly connected with the kind of isothiocyanate (aryl/alkyl). The (1)H NMR, (13)C NMR, MS methods were used to confirm structures of obtained thiourea derivatives. The molecular structure of (1, 17) was determined by an X-ray analysis. Two of the new compounds (8 and 14) were tested for their pharmacological activity on animal central nervous system (CNS) in behavioural animal tests. The results presented in this work indicate the possible involvement of the serotonergic system in the activity of 8 and 14. In the case of 14 is also a possible link between its activity and the endogenous opioid system. All obtained compounds were tested for antibacterial activity against gram-positive cocci, gram-negative rods and antifungal activity. Compounds (1, 2, 5, 7, 9) showed significant inhibition against gram-positive cocci. Microbiological evaluation was carried out over 20 standard strains and 30 hospital strains. Selected compounds (1-13) were examined for cytotoxicity, antitumor, and anti-HIV activity. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

ESTABLISHING NORMAL FECAL FLORA IN WILD AUSTRALIAN PASSERINE BIRDS BY USE OF THE FECAL GRAM STAIN.

PubMed

Latham, Benjamin; Leishman, Alan; Martin, John; Phalen, David

2017-09-01

The purpose of this study was to determine the normal fecal bacterial and fungal flora and parasite prevalence in wild passerine birds found at the Australian Botanic Garden (Mount Annan, New South Wales). Wild passerine birds (n = 186) from 28 species were captured with mist nets. Fecal Gram stains (n = 155) were made from 26 species and analyzed for bacterial density, Gram stain morphology, and the presence of yeast. Fecal wet preparations (n = 139) were made from 24 passerine species and were analyzed for parasites. Our results showed that 81.9% of passerines sampled had bacteria present in their feces. The bacteria found were entirely Gram positive and consisted predominantly of cocci. Individuals that were caught on multiple occasions were found to have stable bacterial populations, apart from the red-browed finch (Neochmia temporalis). Insectivores had higher bacterial densities and cocci proportions than nectarivores had. Yeasts were rare in most species, with the exception of the bell miner (Manorina melanophrys) and noisy miner (Manorina melanocephala). The yeast, Macrorhabdus ornithogaster, and parasites were not observed in any fecal samples. These results will help practitioners to assess the health of Australian passerine species submitted for care or housed in zoological collections.

[Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

PubMed

Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

2014-01-01

The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Tuning bacterial hydrodynamics with magnetic fields

NASA Astrophysics Data System (ADS)

Pierce, C. J.; Mumper, E.; Brown, E. E.; Brangham, J. T.; Lower, B. H.; Lower, S. K.; Yang, F. Y.; Sooryakumar, R.

2017-06-01

Magnetotactic bacteria are a group of motile prokaryotes that synthesize chains of lipid-bound, magnetic nanoparticles called magnetosomes. This study exploits their innate magnetism to investigate previously unexplored facets of bacterial hydrodynamics at surfaces. Through use of weak, uniform, external magnetic fields and local, micromagnetic surface patterns, the relative strength of hydrodynamic, magnetic, and flagellar force components is tuned through magnetic control of the bacteria's orientation. The resulting swimming behaviors provide a means to experimentally determine hydrodynamic parameters and offer a high degree of control over large numbers of living microscopic entities. The implications of this controlled motion for studies of bacterial motility near surfaces and for micro- and nanotechnology are discussed.

Persistence of oxyfluorfen in soil, runoff water, sediment and plants of a sunflower cultivation.

PubMed

Mantzos, N; Karakitsou, A; Hela, D; Patakioutas, G; Leneti, E; Konstantinou, I

2014-02-15

A field dissipation and transport study of oxyfluorfen in a sunflower cultivation under Mediterranean conditions have been conducted in silty clay plots (cultivated and uncultivated) with two surface slopes (1% and 5%). The soil dissipation and transport of oxyfluorfen in runoff water and sediment, as well as the uptake by sunflower plants, were investigated over a period of 191 days. Among different kinetic models assayed, soil dissipation rate of oxyfluorfen was better described by first-order kinetics. The average half-life was 45 and 45.5 days in cultivated plots with soil slopes 5% and 1% respectively, and 50.9 and 52.9 days in uncultivated plots with soil slopes 5% and 1%. The herbicide was detected below the 10 cm soil layer 45 days after application (DAA). Limited amounts of oxyfluorfen were moved with runoff water and the cumulative losses from tilled and untilled plots with slope 5% were estimated at 0.007% and 0.005% of the initial applied active ingredient, while for the plots with slope of 1%, the respective values were 0.002% and 0.001%. The maximum concentration of oxyfluorfen in sediment ranged from 1.46 μg g(-1) in cultivated plot with soil slope 1% to 2.33 μg g(-1) in uncultivated plot with soil slope 5%. The cumulative losses from tilled and untilled plots with slope 5% were estimated at 0.217% and 0.170% while for the plots with slope of 1%, the respective values were 0.055% and 0.025%. Oxyfluorfen was detected in sunflower plants until the day of harvest; maximum concentrations in stems and leaves (0.042 μg g(-1)) were observed 33 DAA and in roots (0.025 μg g(-1)) 36 DAA. In conclusion, oxyfluorfen hardly moves into silty clay soil and exhibited low run-off potential so it represents a low risk herbicide for the contamination of ground and adjacent water resources. Copyright © 2013 Elsevier B.V. All rights reserved.

Phosphorus load to surface water from bank erosion in a Danish lowland river basin.

PubMed

Kronvang, Brian; Audet, Joachim; Baattrup-Pedersen, Annette; Jensen, Henning S; Larsen, Søren E

2012-01-01

Phosphorus loss from bank erosion was studied in the catchment of River Odense, a lowland Danish river basin, with the aim of testing the hypothesis of whether stream banks act as major diffuse phosphorus (P) sources at catchment scale. Furthermore, the study aimed at analyzing the impact of different factors influencing bank erosion and P loss such as stream order, anthropogenic disturbances, width of uncultivated buffer strips, and the vegetation of buffer strips. A random stratified procedure in geographical information system (GIS) was used to select two replicate stream reaches covering different stream orders, channelized vs. naturally meandering channels, width of uncultivated buffer strips (≤ 2 m and ≥ 10 m), and buffer strips with different vegetation types. Thirty-six 100-m stream reaches with 180 bank plots and a total of 3000 erosion pins were established in autumn 2006, and readings were conducted during a 3-yr period (2006-2009). The results show that neither stream size nor stream disturbance measured as channelization of channel or the width of uncultivated buffer strip had any significant ( < 0.05) influence on bank erosion and P losses during each of the 3 yr studied. In buffer strips with natural trees bank erosion was significantly ( < 0.05) lower than in buffer strips dominated by grass and herbs. Gross and net P input from bank erosion amounted to 13.8 to 16.5 and 2.4 to 6.3 t P, respectively, in the River Odense catchment during the three study years. The net P input from bank erosion equaled 17 to 29% of the annual total P export and 21 to 62% of the annual export of P from diffuse sources from the River Odense catchment. Most of the exported total P was found to be bioavailable (71.7%) based on a P speciation of monthly suspended sediment samples collected at the outlet of the river basin. The results found in this study have a great importance for managers working with P mitigation and modeling at catchment scale. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Bioinspired synthesis of magnetic nanoparticles

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

David, Anand

2009-01-01

The synthesis of magnetic nanoparticles has long been an area of active research. Magnetic nanoparticles can be used in a wide variety of applications such as magnetic inks, magnetic memory devices, drug delivery, magnetic resonance imaging (MRI) contrast agents, and pathogen detection in foods. In applications such as MRI, particle uniformity is particularly crucial, as is the magnetic response of the particles. Uniform magnetic particles with good magnetic properties are therefore required. One particularly effective technique for synthesizing nanoparticles involves biomineralization, which is a naturally occurring process that can produce highly complex nanostructures. Also, the technique involves mild conditions (ambientmore » temperature and close to neutral pH) that make this approach suitable for a wide variety of materials. The term 'bioinspired' is important because biomineralization research is inspired by the naturally occurring process, which occurs in certain microorganisms called 'magnetotactic bacteria'. Magnetotactic bacteria use biomineralization proteins to produce magnetite crystals having very good uniformity in size and morphology. The bacteria use these magnetic particles to navigate according to external magnetic fields. Because these bacteria synthesize high quality crystals, research has focused on imitating aspects of this biomineralization in vitro. In particular, a biomineralization iron-binding protein found in a certain species of magnetotactic bacteria, magnetospirillum magneticum, AMB-1, has been extracted and used for in vitro magnetite synthesis; Pluronic F127 gel was used to increase the viscosity of the reaction medium to better mimic the conditions in the bacteria. It was shown that the biomineralization protein mms6 was able to facilitate uniform magnetite synthesis. In addition, a similar biomineralization process using mms6 and a shorter version of this protein, C25, has been used to synthesize cobalt ferrite particles. The overall goal of this project is to understand the mechanism of magnetite particle synthesis in the presence of the biomineralization proteins, mms6 and C25. Previous work has hypothesized that the mms6 protein helps to template magnetite and cobalt ferrite particle synthesis and that the C25 protein templates cobalt ferrite formation. However, the effect of parameters such as the protein concentration on the particle formation is still unknown. It is expected that the protein concentration significantly affects the nucleation and growth of magnetite. Since the protein provides iron-binding sites, it is expected that magnetite crystals would nucleate at those sites. In addition, in the previous work, the reaction medium after completion of the reaction was in the solution phase, and magnetic particles had a tendency to fall to the bottom of the medium and aggregate. The research presented in this thesis involves solid Pluronic gel phase reactions, which can be studied readily using small-angle x-ray scattering, which is not possible for the solution phase experiments. In addition, the concentration effect of both of the proteins on magnetite crystal formation was studied.« less

Coliform bacteria removal from sewage in constructed wetlands planted with Mentha aquatica.

PubMed

Avelar, Fabiana F; de Matos, Antonio T; de Matos, Mateus P; Borges, Alisson C

2014-08-01

The present study evaluated the performance of the species Mentha aquatica in constructed wetlands of horizontal subsurface flow (CW-HSSF) with regard to the removal of coliforms bacteria in an effluent from the primary treatment of sewage as well as to obtain adjustment parameters of the bacterial decay kinetic model along the length of the CW-HSSF. Therefore, four CW-HSSFs measuring 24.0 m x 1.0 m x 0.35 m were built and filled with number 0 gravel as the support medium to a height of 0.20m. Two of the CW-HSSFs were planted with the species M. aquatica, while the other two remained uncultivated. Cultivation of M. aquatica in CW-HSSF resulted in total coliforms (TC) and Escherichia coli (EC) removals from 0.9 to 1.3 log units greater than those obtained in the uncultivated experimental plots, for the hydraulic retention times (HRTs) of 4.5 and 6.0 days. For HRT ranged from 1.5 to 6.0 days, the highest removal efficiencies in counts of TC and EC were obtained when using longer HRT. The mathematical models evaluated showed good fit to average counts of TC and EC highlighting the modified first-order kinetic model with the inclusion of the power parameter in the HRT variable.

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill

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

Handley, K. M.; Piceno, Y. M.; Hu, P.

The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common traitmore » selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.« less

Acceleration of Antimicrobial Susceptibility Testing of Positive Blood Cultures by Inoculation of Vitek 2 Cards with Briefly Incubated Solid Medium Cultures

PubMed Central

Idelevich, Evgeny A.; Schüle, Isabel; Grünastel, Barbara; Wüllenweber, Jörg; Peters, Georg

2014-01-01

Briefly incubated agar cultures from positive blood cultures were used for antimicrobial susceptibility testing (AST) by Vitek 2. The cultivation time until inoculation was 3.8 h for Gram-positive cocci and 2.4 h for Gram-negative rods. The error rates were low, providing early and reliable AST without additional time or cost expenditure. PMID:25165084

Production of deoxyribonuclease, ribonuclease, coagulase, and hemolysins by anaerobic gram-positive cocci.

PubMed Central

Marshall, R; Kaufman, A K

1981-01-01

Clinical isolates of Peptococcus and Peptostreptococcus species and Streptococcus intermedius strains were obtained from local hospitals. After confirmed identification, each isolate was tested for the in vitro production of deoxyribonuclease, ribonuclease, coagulase, and hemolysins. Of the 60 strains studied, 18 had enzymatic activity. The variability of enzyme production suggests that such assays are not suitable as an aid to identification of these organisms. PMID:7229018

In silico analysis of 16S ribosomal RNA gene sequencing‐based methods for identification of medically important anaerobic bacteria

PubMed Central

Woo, Patrick C Y; Chung, Liliane M W; Teng, Jade L L; Tse, Herman; Pang, Sherby S Y; Lau, Veronica Y T; Wong, Vanessa W K; Kam, Kwok‐ling; Lau, Susanna K P; Yuen, Kwok‐Yung

2007-01-01

This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5′‐end 527‐bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin‐Elmer Applied Biosystems Division, Foster City, California, USA) databases for the identification of all existing medically important anaerobic bacteria. Full and 527‐bp 16S rRNA sequencing are able to identify 52–63% of 130 Gram‐positive anaerobic rods, 72–73% of 86 Gram‐negative anaerobic rods and 78% of 23 anaerobic cocci. The existing MicroSeq databases are able to identify only 19–25% of 130 Gram‐positive anaerobic rods, 38% of 86 Gram‐negative anaerobic rods and 39% of 23 anaerobic cocci. These represent only 45–46% of those that should be confidently identified by full and 527‐bp 16S rRNA sequencing. To improve the usefulness of MicroSeq, bacterial species that should be confidently identified by full and/or 527‐bp 16S rRNA sequencing but not included in the existing MicroSeq databases should be included. PMID:17046845

18 GHz electromagnetic field induces permeability of Gram-positive cocci

PubMed Central

Nguyen, The Hong Phong; Shamis, Yury; Croft, Rodney J.; Wood, Andrew; McIntosh, Robert L.; Crawford, Russell J.; Ivanova, Elena P.

2015-01-01

The effect of electromagnetic field (EMF) exposures at the microwave (MW) frequency of 18 GHz, on four cocci, Planococcus maritimus KMM 3738, Staphylococcus aureus CIP 65.8T, S. aureus ATCC 25923 and S. epidermidis ATCC 14990T, was investigated. We demonstrate that exposing the bacteria to an EMF induced permeability in the bacterial membranes of all strains studied, as confirmed directly by transmission electron microscopy (TEM), and indirectly via the propidium iodide assay and the uptake of silica nanospheres. The cells remained permeable for at least nine minutes after EMF exposure. It was shown that all strains internalized 23.5 nm nanospheres, whereas the internalization of the 46.3 nm nanospheres differed amongst the bacterial strains (S. epidermidis ATCC 14990T~ 0%; Staphylococcus aureus CIP 65.8T S. aureus ATCC 25923, ~40%; Planococcus maritimus KMM 3738, ~80%). Cell viability experiments indicated that up to 84% of the cells exposed to the EMF remained viable. The morphology of the bacterial cells was not altered, as inferred from the scanning electron micrographs, however traces of leaked cytosolic fluids from the EMF exposed cells could be detected. EMF-induced permeabilization may represent an innovative, alternative cell permeability technique for applications in biomedical engineering, cell drug delivery and gene therapy. PMID:26077933

18 GHz electromagnetic field induces permeability of Gram-positive cocci.

PubMed

Nguyen, The Hong Phong; Shamis, Yury; Croft, Rodney J; Wood, Andrew; McIntosh, Robert L; Crawford, Russell J; Ivanova, Elena P

2015-06-16

The effect of electromagnetic field (EMF) exposures at the microwave (MW) frequency of 18 GHz, on four cocci, Planococcus maritimus KMM 3738, Staphylococcus aureus CIP 65.8(T), S. aureus ATCC 25923 and S. epidermidis ATCC 14990(T), was investigated. We demonstrate that exposing the bacteria to an EMF induced permeability in the bacterial membranes of all strains studied, as confirmed directly by transmission electron microscopy (TEM), and indirectly via the propidium iodide assay and the uptake of silica nanospheres. The cells remained permeable for at least nine minutes after EMF exposure. It was shown that all strains internalized 23.5 nm nanospheres, whereas the internalization of the 46.3 nm nanospheres differed amongst the bacterial strains (S. epidermidis ATCC 14990(T) ~  0%; Staphylococcus aureus CIP 65.8(T) S. aureus ATCC 25923, ~40%; Planococcus maritimus KMM 3738, ~ 80%). Cell viability experiments indicated that up to 84% of the cells exposed to the EMF remained viable. The morphology of the bacterial cells was not altered, as inferred from the scanning electron micrographs, however traces of leaked cytosolic fluids from the EMF exposed cells could be detected. EMF-induced permeabilization may represent an innovative, alternative cell permeability technique for applications in biomedical engineering, cell drug delivery and gene therapy.

Are there any reasons to change our behavior in necrotizing fasciitis with the advent of new antibiotics?

PubMed

Menichetti, Francesco; Giuliano, Simone; Fortunato, Simona

2017-04-01

The treatment of necrotizing fasciitis requires a multifaceted approach, consisting of surgical source control with immediate surgical debridement along with life support, clinical monitoring, and antimicrobial therapy. Many drugs are now available for the treatment of this life-threatening infectious disease, and the purpose of this review is to provide the reader with an updated overview of the newest therapeutic options. Because most necrotizing soft tissue infections are polymicrobial, broad-spectrum coverage is advisable. Acceptable monotherapy regimens include piperacillin-tazobactam or a carbapenem. However, drugs such as ceftolozane-tazobactam, ceftazidime-avibactam in association with an antianaerobic agent (metronidazole or clindamycin) are currently available as valuable alternatives. The new cephalosporins active against methicillin-resistant Staphylococcus aureus (MRSA), ceftaroline, and ceftobiprole share similar antibacterial activity against Gram-positive cocci, and they might be considered as an alternative to nonbetalactam anti-MRSA agents for necrotizing fasciitis management. Two new long-acting lypoglycopeptides - oritavancin and dalbavancin - share the indications for acute bacterial skin and skin structure infections and had similar activity against Gram-positive cocci including MRSA and streptococci. Carbapenem-sparing agents are particularly suitable for antimicrobial stewardship strategy. The new long-acting lypoglycopeptides are very effective in treating necrotizing fasciitis and are uttermost attractive for patients requiring short hospital stays and early discharge.

Magnetic microbes: Bacterial magnetite biomineralization

DOE PAGES

Prozorov, Tanya

2015-09-14

Magnetotactic bacteria are a diverse group of prokaryotes with the ability to orient and migrate along the magnetic field lines in search for a preferred oxygen concentration in chemically stratified water columns and sediments. These microorganisms produce magnetosomes, the intracellular nanometer-sized magnetic crystals surrounded by a phospholipid bilayer membrane, typically organized in chains. Magnetosomes have nearly perfect crystal structures with narrow size distribution and species-specific morphologies, leading to well-defined magnetic properties. As a result, the magnetite biomineralization in these organisms is of fundamental interest to diverse disciplines, from biotechnology to astrobiology. As a result, this article highlights recent advances inmore » the understanding of the bacterial magnetite biomineralization.« less

Fate of phosphorus in Everglades agricultural soils after fertilizer application

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

Wright, Alan L.; Hanlon, Edward A.; McCray, J. Mabry

2012-07-01

Land use changes, agricultural drainage and conventional cultivation of winter vegetables and sugarcane cropping in the Everglades Agricultural Area (EAA) may alter soil conditions and organic matter decomposition and ultimately influence the fate of phosphorus (P). Theses agricultural practices promote soil subsidence, reduce the soil depth to bedrock limestone and increase the potential for incorporation of limestone into the root zone of crops. The incorporation of limestone into surface soil has significantly increased soil pH which in turns causes greater fixation of P fertilizer into unavailable forms for plant growth. Additional P fertilization is thus required to satisfy crop nutrientmore » requirements in plant-available P form. It is important to determine how the mixing of bedrock limestone into soils influences the behavior of P fertilizers after their application. To accomplish this task, P fertilizers were applied to (1) typical cultivated soils and to (2) soils that have never been fertilized or extensively tilled. The changes in P concentrations over time were then compared between the two land uses, with differences being attributable to the impacts of cultivation practices. The P distribution in soil varied between land uses, with sugarcane having more P in inorganic pools while the uncultivated soil had more in organic pools. Water-soluble P concentrations in soil increased with increasing fertilizer application rates for all sampling times and both land uses. However, concentrations in uncultivated soil increased proportionally to P-fertilized soil due to organic P mineralization. At all sampling times, plant-available P concentrations remained higher for uncultivated than sugarcane soil. Lower P concentrations for sugarcane were related to adsorption by mineral components (e.g. limestone). Cultivated soils have higher calcium concentrations resulting from incorporation of bedrock limestone into soil by tillage, which increased pH and fostered sequestration of plant-available P into stable calcium-bound P pools. This greater P retention for sugarcane was reflected in the greater proportion of P in inorganic pools compared to uncultivated soils. Some lands within the EAA, including wetlands and seasonally-flooded prairies, are being reclaimed for water quality purposes. However, long-term effects of fertilization and cropping practices described in this document indicate that direct conversion from active farming, such as from sugarcane production directly to wetlands, may be problematic due to the changes in nutrient dynamics that may occur. The shift directly to wetlands may, in fact, release considerable amounts of P into the Everglades, thwarting the intent of the land use change. The inorganic P component in sugarcane soils may lead to the regeneration of soluble P in frequently flooded land uses such as wetlands. While most of the inorganic P pools are unavailable to sugarcane, the direct conversion of sugarcane soils to wetlands may facilitate P release. Here, reclamation of sugarcane fields for environment uses would benefit by an intermediate step to allow for a short duration of seasonal flooding allowing for P conversion from inorganic to organic forms. Prolonged flooding of organic soils previously used for intensive agriculture is not recommended.« less

Widespread Magnetofossil Occurrences in Deep-sea Sediments and Implications for Paleo- and Environmental Magnetism (Invited)

NASA Astrophysics Data System (ADS)

Yamazaki, T.; Roberts, A. P.

2013-12-01

Recent progress in rock magnetism has enabled quantitative estimation of magnetizations carried by magnetofossils. Using FORC diagrams, IRM component analyses, ferromagnetic resonance spectroscopy, low-temperature magnetometry, and transmission electron microscopy, it has been found that magnetofossils are widespread in deep-sea sediments and are often a dominant constituent of magnetic mineral assemblages. Some studies have documented a relationship between increased magnetofossil abundances and enhanced oceanic productivity induced by iron fertilization via eolian dust. The morphology of magnetosomes, which is species specific, may reflect a preference of magnetotactic bacteria for particular redox conditions. Dominant magnetofossil morphologies in sediments (cubo-octahedral vs. elongated) can be detected with rock magnetic techniques. Thus, magnetofossil abundance and morphology have considerable potential as paleoenvironmental indicators. It is widely held that magnetotactic bacteria live at or below the oxic-anoxic transition zone (OATZ) in chemically stratified aquatic environments. If so, it is expected that sediments that contain magnetofossils would have acquired their remanent magnetization at around the OATZ, and that the magnetization carried by magnetofossils will be delayed with respect to a pDRM carried by detrital magnetic minerals if the OATZ lies below the surface mixed layer and the pDRM acquisition zone. However, magnetofossils often dominate the magnetic mineral assemblage even in marine red clays that lack an OATZ. Changes in the relative abundance of biogenic and detrital magnetic components can be estimated from the ratio of ARM susceptibility to SIRM; a smaller average magnetic grain size and weaker magnetostatic interactions in the biogenic component causes higher ARM susceptibility. In relative paleointensity estimations, the kARM/SIRM ratio sometimes anti-correlates with normalized intensity regardless of the choice of normalizer (ARM or IRM). This implies that changes in relative abundance of biogenic magnetite may not be well compensated for by the widely used normalizers and may contaminate relative paleointensity records.

Magnetic enhancement of Baltic Sea sapropels by greigite magnetofossils

NASA Astrophysics Data System (ADS)

Reinholdsson, M.; Snowball, I.; Zillén, L.; Lenz, C.; Conley, D. J.

2013-03-01

Magnetotactic bacteria (MTB) are known to biosynthesise single-domain magnetite (Fe3O4) for geomagnetic navigation and their relict magnetosomes (called magnetofossils) can control the magnetic properties of lake and marine sediments. Magnetotactic bacteria also produce greigite (Fe3S4) magnetosomes but, compared to those made of magnetite, relatively little is known about the sedimentary environments where they are produced and the magnetic properties of the preserved particles. We studied the magnetic properties of sediment cores from two basins (the North Central Baltic Proper and eastern Gotland Basin) that currently experience hypoxia and we discovered the magnetic enhancement of older laminated sapropels, which are a signal of past occurrences of anoxia and hypoxia in the Baltic Sea. Magnetic concentrates extracted from the laminated sapropels were characterised by transmission electron microscopy and energy dispersive X-ray spectrometry and we identified only single-domain greigite (Fe3S4) particles with a mean size of 55×75 nm, which we interpret as magnetofossils due to diagnostic chains of individual particles separated by an intact dividing membrane. The degree of magnetic enhancement in the laminated sapropels has a positive relationship with loss-on-ignition data, which indicates a link between the production of greigite magnetosomes, organic matter supply and preservation and redox conditions. The coercive force of collections of non-interacting greigite magnetofossils is ∼13 mT, which is considerably lower than the magnetite counterparts (∼30 mT) and strictly non-bacterial and larger greigite single-domain grains (∼60 mT). The values of the interparametric ratios of SIRM/χ, χARM/SIRM and χARM/χ that we obtain for our greigite magnetofossils overlap with those previously considered to be diagnostic of magnetosomal magnetite. The presence of bacterial greigite, which is easily detected by magnetic measurements, forms a proxy for hypoxia and anoxia, thus aiding the palaeoenvironmental interpretation of how oxygen conditions in the Baltic Sea have changed over time.

Biocompatible coated magnetosome minerals with various organization and cellular interaction properties induce cytotoxicity towards RG-2 and GL-261 glioma cells in the presence of an alternating magnetic field.

PubMed

Hamdous, Yasmina; Chebbi, Imène; Mandawala, Chalani; Le Fèvre, Raphael; Guyot, François; Seksek, Olivier; Alphandéry, Edouard

2017-10-17

Biologics magnetics nanoparticles, magnetosomes, attract attention because of their magnetic characteristics and potential applications. The aim of the present study was to develop and characterize novel magnetosomes, which were extracted from magnetotactic bacteria, purified to produce apyrogen magnetosome minerals, and then coated with Chitosan, Neridronate, or Polyethyleneimine. It yielded stable magnetosomes designated as M-Chi, M-Neri, and M-PEI, respectively. Nanoparticle biocompatibility was evaluated on mouse fibroblast cells (3T3), mouse glioblastoma cells (GL-261) and rat glioblastoma cells (RG-2). We also tested these nanoparticles for magnetic hyperthermia treatment of tumor in vitro on two tumor cell lines GL-261 and RG-2 under the application of an alternating magnetic field. Heating, efficacy and internalization properties were then evaluated. Nanoparticles coated with chitosan, polyethyleneimine and neridronate are apyrogen, biocompatible and stable in aqueous suspension. The presence of a thin coating in M-Chi and M-PEI favors an arrangement in chains of the magnetosomes, similar to that observed in magnetosomes directly extracted from magnetotactic bacteria, while the thick matrix embedding M-Neri leads to structures with an average thickness of 3.5 µm 2 per magnetosome mineral. In the presence of GL-261 cells and upon the application of an alternating magnetic field, M-PEI and M-Chi lead to the highest specific absorption rates of 120-125 W/g Fe . Furthermore, while M-Chi lead to rather low rates of cellular internalization, M-PEI strongly associate to cells, a property modulated by the application of an alternating magnetic field. Coating of purified magnetosome minerals can therefore be chosen to control the interactions of nanoparticles with cells, organization of the minerals, as well as heating and cytotoxicity properties, which are important parameters to be considered in the design of a magnetic hyperthermia treatment of tumor.

Starvation-Survival in Haloarchaea.

PubMed

Winters, Yaicha D; Lowenstein, Tim K; Timofeeff, Michael N

2015-11-12

Recent studies claiming to revive ancient microorganisms trapped in fluid inclusions in halite have warranted an investigation of long-term microbial persistence. While starvation-survival is widely reported for bacteria, it is less well known for halophilic archaea-microorganisms likely to be trapped in ancient salt crystals. To better understand microbial survival in fluid inclusions in ancient evaporites, laboratory experiments were designed to simulate growth of halophilic archaea under media-rich conditions, complete nutrient deprivation, and a controlled substrate condition (glycerol-rich) and record their responses. Haloarchaea used for this work included Hbt. salinarum and isolate DV582A-1 (genus Haloterrigena) sub-cultured from 34 kyear Death Valley salt. Hbt. salinarum and DV582A-1 reacted to nutrient limitation with morphological and population changes. Starved populations increased and most cells converted from rods to small cocci within 56 days of nutrient deprivation. The exact timing of starvation adaptations and the physical transformations differed between species, populations of the same species, and cells of the same population. This is the first study to report the timing of starvation strategies for Hbt. salinarum and DV582A-1. The morphological states in these experiments may allow differentiation between cells trapped with adequate nutrients (represented here by early stages in nutrient-rich media) from cells trapped without nutrients (represented here by experimental starvation) in ancient salt. The hypothesis that glycerol, leaked from Dunaliella, provides nutrients for the survival of haloarchaea trapped in fluid inclusions in ancient halite, is also tested. Hbt. salinarum and DV582A-1 were exposed to a mixture of lysed and intact Dunaliella for 56 days. The ability of these organisms to utilize glycerol from Dunaliella cells was assessed by documenting population growth, cell length, and cell morphology. Hbt. salinarum and DV582A-1 experienced size reductions and shape transitions from rods to cocci. In the short-term, these trends more closely resembled the response of these organisms to starvation conditions than to nutrient-rich media. Results from this experiment reproduced the physical state of cells (small cocci) in ancient halite where prokaryotes co-exist with single-celled algae. We conclude that glycerol is not the limiting factor in the survival of haloarchaea for thousands of years in fluid inclusions in halite.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium. Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result. Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our approach allowed an optimized treatment recommendation. MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation. Copyright © 2015 Elsevier GmbH. All rights reserved.

Performance of Two Resin-Containing Blood Culture Media in Detection of Bloodstream Infections and in Direct Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS) Broth Assays for Isolate Identification: Clinical Comparison of the BacT/Alert Plus and Bactec Plus Systems

PubMed Central

Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Spanu, Teresa

2014-01-01

We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P < 0.001). Similarly high percentages of microorganisms in BacT/Alert and Bactec cultures (93.8% and 93.3%, respectively) were identified by direct matrix-assisted laser desorption ionization–time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. PMID:25031441

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle.

PubMed

He, Xuesong; McLean, Jeffrey S; Edlund, Anna; Yooseph, Shibu; Hall, Adam P; Liu, Su-Yang; Dorrestein, Pieter C; Esquenazi, Eduardo; Hunter, Ryan C; Cheng, Genhong; Nelson, Karen E; Lux, Renate; Shi, Wenyuan

2015-01-06

The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200-300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype.

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

PubMed Central

He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su-Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo; Hunter, Ryan C.; Cheng, Genhong; Nelson, Karen E.; Lux, Renate; Shi, Wenyuan

2015-01-01

The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200–300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype. PMID:25535390

The relationship between Anopheles gambiae density and rice cultivation in the savannah zone and forest zone of Côte d'Ivoire.

PubMed

Briët, Olivier J T; Dossou-Yovo, Joel; Akodo, Elena; van de Giesen, Nick; Teuscher, Thomas M

2003-05-01

In 13 villages in the savannah zone and 21 villages in the forest zone of Côte d'Ivoire, the biting density of the principal malaria vector, Anopheles gambiae, was studied as a function of rice cultivation in the inland valleys in a 2-km radius around each village. In the savannah villages, during the main season cropping period, surface water on rice-cultivated and to a lesser extent on uncultivated inland valleys seems to contribute strongly to the A. gambiae population density. For the off-season cropping period (which starts after the first light rains in the savannah zone), correlations were weaker. Breeding sites other than in inland valleys may play an important role in the savannah zone. In the forest zone, however, the A. gambiae population density was strongly correlated with the surface water availability (SWA) in the rice-cultivated inland valleys, whereas the correlation with the SWA in other (uncultivated) inland valleys was weak. The requirement of sunlit breeding sites for A. gambiae might explain this difference between zones. In the forest zone, only inland valleys cleared for rice cultivation meet this requirement, whereas all other inland valleys are covered with dense vegetation. In the savannah zone, however, most undergrowth is burnt during the dry season, which permits sunlight to reach puddles resulting from the first rains.

The human gut microbiome and its dysfunctions through the meta-omics prism.

PubMed

Mondot, Stanislas; Lepage, Patricia

2016-05-01

The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual). It is now acknowledged that the microbiota has coevolved with its host to achieve a symbiotic relationship, leading to physiological homeostasis. The gut microbiota ensures vital functions, such as food digestibility, maturation of the host immune system, and protection against pathogens. Over the last few decades, the gut microbiota has also been associated with numerous diseases, such as inflammatory bowel disease, irritable bowel syndrome, obesity, and metabolic diseases. In most of these pathologies, a microbial dysbiosis has been found, indicating shifts in the taxonomic composition of the gut microbiota and changes in its functionality. Our understanding of the influence of the gut microbiota on human health is still growing. Working with microorganisms residing in the gut is challenging since most of them are anaerobic and a vast majority (approximately 75%) are uncultivable to date. Recently, a wide range of new approaches (meta-omics) has been developed to bypass the uncultivability and reveal the intricate mechanisms that sustain gut microbial homeostasis. After a brief description of these approaches (metagenomics, metatranscriptomics, metaproteomics, and metabolomics), this review will discuss the importance of considering the gut microbiome as a structured ecosystem and the use of meta-omics to decipher dysfunctions of the gut microbiome in diseases. © 2016 New York Academy of Sciences.

A structural equation model analysis of phosphorus transformations in global unfertilized and uncultivated soils

NASA Astrophysics Data System (ADS)

Hou, Enqing; Chen, Chengrong; Kuang, Yuanwen; Zhang, Yuguang; Heenan, Marijke; Wen, Dazhi

2016-09-01

Understanding the soil phosphorus (P) cycle is a prerequisite for predicting how environmental changes may influence the dynamics and availability of P in soil. We compiled a database of P fractions sequentially extracted by the Hedley procedure and its modification in 626 unfertilized and uncultivated soils worldwide. With this database, we applied structural equation modeling to test hypothetical soil P transformation models and to quantify the importance of different soil P pools and P transformation pathways in shaping soil P availability at a global scale. Our models revealed that soluble inorganic P (Pi, a readily available P pool) was positively and directly influenced by labile Pi, labile organic P (Po), and primary mineral P and negatively and directly influenced by secondary mineral P; soluble Pi was not directly influenced by moderately labile Po or occluded P. The overall effect on soluble Pi was greatest for labile Pi followed by the organic P pools, occluded P, and then primary mineral P; the overall influence from secondary mineral P was small. Labile Pi was directly linked to all other soil P pools and was more strongly linked than soluble Pi to labile Po and primary mineral P. Our study highlights the important roles of labile Pi in mediating P transformations and in determining overall P availability in soils throughout the world.

Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.

PubMed

Bernardo, Pauline; Charles-Dominique, Tristan; Barakat, Mohamed; Ortet, Philippe; Fernandez, Emmanuel; Filloux, Denis; Hartnady, Penelope; Rebelo, Tony A; Cousins, Stephen R; Mesleard, François; Cohez, Damien; Yavercovski, Nicole; Varsani, Arvind; Harkins, Gordon W; Peterschmitt, Michel; Malmstrom, Carolyn M; Martin, Darren P; Roumagnac, Philippe

2018-01-01

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km 2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.

Effects of Land Use on Concentrations and Chemical Forms of Phosphorus in Different-Size Aggregates

NASA Astrophysics Data System (ADS)

Ahmad, E. H.; Demisie, W.; Zhang, M.

2017-12-01

Land use has been recognized as an important driver of environmental change on all spatial and temporal scales. This study was conducted to determine the effects of land uses on phosphorus concentration in bulk soil and in water-stable aggregates in different soils. The study was conducted on three soil types (Ferrosols, Cambosols, and Primosols), which were collected from three different locations from southeast China and under three land uses (Uncultivated, Vegetable and forest land) the region is characterized as a hill and plain area. Accordingly, a total of 24 soil samples were collected. The results showed that average contents of total P were 0.55-1.55 g/kg, 0.28-1.03 g/kg and 0.14-0.8 g/kg for the soils: Cambosols, Ferrosols and Primosols respectively. Vegetable and forest land led to higher total phosphorus contents in these soils than in the uncultivated land. An aggregate fraction of >2 mm under forest land made up the largest percentage (30 up to 70%), whereas the size fraction <0.106 mm made the least contribution (5 up to 20%) in all soil types. Vegetable land increased the total phosphorus, organic phosphorus and Olsen P and phosphorus forms in the soils. It implies that the conversion of natural ecosystem to vegetable land increased the phosphorus proportion in the soils, which could have negative impact on the environmental quality.

The in vitro activity of flomoxef compared to four other cephalosporins and imipenem.

PubMed

Shah, P M; Knothe, H

1991-01-01

The antibacterial activity of the oxacephalosporin flomoxef was evaluated in comparison to cefpirome, cefuzoname, cefotaxime, ceftazidime, and imipenem against fresh clinical isolates. Flomoxef is an antibiotic with strong antibacterial activity against staphylococci including methicillin-resistant strains and streptococci with the exception of Enterococcus faecalis and Enterococcus faecium. It is very active against gram-negative cocci and rods including gram-positive and gram-negative anaerobes. Against Pseudomonas sp. flomoxef has no activity.

Direct detection of Streptococcus mutans in human dental plaque by polymerase chain reaction.

PubMed

Igarashi, T; Yamamoto, A; Goto, N

1996-10-01

Streptococcus mutans is an etiological agent in human dental caries. A method for the detection of S. mutans directly from human dental plaque by polymerase chain reaction has been developed. Oligonucleotide primers specific for a portion of the dextranase gene (dexA) of S. mutans Ingbritt (serotype c) were designed to amplify a 1272-bp DNA fragment by polymerase chain reaction. The present method specifically detected S. mutans (serotypes c, e and f), but none of the other mutans streptococci: S. cricetus (serotype a), S. rattus (serotype b), S. sobrinus (serotypes d and g), and S. downei (serotype h), other gram-positive bacteria (16 strains of 12 species of cocci and 18 strains of 12 species of bacilli) nor gram-negative bacteria (1 strain of 1 species of cocci and 20 strains of 18 species of bacilli). The method was capable of detecting 1 pg of the chromosomal DNA purified from S. mutans Ingbritt and as few as 12 colony-forming units of S. mutans cells. The S. mutans cells in human dental plaque were also directly detected. Seventy clinical isolates of S. mutans isolated from the dental plaque of 8 patients were all positive by the polymerase chain reaction. These results suggest that the dexA polymerase chain reaction is suitable for the specific detection and identification of S. mutans.

Gram-positive anaerobic cocci--commensals and opportunistic pathogens.

PubMed

Murphy, Elizabeth Carmel; Frick, Inga-Maria

2013-07-01

Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Biofilm formation in an ice cream plant.

PubMed

Gunduz, Gulten Tiryaki; Tuncel, Gunnur

2006-01-01

The sites of biofilm formation in an ice cream plant were investigated by sampling both the production line and the environment. Experiments were carried out twice within a 20-day period. First, stainless steel coupons were fixed to surfaces adjacent to food contact surfaces, the floor drains and the doormat. They were taken for the analysis of biofilm at three different production stages. Then, biofilm forming bacteria were enumerated and also presence of Listeria monocytogenes was monitored. Biofilm forming isolates were selected on the basis of colony morphology and Gram's reaction; Gram negative cocci and rod, Gram positive cocci and spore forming isolates were identified. Most of the biofilm formations were seen on the conveyor belt of a packaging machine 8 h after the beginning of the production, 6.5 x 10(3) cfu cm(-2). Most of the Gram negative bacteria identified belong to Enterobacteriaceae family such as Proteus, Enterobacter, Citrobacter, Shigella, Escherichia, Edwardsiella. The other Gram negative microflora included Aeromonas, Plesiomonas, Moraxella, Pseudomonas or Alcaligenes spp. were also isolated. Gram positive microflora of the ice cream plant included Staphyloccus, Bacillus, Listeria and lactic acid bacteria such as Streptococcus, Leuconostoc or Pediococcus spp. The results from this study highlighted the problems of spread of pathogens like Listeria and Shigella and spoilage bacteria. In the development of cleaning and disinfection procedures in ice cream plants, an awareness of these biofilm-forming bacteria is essential for the ice cream plants.

The impact of soil redistribution on SOC pools in a Mediterranean agroforestry catchment

NASA Astrophysics Data System (ADS)

Quijano, Laura; Gaspar, Leticia; Lizaga, Iván; Navas, Ana

2017-04-01

Soil redistribution processes play an important role influencing the spatial distribution patterns of soil and associated soil organic carbon (SOC) at landscape scale. Information on drivers of SOC dynamics is key for evaluating both soil degradation and SOC stability that can affect soil quality and sustainability. 137Cs measurements provide a very effective tool to infer spatial patterns of soil redistribution and quantify soil redistribution rates in different landscapes, but to date these data are scarce in mountain Mediterranean agroecosystems. We evaluate the effect of soil redistribution on SOC and SOC pools in relation to land use in a Mediterranean mountain catchment (246 ha). To this purpose, two hundred and four soil bulk cores were collected on a 100 m grid in the Estaña lakes catchment located in the central sector of the Spanish Pyrenees (31T 4656250N 295152E). The study area is an agroforestry and endorheic catchment characterized by the presence of evaporite dissolution induced dolines, some of which host permanent lakes. The selected landscape is representative of rainfed areas of Mediterranean continental climate with erodible lithology and shallow soils, and characterized by an intense anthropogenic activity through cultivation and water management. The cultivated and uncultivated areas are heterogeneously distributed. SOC and SOC pools (the active and decomposable fraction, ACF and the stable carbon fraction SCF) were measured by the dry combustion method and soil redistribution rates were derived from 137Cs measurements. The results showed that erosion predominated in the catchment, most of soil samples were identified as eroded sites (n=114) with an average erosion rate of 26.9±51.4 Mg ha-1 y-1 whereas the mean deposition rate was 13.0±24.2 Mg ha-1 y-1. In cultivated soils (n=54) the average of soil erosion rate was significantly higher (78.5±74.4 Mg ha-1 y-1) than in uncultivated soils (6.8±10.4 Mg ha-1 y-1). Similarly, the mean of soil deposition rate in cultivated soils (n=22) was significantly higher (42.6±35.1 Mg ha-1 y-1) than in uncultivated soils (3.4±3.2 Mg ha-1 y-1). The mean SOC content for all soil samples was 2.5±2.0%. In uncultivated soils, significantly higher (P<0.01) amounts of SOC (3.0±2.6%), ACF (2.1±0.7%) and SCF (0.9±0.4%) were found compared to cultivated soils where the means were 1.1±0.7%, 0.7±0.5% and 0.4±0.3%, respectively. Significant (P<0.05) correlations between SOC, SOC pools and soil redistribution rates indicate that the distribution of SOC pools were significantly affected by soil redistribution in the study area. SOC and SOC pools were significantly higher at depositional (n=90, 2.8±1.8%) than at eroded sampling points (2.2±2.1%). ACF shows greater differences at eroding sites and at depositional sites than SCF reflecting that ACF is more sensitive to soil redistribution processes. Our findings emphasize the role of soil redistribution and land use in influencing the dynamics of SOC, information that can be also relevant in soil management. Improving the knowledge on the relationships between land use, soil redistribution processes and SOC fractions is of interest, especially in these Mediterranean rapidly changing landscapes.

Effects of sample treatments on genome recovery via single-cell genomics

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

Clingenpeel, Scott; Schwientek, Patrick; Hugenholtz, Philip

2014-06-13

It is known that single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we demonstrate that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

“Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

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

Naas, A. E.; Solden, L. M.; Norbeck, A. D.

2018-03-01

In Nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family (“Candidatus MH11”) composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa.

Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes.

PubMed

Ufarté, Lisa; Bozonnet, Sophie; Laville, Elisabeth; Cecchini, Davide A; Pizzut-Serin, Sandra; Jacquiod, Samuel; Demanèche, Sandrine; Simonet, Pascal; Franqueville, Laure; Veronese, Gabrielle Potocki

2016-01-01

Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.

Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)▿

PubMed Central

Evans, Paul N.; Hinds, Lyn A.; Sly, Lindsay I.; McSweeney, Christopher S.; Morrison, Mark; Wright, André-Denis G.

2009-01-01

The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight. PMID:19218421

Gigantism in unique biogenic magnetite at the Paleocene-Eocene Thermal Maximum.

PubMed

Schumann, Dirk; Raub, Timothy D; Kopp, Robert E; Guerquin-Kern, Jean-Luc; Wu, Ting-Di; Rouiller, Isabelle; Smirnov, Aleksey V; Sears, S Kelly; Lücken, Uwe; Tikoo, Sonia M; Hesse, Reinhard; Kirschvink, Joseph L; Vali, Hojatollah

2008-11-18

We report the discovery of exceptionally large biogenic magnetite crystals in clay-rich sediments spanning the Paleocene-Eocene Thermal Maximum (PETM) in a borehole at Ancora, NJ. Aside from previously described abundant bacterial magnetofossils, electron microscopy reveals novel spearhead-like and spindle-like magnetite up to 4 microm long and hexaoctahedral prisms up to 1.4 microm long. Similar to magnetite produced by magnetotactic bacteria, these single-crystal particles exhibit chemical composition, lattice perfection, and oxygen isotopes consistent with an aquatic origin. Electron holography indicates single-domain magnetization despite their large crystal size. We suggest that the development of a thick suboxic zone with high iron bioavailability--a product of dramatic changes in weathering and sedimentation patterns driven by severe global warming--drove diversification of magnetite-forming organisms, likely including eukaryotes.

Chemolithoautotrophy and its Relation to Magnetism and Biomineralization in Marine Magnetotactic Bacteria

NASA Astrophysics Data System (ADS)

Bazylinski, D. A.; Williams, T. J.; Zhang, C. L.; Scott, J. H.

2005-12-01

All cultured, marine, magnetite-producing, magnetotactic bacteria (MB) are capable of chemolithoautotrophy and use a number of electron donors to support this mode of growth including reduced sulfur compounds. Several vibrioid strains are known to rely on the Calvin-Benson-Bassham (CBB) cycle for autotrophy. An obligately microaerophilic, magnetite-producing, coccoid strain (MC-1) grew with sulfide and thiosulfate as electron donors and 14C-labelling experiments showed that virtually all cell C was derived from H14CO3-/14CO2 confirming autotrophy in this strain. Cell-free extracts of strain MC-1 did not exhibit ribulose-1,5-bisphosphate carboxylase-oxygenase (RubisCO) activity and nor were RubisCO genes found in the draft genome of the organism. Cell extracts also did not exhibit carbon monoxide dehydrogenase activity indicating that the acetyl-CoA pathway also does not function in strain MC-1. The 13C content of whole cells of strain MC-1 relative to the 13C content of the H14CO3-/14CO2 used for growth (Δδ13C) was -11.4 ppt. Cellular fatty acids showed enrichment of 13C relative to biomass. Activities for three key enzymes of the reverse or reductive tricarboxylic acid (rTCA) cycle were demonstrated for MC-1: fumarate reductase, pyruvate: acceptor oxidoreductase and 2-oxoglutarate: acceptor oxidoreductase. Although ATP citrate lyase (another key enzyme of the rTCA cycle) activity was not detected in cell-free extracts of strain MC-1 using commonly used assays for this enzyme, cell-free extract was found to rapidly cleave citrate, and the reaction was dependent upon the presence of ATP, coenzyme A and NADH. Thus, we infer the presence of an ATP-dependent citrate-cleaving enzyme or enzymes. The Δδ13C value and results from enzyme studies are consistent with the operation of the rTCA cycle for autotrophy in strain MC-1. Strain MC-1 appears to be the first known member of the alpha-Proteobacteria to assimilate CO2 during autotrophic growth using the rTCA cycle. Based on the type of chemolithoautotrophy described above, it is clear why marine magnetite-producing MB occupy a precise location, the oxic-anoxic interface, in vertical chemical gradients within chemically-stratified coastal environments: they must have an electron donor, sulfide and perhaps others, and an electron acceptor, O2. The presumed function of magnetosomes is that the magnetic dipole resulting from the magnetosomes aids the cell in locating and maintaining an optimal position within vertical chemical gradients. MB process large amounts of Fe in the biomineralization of magnetosomes: cells consist of 1-3% Fe (dry wt). Because of this, and the fact that many chemolithoautotrophic, non-magnetotactic bacteria occupy a similar niche, we have been investigating possible physiological reasons for the production of magnetosomes and the processing of such large amounts of Fe. We have found that some marine vibrioid strains grow in O2-gradient medium with Fe(II) as the electron donor. Cells appear to oxidize the Fe(II) and produce a layer of Fe oxyhydroxides within the gradient suggesting that cells obtain energy from the oxidation of Fe(II).

Tropical Archaea: Diversity associated with the surface microlayer of corals

USGS Publications Warehouse

Kellogg, C.A.

2004-01-01

Recent 16S rDNA studies have focused on detecting uncultivated bacteria associated with Caribbean reef corals in an effort to address the ecological roles of coral-associated microbes. Reports of Archaea associated with fishes and marine invertebrates raised the question of whether Archaea might also be part of the coral-associated microbial community. DNA analysis of mucus from 3 reef-building species of Caribbean corals, Montastraea annularis complex, Diploria strigosa and D. labyrinthiformis in the US Virgin Islands yielded 34 groups of archaeal 16S ribotypes (defined at the level of 97% similarity). The majority (75%) was most closely matched by BLAST searches to sequences derived from marine water column samples, whereas the remaining ribotypes were most similar to sequences isolated from anoxic environments (15%) and hydrothermal vents (9%). Unlike previous 16S studies of coral-associated Bacteria, the results do not suggest specific associations between particular archaeal sequences and individual coral species. Marine Archaea (Groups I, II and III) in addition to Thermoplasma-like, methanogen, and marine benthic crenarchaeote phylotypes, were detected in the mucus of tropical corals. The finding of sequences from coral-associated Archaea that are closely related to strict and facultative anaerobes, as well as to uncultivated Archaea from other types of anoxic environments, suggests that anaerobic micro-niches may exist in coral mucus layers. Archaea, with their unique biogeochemical capabilities, broaden the scope of possible interactions between corals and their associated microbial communities.

Phosphorus content as a function of soil aggregate size and paddy cultivation in highly weathered soils.

PubMed

Li, Baozhen; Ge, Tida; Xiao, Heai; Zhu, Zhenke; Li, Yong; Shibistova, Olga; Liu, Shoulong; Wu, Jinshui; Inubushi, Kazuyuki; Guggenberger, Georg

2016-04-01

Red soils are the major land resource in subtropical and tropical areas and are characterized by low phosphorus (P) availability. To assess the availability of P for plants and the potential stability of P in soil, two pairs of subtropical red soil samples from a paddy field and an adjacent uncultivated upland were collected from Hunan Province, China. Analysis of total P and Olsen P and sequential extraction was used to determine the inorganic and organic P fractions in different aggregate size classes. Our results showed that the soil under paddy cultivation had lower proportions of small aggregates and higher proportions of large aggregates than those from the uncultivated upland soil. The portion of >2-mm-sized aggregates increased by 31 and 20 % at Taoyuan and Guiyang, respectively. The total P and Olsen P contents were 50-150 and 50-300 % higher, respectively, in the paddy soil than those in the upland soil. Higher inorganic and organic P fractions tended to be enriched in both the smallest and largest aggregate size classes compared to the middle size class (0.02-0.2 mm). Furthermore, the proportion of P fractions was higher in smaller aggregate sizes (<2 mm) than in the higher aggregate sizes (>2 mm). In conclusion, soils under paddy cultivation displayed improved soil aggregate structure, altered distribution patterns of P fractions in different aggregate size classes, and to some extent had enhanced labile P pools.

New CRISPR-Cas systems from uncultivated microbes

NASA Astrophysics Data System (ADS)

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

2017-02-01

CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

New CRISPR–Cas systems from uncultivated microbes

DOE PAGES

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; ...

2016-12-22

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less

New CRISPR–Cas systems from uncultivated microbes

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

Burstein, David; Harrington, Lucas B.; Strutt, Steven C.

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less

Dissipation and runoff transport of metazachlor herbicide in rapeseed cultivated and uncultivated plots in field conditions.

PubMed

Mantzos, Nikolaos; Hela, Dimitra; Karakitsou, Anastasia; Antonopoulou, Maria; Konstantinou, Ioannis

2016-10-01

The environmental fate of metazachlor herbicide was investigated under field conditions in rapeseed cultivated and uncultivated plots, over a period of 225 days. The cultivation was carried out in silty clay soil plots with two surface slopes, 1 and 5 %. The herbicide was detectable in soil up to 170 days after application (DAA), while the dissipation rate was best described by first-order kinetics and its half-life ranged between 10.92 and 12.68 days. The herbicide was detected in the soil layer of 10-20 cm from 5 to 48 DAA, and its vertical movement can be described by the continuous stirred tank reactor (CSTR) in series model. Relatively low amounts of metazachlor (less than 0.31 % of the initial applied active ingredient) were transferred by runoff water. More than 80 % of the total losses were transferred at the first runoff event (12 DAA), with herbicide concentrations in runoff water ranging between 70.14 and 79.67 μg L -1 . Minor amounts of the herbicide (less than 0.07 % of the initial applied active ingredient) were transferred by the sediment, with a maximum concentration of 0.57 μg g -1 (12 DAA), in plots with 5 % inclination. Finally, in rapeseed plants, metazachlor was detected only in the first sampling (28 DAA) at concentrations slightly higher than the limit of quantification; when in seeds, no residues of the herbicide were detected.

In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina.

PubMed

Behrendt, Lars; Raina, Jean-Baptiste; Lutz, Adrian; Kot, Witold; Albertsen, Mads; Halkjær-Nielsen, Per; Sørensen, Søren J; Larkum, Anthony Wd; Kühl, Michael

2017-10-31

The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO 2 fixing pathways, likely a result of O 2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.192.

Analysis of sepsis in allogeneic bone marrow transplant recipients: a single-center study.

PubMed

Mitsui, Hideki; Karasuno, Takahiro; Santo, Taisuke; Fukushima, Kentaro; Matsunaga, Hitomi; Nakamura, Hiroyuki; Hiraoka, Akira

2003-09-01

We reviewed the records of 235 consecutive recipients of allogeneic bone marrow transplantation (allo-BMT) at our center between February 1983 and October 2000. Sepsis occurred in 25 patients (10.6%) at a median of 10 days (range, 1-280 days) after BMT. Five of the 25 patients (20%) died of sepsis. Pathogens isolated from blood culture were gram-positive cocci in 19 patients, gram-negative rods in 7, fungi in 2, and others in 1 patient. Two pathogens were detected concomitantly in 4 patients. Univariate analysis revealed that risk factors for sepsis were selective gut decontamination using lomefloxacin hydrochloride and nystatin, an unrelated donor, HLA mismatched BMT, and stomatitis. Multivariate logistic regression analysis revealed that an unrelated donor was the only significant independent risk factor, with a relative risk of 5.432. In 12 of 25 patients with sepsis, the pathogens of sepsis were sensitive to antibiotics used for gut decontamination. Selective gut decontamination significantly increased the incidence of sepsis, especially that with gram-positive cocci, but not the mortality rate of sepsis, compared with total gut decontamination using vancomycin. We also found a significant relationship between pathogens isolated from blood culture and those isolated from surveillance cultures of stool, urine, and gargled water in the period before sepsis occurred. The present study revealed an independent risk factor for sepsis (unrelated donor), the feasibility of selective gut decontamination, and the importance of surveillance culture.

Identification and susceptibility testing of microorganism by direct inoculation from positive blood culture bottles by combining MALDI-TOF and Vitek-2 Compact is rapid and effective.

PubMed

Romero-Gómez, María-Pilar; Gómez-Gil, Rosa; Paño-Pardo, Jose Ramón; Mingorance, Jesús

2012-12-01

The objective of this study was to evaluate the reliability and accuracy of the combined use of MALDI-TOF MS bacterial identification and the Vitek-2 Compact antimicrobial susceptibility testing (AST) directly from positive blood cultures. Direct identification by MALDI-TOF MS and AST were performed in parallel to the standard methods in all positively flagged blood cultures bottles during the study period. Three hundred and twenty four monomicrobial positive blood cultures were included in the present study, with 257 Gram-negative and 67 Gram-positive isolates. MALDI-TOF MS identification directly from blood bottles reported the correct identification for Enterobacteriaceae in 97.7%, non-fermentative Gram-negative bacilli 75.0%, Staphylococcus aureus 75.8%, coagulase negative staphylococci 63.3% and enterococci 63.3%. A total 6156 isolate/antimicrobial agent combinations were tested. Enterobacteriaceae group and non-fermentative Gram-negative Bacilli showed an agreement of 96.67% and 92.30%, respectively, for the Gram-positive cocci the overall agreement found was 97.84%. We conclude that direct identification by MALDI-TOF and inoculation of Vitek-2 Compact AST with positive blood culture bottles yielded very good results and decreased time between initial inoculation of blood culture media and determination of the antibiotic susceptibility for Gram-negative rods and Gram-positive cocci causing bacteremia. Copyright © 2012 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Clinical evaluation of the Vitek ANI card for identification of anaerobic bacteria.

PubMed Central

Schreckenberger, P C; Celig, D M; Janda, W M

1988-01-01

An evaluation of the Vitek Anaerobe Identification (ANI) card was performed with 341 bacterial isolates, including 313 clinical isolates and 28 stock strains of anaerobic microorganisms. Identifications obtained with the ANI card were compared with those determined by conventional methods. The card identified 73.2% of 149 anaerobic gram-negative bacilli, 63.6% of 44 Clostridium spp., 65.8% of 38 anaerobic nonsporeforming gram-positive bacilli, and 69.1% of 110 anaerobic cocci, with no further testing required. When genus-level identifications were included, 83.9% of the anaerobic gram-negative bacilli, 70.5% of Clostridium spp., 73.7% of the anaerobic nonsporeforming gram-positive bacilli, and 73.6% of the anaerobic cocci were identified. Nineteen isolates (5.6%) produced identifications of good confidence but marginal separation or questionable biotype, in which the correct identification was listed with one or two other possible choices and extra tests were required and suggested. A total of 28 (8.2%) were not identified and 29 isolates (8.5%) were misidentified by the ANI card. Among the commonly isolated clinically significant anaerobes, the ANI card identified 100% of 55 Bacteroides fragilis and 100% of 8 Clostridium perfringens. Use of supplemental tests and expansion of the data base to include additional strains of organisms that are difficult to separate even with conventional methods may improve the accuracy of the ANI card as a method for identification of anaerobic bacteria in the clinical laboratory. PMID:3343321

Accuracy of the cytopathology, bacterioscopy, and vaginal flora culture.

PubMed

Almeida, P Q; Pereira, M A P; Palomo, F S; Okazaki, C; Schimidt, M A; Speck, N M G; Ribalta, J C L

2013-01-01

An over-population of vaginal microorganisms causing inflammatory processes renders it difficult to properly assess the cytopathological exam that aims to screen precedent cervical lesions. On the contrary, the occurrence of the microbial flora saprophyte does not influence correct cythodiagnosis. To assess the composition of vaginal tract aerobic microorganisms of asymptomatic women in menacme and post-menopause, and to analyze the accuracy of cytopathologic, bacterioscopic exams, and culturing of the flora. The women were first submitted to a focused anamnestic interrogatory and then submitted to gynecological exam. A sample of the vaginal fluid was collected with a culture swab and a smear was made on two glass slides for stained bacterioscopic exam (GRAM). The collection of material was then compiled in a cytopathologic smear analysis. All women signed the free and informed consent letter and the project was approved by the Ethics Research Board of Hospital São Paulo - UNIFESP. Bacterioscopy and culture proved to be better than the cytopathologic exam in featuring the bacilli and cocci. The bacterioscopy provided a better detection of the presence of bacilli (p < 0.001); no statistical difference was seen between both exams with respect to the detected cocci. The beta-hemolytic Streptococcus group was of significance in post-menopausal women (p < 0.05). In this study, the bacterioscopic and culture exams of the vaginal fluid were more effective in assessing the vaginal flora and in the detection of bacilli, compared to the cytopathological exam.

Rapid identification of pneumococci, enterococci, beta-haemolytic streptococci and S. aureus from positive blood cultures enabling early reports.

PubMed

Larsson, Marie C; Karlsson, Ewa; Woksepp, Hanna; Frölander, Kerstin; Mårtensson, Agneta; Rashed, Foad; Annika, Wistedt; Schön, Thomas; Serrander, Lena

2014-03-19

The aim of this study was to evaluate diagnostic tests in order to introduce a diagnostic strategy to identify the most common gram-positive bacteria (pneumococci, enterococci, β-haemolytic streptococci and S. aureus) found in blood cultures within 6 hours after signalling growth. The tube coagulase test was optimized and several latex agglutination tests were compared and evaluated before a validation period of 11 months was performed on consecutive positive blood culture patient samples from Kalmar County Hospital, Sweden. During the validation period 150 (91%) of a total of 166 gram-positive cocci (119 in clusters, 45 in chains or pairs and 2 undefined morphology) were correctly identified as S. aureus, CoNS, Pneumococci, Enterococci or group A streptococci (GAS), group B streptococci (GBS), group G streptococci (GGS) within 6 hours with a minimal increase in work-load and costs. The remaining samples (9%) were correctly identified during the next day. No samples were incorrectly grouped with this diagnostic strategy and no patient came to risk by early reporting. A simple strategy gives reliable and cost-effective reporting of >90% of the most common gram-positive cocci within 6 hours after a blood cultures become positive. The high specificity of the tests used makes preliminary reports reliable. The reports can be used to indicate the focus of infection and not the least, support faster administration of proper antimicrobial treatment for patients with serious bacterial infections.

A super-infection in the cornea caused by Stemphylium, Acremonium, and α-Streptococcus.

PubMed

Hotta, Fumika; Eguchi, Hiroshi; Nishimura, Keiko; Kogiso, Masahiro; Ishimaru, Mayumi; Kusaka, Shunji; Shimomura, Yoshikazu; Yaguchi, Takashi

2017-03-09

Polymicrobial keratitis with fungus and bacteria can lead to blindness and is challenging to treat. Here, we introduce a case of fungal keratitis caused by two different strains in addition to definite bacterial super-infection caused by an α-Streptococcus sp., and describe the importance of microscopic examination. A 74-year-old woman, who had a past history of infection with leprosy, presented with conjunctival hyperaemia, pain, and corneal opacity in her right eye. Under the presumptive diagnosis of infectious keratitis, corneal scrapings were stained by various reagents and inoculated on several agar plates. Microscopic findings of the scrapings revealed fungi and a small number of Gram-positive cocci. Multiple anti-fungal therapies with levofloxacin ophthalmic solution were administered. Although empiric treatment was initially effective, keratitis recurred 10 days after its initiation. Repeated corneal scraping revealed an abundance of Gram-positive chain cocci and a small amount of fungi, resulting in the switching of an antibiotic medication from levofloxacin to moxifloxacin and cefmenoxime. Keratitis resolved gradually after the conversion. Stemphylium sp., Acremonium sp., and α-Streptococcus sp. were simultaneously isolated from the corneal scrapings. To the best of our knowledge, this is the first case of fungal keratitis caused by Stemphylium sp., and also the first case of super-infection in the cornea caused by two different fungi and one bacterium. Microscopic examination of the corneal scrapings was beneficial in rapid decision of changing to appropriate drug according to the dominancy of pathogenicity.

Variations in the natural ¹⁵N abundance of Brassica chinensis grown in uncultivated soil affected by different nitrogen fertilizers.

PubMed

Yuan, Yuwei; Hu, Guixian; Zhao, Ming; Chen, Tianjin; Zhang, Yongzhi; Zhu, Jiahong; Wang, Qiang

2014-11-26

To further investigate the method of using δ(15)N as a marker for organic vegetable discrimination, the effects of different fertilizers on the δ(15)N in different growing stages of Brassica chinensis (B. chinensis) grown in uncultivated soil were investigated with a pot experiment. B. chinensis was planted with uncultivated soil and different fertilizer treatments and then harvested three times in three seasons consecutively. For the spring experiments in the years of 2011 and 2012, the δ(15)N value of B. chinensis, which increased due to organic manure application and decreased due to chemical fertilizer application, was significantly different (p < 0.05) with manure treatment and chemical treatment. The δ(15)N value of vegetables varied among three growing stages and ranged from +8.6‰ to +11.5‰ for the control, from +8.6‰ to +12.8‰ for the compost chicken manure treatment, from +2.8‰ to +7.7‰ for the chemical fertilizer urea treatment, and from +7.7‰ to +10.9‰ for the compost-chemical fertilizer treatment. However, the δ(15)N values observed in the autumn experiment of 2011 without any fertilizer application increased ranging from +13.4‰ to +15.4‰, + 11.2‰ to +17.7‰, +10.7‰ to +17.1‰, and +10.6‰ to +19.1‰, respectively, for the same treatments mentioned above. This result was not significantly different between manure treatment and chemical treatment. The δ(15)N values of soil obtained in the spring of 2011 during three growing stages were slightly affected by fertilizers and varied in the range of +1.6‰ to +2.5‰ for CK, +4.7‰ to +6.5‰ for compost treatment, +2.1‰ to +2.4‰ for chemical treatment, and +2.7‰ to +4.6‰ for chemical-compost treatment, respectively. High δ(15)N values of B. chinensis were observed in these experiments, which would be useful to supplement a δ(15)N database for discriminating organic vegetables. Although there was a significant difference between manure treatment and chemical treatment, it was still difficult to discriminate whether a labeled organic vegetable was really grown without chemical fertilizer just with a fixed high δ(15)N value, especially for the vegetables planted simultaneously with chemical and compost fertilizer.

Performance of two resin-containing blood culture media in detection of bloodstream infections and in direct matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) broth assays for isolate identification: clinical comparison of the BacT/Alert Plus and Bactec Plus systems.

PubMed

Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Sanguinetti, Maurizio; Spanu, Teresa

2014-10-01

We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥ 16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤ 5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P < 0.001). Similarly high percentages of microorganisms in BacT/Alert and Bactec cultures (93.8% and 93.3%, respectively) were identified by direct matrix-assisted laser desorption ionization-time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

[Analysis of the drug-resistance of Pseudomonas aeruginosa and the use of antibiotics in burn wards].

PubMed

Dou, Yi; Zhang, Xiong; Zhang, Qin; Shi, Yan

2011-04-01

To study changes in the drug-resistance of Pseudomonas aeruginosa (PA) and the use of antibiotics in burn wards so as to optimize the use of antibiotic in the future. Bacteria were isolated from specimens of blood, venous catheter, stool, sputum, urine, wound tissue from 5717 patients hospitalized in our burn wards within the duration of January 2005 to December 2009. The number of specimens examined and positive rates of bacteria were calculated. Changes in constituent ratio of cocci and bacilli, spectrum of bacteria, the drug-resistance rate of PA, and the usage of antibiotics were analyzed. The number of specimens examined, constituent ratio of cocci and bacilli, drug-resistance rate were processed with chi-square test. Bivariate correlation analysis was performed between the usage of antibiotics and the drug-resistance rate. (1) The number of specimens examined showed no statistical difference during the five years (with rates from 73.2% to 76.1%, χ(2) = 5.583, P > 0.05), while constituent ratio of cocci and bacilli showed statistical difference (with ratios from 105:134 to 169:126, χ(2) = 14.806, P < 0.01). The positive rates of bacteria were increasing in the five years. (2) One thousand six hundred and seventy-five strains were identified during the five years from different kinds of specimens, with 29 from blood, 39 from venous catheter, 3 from stool, 157 from sputum, 13 from urine, and 1434 from wound tissue. Among them, Staphylococcus aureus accounted for 28% to 42%, PA accounted for 10% to 25%, Acinetobacter baumannii accounted for 10% to 19%, and they were the predominant strains. (3) The difference among drug-resistance rates of PA to each kind of 12 antibiotics during the five years were statistically significant (with χ(2) values from 47.911 to 308.095, P values all below 0.01). The drug-resistance rates of PA to some antibiotics showed downward trend in the former four years, including amikacin, ceftazidime, and imipenem/cilastatin, but it rebounded in the fifth year. (4) There was descending trend in usage of cefoperazone/sulbactam and levofloxacin, but vancomycin was always used widely. (5) Drug-resistance rates of PA to 7 antibiotics, including amikacin, imipenem/cilastatin, and ciprofloxacin, etc., were positively correlated with usage of various antibiotics (with r values from 0.879 to 0.978, P < 0.05 or P < 0.01). In our burn wards, drug-resistant PA was prevalent. Disinfection and isolation measures, appropriate use of antibiotics, etc. can reduce PA infection.

Linkage between the Biosphere and Geomagnetic field: Knowns and Unknowns

NASA Astrophysics Data System (ADS)

Pan, Y.; Zhu, R.

2017-12-01

The geomagnetic field extends from Earth's interior into space, and protects our planets habitability by shielding the planet from solar winds and cosmic rays. Recently, single zircon paleomagnetic study provides evidence of the field to ages as old as 4.2 Ga. Many great questions remain, including whether the emergence of life on Earth was a consequence of the field's protection, how organisms utilize the field, and if field variations (polarity reversal, excursion and secular variation) impact the evolution of the biosphere. In the past decade, great efforts have been made to probe these very complex and great challenging questions through the inter-disciplinary subject of biogeomagnetism. Numerous birds, fish, sea turtles, bats and many other organisms utilize the geomagnetic field during orientation and long-distance navigation. We recently found that bats, the second most abundant order of mammals, can use the direction of magnetic field with a weak strength comparable to polarity transitions/excursions, which is indicative of advanced magnetoreception developed in bats co-evolving with the geomagnetic field since the Eocene. Magnetotactic bacteria swim along the geomagnetic field lines by synthesizing intracellular nano-sized and chain-arranged magnetic minerals (magnetosomes). Recent field surveys in China, Europe, America and Australia have shown that these microbes are ubiquitous in aqueous habitats. Both their biogeography distribution and magnetotactic swimming speed are field intensity dependent. On the other hand, it is increasingly accepted that the geomagnetic field influences life through several indirect pathways. For example, it has been discovered that solar wind erosion enhanced the atmospheric oxygen escape during periods of weak magnetic field and global mean ionospheric electron density profiles can be affected by geomagnetic field strength variation. In addition, depletion of the ozone layer during a weak magnetic field could result in strong solar irradiation, which is harmful to many organisms. Together, newly accumulated lines of evidence strongly indicate that the geomagnetic field and its variations have important impacts on life and its evolution. In this paper we will provide an overview of recent observations, progresses and perspectives in this subject.

Phytoparasitic Nematodes Adjacent to Established Strawberry Plantations

PubMed Central

Crow, R. V.; MacDonald, D. H.

1978-01-01

Plant-nematode populations associated with uncultivated vegetation, adjacent strawberry plants, and alternate crop sites were studied at three locations in Minnesota. At one site (Forest Lake), Paratylenchus projectus, Meloidogyne hapla, and Pratylenchus tenuis were frequently associated with the roots of native vegetation. These nematode species were also present in adjacent strawberry beds. Among alternate crops observed, oats and muskmelon usually supported the fewest nematodes although moderate densities of Xiphinema americanum and P. tenuis were found at one location in plots planted to oats. Pratylenchus tenuis was also found on rye at one location. PMID:19305841

Genomics of Staphylococcus

NASA Astrophysics Data System (ADS)

Lindsay, Jodi A.

The staphylococci are Gram-positive cocci that divide to form clusters that look like grapes. By 16S ribosomal sequencing, they are most closely related to the Gram-positive, low G+C content Bacillus-Lactobacillus-Staphylococcus genera (Woese, 1987). There are over 30 species of staphylococci identified, and they are typically found on the skin and mucous membranes of mammals. About a dozen species are frequently carried on humans, including Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus capitis, Staphylococcus hominis, Staphylococcus cohnii, Staphylococcus lugdunensis, Staphylococcus schleiferi, Staphylococcus saprophyticus, Staphylococcus simulans, Staphylococcus warneri and Staphylococcus xylosus.

Comparative in-vitro activities of quinupristin-dalfopristin against Gram-positive bloodstream isolates.

PubMed

Schouten, M A; Hoogkamp-Korstanje, J A

1997-08-01

The in-vitro activity of quinupristin-dalfopristin was compared with those of vancomycin, teicoplanin, erythromycin, clarithromycin, rifampicin, imipenem, meropenem, ciprofloxacin and sparfloxacin against 414 bloodstream isolates of Gram-positive cocci. Quinupristin-dalfopristin inhibited strains of Streptococcus pyogenes and Streptococcus agalactiae at 0.12 mg/L, methicillin- and/or erythromycin-resistant Staphylococcus aureus and Staphylococcus epidermidis at 0.5 mg/L, Staphylococcus haemolyticus, Enterococcus faecium, Streptococcus pneumoniae, Streptococcus mitis, Streptococcus bovis, Streptococcus sanguis and Streptococcus anginosus at 1 mg/L and Enterococcus faecalis at 8 mg/L.

[Epidemiology of nosocomial infections].

PubMed

Astagneau, P

1998-09-15

The frequency of nosocomial infections lies between 5 and 10%, and varies according to the type of hospital and service. Age, underlying disease invasive devices (such as catheters) or procedures are the main risk factors. Common nosocomial infections are urinary tract infections, pneumonia, surgical site infections, bacteremia/septicemia and intravascular catheter-related infections. Gram positive cocci and gram negative bacilli account for one third and two thirds of microorganisms respectively, Staphylococcus aureus being frequently resistant to antibiotics. Prevention is based on a better control of infection risk related to the use of invasive devices.

In Vitro Activities of Y-688, a New 7-Substituted Fluoroquinolone, against Anaerobic Bacteria

PubMed Central

MacGowan, A. P.; Bowker, K. E.; Wootton, M.; Holt, H. A.; Reeves, D. S.

1998-01-01

The in vitro activities of Y-688, a new 7-substituted fluoroquinolone derivative, against 317 nonduplicate anaerobic isolates were determined. Eighty-five percent of the Bacteroides fragilis group (n = 89) were inhibited by ≤2 mg of Y-688 per liter, while 78, 100, 89, and 98% of gram-negative bacilli (n = 135), gram-positive cocci (n = 59), and non-spore-forming (n = 58) and spore-forming (n = 51) gram-positive bacilli, respectively, were inhibited by ≤1 mg of Y-688 per liter. PMID:9527797

Quinupristin-Dalfopristin Resistance in Streptococcus pneumoniae: Novel L22 Ribosomal Protein Mutation in Two Clinical Isolates from the SENTRY Antimicrobial Surveillance Program

PubMed Central

Jones, Ronald N.; Farrell, David J.; Morrissey, Ian

2003-01-01

Resistance to quinupristin-dalfopristin (Q/D) among gram-positive cocci has been very uncommon. Two clinical isolates among 8,837 (0.02%) Streptococcus pneumoniae isolates were discovered in 2001 to 2002 with Q/D MICs of 4 μg/ml. Each had a 5-amino-acid tandem duplication (RTAHI) in the L22 ribosomal protein gene (rplV) preventing synergistic ribosomal binding of the streptogramin combination. Similar gene duplication has been reported in Q/D-resistant Staphylococcus aureus. PMID:12878545

[Rare and severe complication of spinal anesthesia: bacterial meningitis (about a case and literature review)].

PubMed

Chouaib, Naoufal; Jidane, Said; Rafai, Mostafa; Belkouch, Ahmed; Zidouh, Saad; Belyamani, Lahcen

2017-01-01

Spinal anesthesia (SA) is the first locoregional anesthesia. It can cause side effects and carry risks that need to be avoided, prevented or treated early. We here report the case of a female patient operated under spinal anesthesia who had intense headache associated with nausea and vomiting evolving in the context of fever within a few days after surgeryLumbar puncture showed cloudy liquid revealing Gram + cocci on direct examination. This allowed the diagnosis of bacterial meningitis. Patient's evolution was favorable after antibiotic therapy.

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC

DOE PAGES

Kashyap, Sanjay; Woehl, Taylor; Valverde-Tercedor, Carmen; ...

2014-01-01

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus , strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation ofmore » biotemplated inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.« less

Fission and fusion scenarios for magnetic microswimmer clusters

PubMed Central

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

2016-01-01

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethora of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria. PMID:27874006

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC

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

Kashyap, Sanjay; Woehl, Taylor; Valverde-Tercedor, Carmen

2014-03-07

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus, strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation of biotemplatedmore » inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.« less

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

PubMed Central

Wrighton, Kelly C; Castelle, Cindy J; Varaljay, Vanessa A; Satagopan, Sriram; Brown, Christopher T; Wilkins, Michael J; Thomas, Brian C; Sharon, Itai; Williams, Kenneth H; Tabita, F Robert; Banfield, Jillian F

2016-01-01

Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete (>93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency. PMID:27137126

Enigmatic, ultrasmall, uncultivated Archaea

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

Baker, Brett J.; Comolli, Luis; Dick, Gregory J.

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge particularly for Archaea that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher codingmore » density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159 167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.« less

Enigmatic, ultrasmall, uncultivated Archaea

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

Baker, Brett J.; Comolli, Luis; Dick, Gregory J.

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete similar to 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher codingmore » density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3: 159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.« less

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

DOE PAGES

Wrighton, Kelly C.; Castelle, Cindy J.; Varaljay, Vanessa A.; ...

2016-05-03

Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates andmore » WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete ( > 93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO 2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.« less

Bacterial succession within an ephemeral hypereutrophic Mojave Desert playa Lake.

PubMed

Navarro, Jason B; Moser, Duane P; Flores, Andrea; Ross, Christian; Rosen, Michael R; Dong, Hailiang; Zhang, Gengxin; Hedlund, Brian P

2009-02-01

Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by approximately 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of approximately 1x10(6) cells ml(-1) of culturable heterotrophs was replaced by a dense population of more than 1x10(9) cells ml(-1), which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria.

Plutonium as a tracer for soil erosion assessment in northeast China.

PubMed

Xu, Yihong; Qiao, Jixin; Pan, Shaoming; Hou, Xiaolin; Roos, Per; Cao, Liguo

2015-04-01

Soil erosion is one of the most serious environmental and agricultural problems faced by human society. Assessing intensity is an important issue for controlling soil erosion and improving eco-environmental quality. The suitability of the application of plutonium (Pu) as a tracer for soil erosion assessment in northeast China was investigated by comparing with that of 137Cs. Here we build on preliminary work, in which we investigated the potential of Pu as a soil erosion tracer by sampling additional reference sites and potential erosive sites, along the Liaodong Bay region in northeast China, for Pu isotopes and 137Cs. 240Pu/239Pu atomic ratios in all samples were approximately 0.18, which indicated that the dominant source of Pu was the global fallout. Pu showed very similar distribution patterns to those of 137Cs at both uncultivated and cultivated sites. 239+240Pu concentrations in all uncultivated soil cores followed an exponential decline with soil depth, whereas at cultivated sites, Pu was homogenously distributed in plow horizons. Factors such as planted crop types, as well as methods and frequencies of irrigation and tillage were suggested to influence the distribution of radionuclides in cultivated land. The baseline inventories of 239+240Pu and 137Cs were 88.4 and 1688 Bq m(-2) respectively. Soil erosion rates estimated by 239+240Pu tracing method were consistent with those obtained by the 137Cs method, confirming that Pu is an effective tracer with a similar tracing behavior to that of 137Cs for soil erosion assessment. Copyright © 2014 Elsevier B.V. All rights reserved.

Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

USGS Publications Warehouse

Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

2009-01-01

Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

USGS Publications Warehouse

Urbach, Ena; Vergin, Kevin L.; Morse, Ariel

2001-01-01

The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (<=16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

Evolution of sensitivity to fosfomycin in bacteria isolated in 1973, 1974 and 1975 in the Servicio de Microbiologia y Epidemiologia of the 'Clinica Puerta de Hierro', Madrid.

PubMed

Dámaso, D; Moreno-López, M; Martínez-Beltrán, J

1977-01-01

The bacteriostatic activity of fosfomycin was studied in vitro against 1,243 clinical isolations of gram-positive cocci and 4,086 isolations of gram-negative bacilli that were obtained in 1973, 1974 and in the period from January to May of 1975. MIC was determined by the agar diffusion method, quantifying it by means of the standard curve that was worked out with the strain of E. coli NCTC 10,418. A slight increase in resistance was observed in the gram-positive cocci: 64 mug/ml were inhibitory for 63% of the 249 isolations obtained in 1973, 59.1% of the 716 isolations obtained in 1974, and 57.5% of the 278 isolations from 1975. A slight loss of sensitivity was also observed in the gram-negative bacilli: the aforementioned concentration of fosfomycin inhibited 36% of the 742 isolations from 1973, 33.6% of the 2,387 isolations from 1974 and 32.6% of the 957 isolations from 1975. 933 g of this antibiotic were consumed in our hospital in 1973, 4,203 g in 1974 and 957 g in 1975. The consumption rate per patient per year was 0.15, 0.72 and 0.20 g, respectively. In conclusion, although no change was observed in the sensitivity of some bacterial strains to fosfomycin, the overall study indicates a slight decrease in the sensitivity, although it does not apparently have any relationship to the consumption of fosfomycin in our hospital.

Biogenicity of terrestrial oncoids formed in soil pockets, Cayman Brac, British West Indies

NASA Astrophysics Data System (ADS)

Jones, Brian

2011-05-01

Terrestrial oncoids, up to 85 mm long, are common in some of the soil-filled pockets found in the finely crystalline dolostones of the Cayman Formation on Cayman Brac. Each of these coated grains has a nucleus formed of a white, finely crystalline dolostone lithoclast (derived from the Cayman Formation) that is encased by a light brown to tan cortex that is formed largely of micrite and minimicrite, is vaguely laminated, and lacks obvious biogenic structures. The cortex, typically < 10 mm thick, is variable in thickness around individual grains and from grain to grain. On the surfaces of the oncoids there is a diverse microbiota that includes various reticulate filaments that are typically < 1 μm in diameter, cocci, some large-diameter collapsed and calcified filaments, sporangia-like structures, and locally, exopolysaccharides (EPS). In the subsurface parts of the cortices, however, filaments are very rare and there are only scattered cocci. Evidence derived from the surface microbes indicates that they played an active role in the growth of the cortical laminae by binding material to their surfaces, calcification of the microbes, providing substrates on which calcite was precipitated, and forming cavities in which calcite cement was later precipitated. In stark contrast, it is difficult to ascribe a biotic influence to the formation of the subsurface laminae because of the paucity of preserved microbes. The lack of microbes, however, probably reflects the fact that the formative microbes were destroyed during diagenesis. This example clearly demonstrates that the lack of preserved microbes cannot be taken as an indication that the grains formed as a result of abiogenic processes.

Surgical management of maxillary and premaxillary osteomyelitis in a reticulated python (Python reticulatus).

PubMed

Latney, La'Toya V; McDermott, Colin; Scott, Gregory; Soltero-Rivera, Maria M; Beguesse, Kyla; Sánchez, Melissa D; Lewis, John R

2016-05-01

CASE DESCRIPTION A 1-year-old reticulated python (Python reticulatus) was evaluated because of a 2-week history of wheezing and hissing. CLINICAL FINDINGS Rostral facial cellulitis and deep gingival pockets associated with missing rostral maxillary teeth were evident. Tissues of the nares were swollen, resulting in an audible wheeze during respiration. Multiple scars and superficial facial wounds attributed to biting by live prey were apparent. Radiographic examination revealed bilateral, focal, rostral maxillary osteomyelitis. TREATMENT AND OUTCOME Wound irrigation, antimicrobials, and anti-inflammatory drug treatment resulted in reduced cellulitis. A 3-week regimen that included empirical antimicrobial treatment and improved husbandry resulted in resolution of the respiratory sounds and partial healing of bite wounds, but radiographic evaluation revealed progressive maxillary osteomyelitis. Microbial culture of blood yielded scant gram-positive cocci and Bacillus spp, which were suspected sample contaminants. Bilateral partial maxillectomies were performed; microbial culture and histologic examination of resected bone confirmed osteomyelitis with gram-positive cocci. Treatment with trimethoprim-sulfamethoxazole was initiated on the basis of microbial susceptibility tests. Four months later, follow-up radiography revealed premaxillary osteomyelitis; surgery was declined, and treatment with trimethoprim-sulfamethoxazole was reinstituted. Eight months after surgery, the patient was reevaluated because of recurrent clinical signs; premaxillectomy was performed, and treatment with trimethoprim-sulfamethoxazole was prescribed on the basis of microbial culture of bone and microbial susceptibility testing. Resolution of osteomyelitis was confirmed by CT 11 months after the initial surgery. CONCLUSIONS AND CLINICAL RELEVANCE Focal maxillectomies and premaxillectomy were successfully performed in a large python. Surgical management and appropriate antimicrobial treatment resulted in a good outcome.

Accuracy of tracheal aspirate gram stain in predicting Staphylococcus aureus infection in ventilator-associated pneumonia.

PubMed

Seligman, Renato; Seligman, Beatriz Graeff Santos; Konkewicz, Loriane; Dos Santos, Rodrigo Pires

2015-01-01

The Gram stain can be used to direct initial empiric antimicrobial therapy when complete culture is not available. This rapid test could prevent the initiation of inappropriate therapy and adverse outcomes. However, several studies have attempted to determine the value of the Gram stain in the diagnosis and therapy of bacterial infection in different populations of patients with ventilator-associated pneumonia (VAP) with conflicting results. The objective of this study is to evaluate the accuracy of the Gram stain in predicting the existence of Staphylococcus aureus infections from cultures of patients suspected of having VAP. This prospective single-center open cohort study enrolled 399 patients from December 2005 to December 2010. Patients suspected of having VAP by ATS IDSA criteria were included. Respiratory secretion samples were collected by tracheal aspirate (TA) for standard bacterioscopic analysis by Gram stain and culture. Respiratory secretion samples collected by tracheal aspirates of 392 patients were analyzed by Gram stain and culture. When Gram-positive cocci were arranged in clusters, the sensitivity was 68.4%, specificity 97.8%, positive predictive value 88.1% and negative predictive value 92.8% for predicting the presence of Staphylococcus aureus in culture (p < 0.001). A tracheal aspirate Gram stain can be used to rule out the presence of Staphylococcus aureus in patients with a clinical diagnosis of VAP with a 92.8% Negative Predictive Value. Therefore, 7.2% of patients with Staphylococcus aureus would not be protected by an empiric treatment that limits antimicrobial coverage to Staphylococcus aureus only when Gram positive cocci in clusters are identified.

The accuracy of Gram stain of respiratory specimens in excluding Staphylococcus aureus in ventilator-associated pneumonia.

PubMed

Gottesman, Tamar; Yossepowitch, Orit; Lerner, Evgenia; Schwartz-Harari, Orna; Soroksky, Arie; Yekutieli, Daniel; Dan, Michael

2014-10-01

To evaluate the Gram stain of deep tracheal aspirate as a tool to direct empiric antibiotic therapy, and more specifically as a tool to exclude the need for empiric antibiotic coverage against Staphylococcus aureus in ventilator-associated pneumonia (VAP). A prospective, single-center, observational, cohort study. All wards at a community hospital. Adult patients requiring mechanical ventilation, identified as having VAP in a 54-month prospective surveillance database. Sampling of lower airway secretions by deep endotracheal aspiration was taken from each patient who developed VAP. Samples were sent immediately for Gram stain and qualitative bacterial cultures. Demographic and relevant clinical data were collected; Gram stain, culture, and antibiotic susceptibility results were documented; and outcome was followed prospectively. The analysis included 114 consecutive patients with 115 episodes of VAP from June 2007 to January 2012. Sensitivity of Gram stain compared with culture was 90.47% for gram-positive cocci, 69.6% for gram-negative rods, and 50% for sterile cultures. Specificity was 82.5%, 77.8%, and 79%, respectively. Negative predictive value was high for gram-positive cocci (97%) and sterile cultures (96%) but low for gram-negative rods (20%). Acinetobacter baumanii (45%) and Pseudomonas aeruginosa (38 %) were the prevailing isolates. S aureus was found in 18.3% of the patients. Most isolates were multiresistant. Absence of gram-positive bacteria on Gram stain had a high negative predictive value. These data can be used to narrow the initial empiric antibiotic regimen and to avoid unnecessary exposure of patients to vancomycin and other antistaphyloccocal agents. Copyright © 2014 Elsevier Inc. All rights reserved.

A comparison of neonatal Gram-negative rod and Gram-positive cocci meningitis.

PubMed

Smith, P B; Cotten, C M; Garges, H P; Tiffany, K F; Lenfestey, R W; Moody, M A; Li, J S; Benjamin, D K

2006-02-01

Neonatal meningitis is an illness with potentially devastating consequences. Early identification of potential risk factors for Gram-negative rod (GNR) infections versus Gram-positive cocci (GPC) infection prior to obtaining final culture results is of value in order to appropriately guide expirical therapy. We sought to compare laboratory and clinical parameters of GNR and GPC meningitis in a cohort of term and premature infants. We evaluated lumbar punctures from neonates cared for at 150 neonatal intensive care units managed by the Pediatrix Medical Group Inc. We compared cerebrospinal fluid (CSF) parameters (white blood cell count, red blood cell count, glucose, and protein), demographics, and outcomes between infants with GNR and GPC meningitis. CSF cultures positive with coagulase-negative staphylococci were excluded. We identified 77 infants with GNR and 86 with GPC meningitis. There were no differences in gestational age, birth weight, infant sex, race, or rate of Caesarean section. GNR meningitis was more often diagnosed after the third postnatal day and was associated with higher white blood cell and red blood cell counts. GNR meningitis diagnosed in the first 3 days of life was associated with antepartum antibiotic exposure. No difference was noted in either CSF protein or glucose levels. After correcting for gestational age, there was no observed difference in mortality between infants infected with GNR or GPC. Compared to GPC meningitis, GNR meningitis was associated with several aspects of the clinical history and laboratory findings including older age of presentation, antepartum exposure to antibiotics, and elevated CSF white blood cell and red blood cell counts.

Isolation and determination of four potential antimicrobial components from Pseudomonas aeruginosa extracts

PubMed Central

Xu, Ling-Qing; Zeng, Jian-Wen; Jiang, Chong-He; Wang, Huan; Li, Yu-Zhen; Wen, Wei-Hong; Li, Jie-Hua; Wang, Feng; Ting, Wei-Jen; Sun, Zi-Yong; Huang, Chih-Yang

2017-01-01

Background: Pseudomonas aeruginosa can cause disease and also can be isolated from the skin of healthy people. Additionally, it exhibits certain antimicrobial effects against other microorganisms. Methods: We collected 60 strains of P. aeruginosa and screened their antimicrobial effects against Staphylococcus aureus (ATCC 25923) using the filter paper-disk method, the cross-streaking method and the co-culture method and then evaluated the antimicrobial activity of the chloroform-isolated S. aureus extracts against methicillin-resistant S. aureus (MRSA, Gram-positive cocci), vancomycin intermediate-resistant S. aureus (VISA, Gram-positive cocci), Corynebacterium spp. (CS, Gram-positive bacilli), Acinetobacter baumannii (AB, Gram-negative bacilli), Moraxella catarrhalis (MC, Gram-negative diplococcus), Candida albicans (CA, fungi), Candida tropicalis (CT, fungi), Candida glabrata (CG, fungi) and Candida parapsilosis (CP, fungi). Results: The PA06 and PA46 strains have strong antimicrobial effects. High-performance liquid chromatography (HPLC) analysis revealed that the major components of PA06 and PA46 that exhibit antimicrobial activity are functionally similar to phenazine-1-carboxylic acid (PCA) and pyocyanin. Preparative HPLC was performed to separate and isolate the 4 major potential antimicrobial components: PA06ER10, PA06ER16, PA06ER23 and PA06ER31. Further, the molecular masses of PA06ER10 (260.1), PA06ER16 (274.1), PA06ER23 (286.1) and PA06ER31 (318.2) were determined by electrospray ionization (ESI) mass spectrometry. Conclusion: P. aeruginosa can produce small molecules with potential antimicrobial activities against MRSA, VISA, CS, MC, CA, CT, CG and CP but not against AB. PMID:29200950

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

PubMed Central

Spang, Anja; Saw, Jimmy H.; Lind, Anders E.; Ettema, Thijs J. G.

2013-01-01

The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. PMID:24348093

Diversity of the human intestinal microbial flora.

PubMed

Eckburg, Paul B; Bik, Elisabeth M; Bernstein, Charles N; Purdom, Elizabeth; Dethlefsen, Les; Sargent, Michael; Gill, Steven R; Nelson, Karen E; Relman, David A

2005-06-10

The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.

Anaerococcus degenerii sp. nov., isolated from human clinical specimens.

PubMed

Veloo, A C M; Elgersma, P E; van Winkelhoff, A J

2015-06-01

Four clinical isolates of gram-positive strict anaerobic cocci were isolated from four different human mixed anaerobic infections. The taxonomical status of the four strains could not be established using standard identification techniques. The biochemical features of the strains were established and their taxonomic position was determined using 16S rRNA sequencing. The four strains form a homogeneous phenotypical and genotypical cluster. A new Anaerococcus species is proposed for these isolates: Anaerococcus degenerii sp. nov. The type strain is UMCG-104(T) = DSM29674(T) (accession number AM176528). Copyright © 2015 Elsevier Ltd. All rights reserved.

Soft x-ray microscope with zone plates at UVSOR

NASA Astrophysics Data System (ADS)

Watanabe, Norio; Shimanuki, Yoshio; Taniguchi, Mieko; Kihara, Hiroshi

1993-01-01

A soft x-ray microscope with zone plates was set up at UVSOR (Okazaki, Japan). A 0.41 micrometers line and space pattern was clearly distinguished using an objective zone plate with the outermost zone width of 0.41 micrometers . Modulation transfer functions were measured at wavelengths of 3.1 nm and 5.4 nm, and compared with theoretical calculations. Considering the resolution of a microchannel plate used as a detector, the agreement is fairly good. With this microscope, some biological specimens such as diatoms, spicule of trepang, crab and rabbit muscles, human blood cells, human chromosomes, and magnetotactic bacterium were observed at 3.1 nm and 5.4 nm. With an environmental chamber (wet cell) using polypropylene foils as windows, wet specimens were observed at a wavelength of 4.6 nm. Images of spicule of trepang, human blood cell, and cultured protoplast of plant cell stained by methyl mercury were observed with good contrast.

Fission and fusion scenarios for magnetic microswimmer clusters

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

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethoramore » of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Lastly, our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria.« less

Time-resolved 2-million-year-old supernova activity discovered in Earth's microfossil record.

PubMed

Ludwig, Peter; Bishop, Shawn; Egli, Ramon; Chernenko, Valentyna; Deneva, Boyana; Faestermann, Thomas; Famulok, Nicolai; Fimiani, Leticia; Gómez-Guzmán, José Manuel; Hain, Karin; Korschinek, Gunther; Hanzlik, Marianne; Merchel, Silke; Rugel, Georg

2016-08-16

Massive stars ([Formula: see text]), which terminate their evolution as core-collapse supernovae, are theoretically predicted to eject [Formula: see text] of the radioisotope (60)Fe (half-life 2.61 Ma). If such an event occurs sufficiently close to our solar system, traces of the supernova debris could be deposited on Earth. Herein, we report a time-resolved (60)Fe signal residing, at least partially, in a biogenic reservoir. Using accelerator mass spectrometry, this signal was found through the direct detection of live (60)Fe atoms contained within secondary iron oxides, among which are magnetofossils, the fossilized chains of magnetite crystals produced by magnetotactic bacteria. The magnetofossils were chemically extracted from two Pacific Ocean sediment drill cores. Our results show that the (60)Fe signal onset occurs around 2.6 Ma to 2.8 Ma, near the lower Pleistocene boundary, terminates around 1.7 Ma, and peaks at about 2.2 Ma.

In Vivo Coating of Bacterial Magnetic Nanoparticles by Magnetosome Expression of Spider Silk-Inspired Peptides.

PubMed

Mickoleit, Frank; Borkner, Christian B; Toro-Nahuelpan, Mauricio; Herold, Heike M; Maier, Denis S; Plitzko, Jürgen M; Scheibel, Thomas; Schüler, Dirk

2018-03-12

Magnetosomes are natural magnetic nanoparticles with exceptional properties that are synthesized in magnetotactic bacteria by a highly regulated biomineralization process. Their usability in many applications could be further improved by encapsulation in biocompatible polymers. In this study, we explored the production of spider silk-inspired peptides on magnetosomes of the alphaproteobacterium Magnetospirillum gryphiswaldense. Genetic fusion of different silk sequence-like variants to abundant magnetosome membrane proteins enhanced magnetite biomineralization and caused the formation of a proteinaceous capsule, which increased the colloidal stability of isolated particles. Furthermore, we show that spider silk peptides fused to a magnetosome membrane protein can be used as seeds for silk fibril growth on the magnetosome surface. In summary, we demonstrate that the combination of two different biogenic materials generates a genetically encoded hybrid composite with engineerable new properties and enhanced potential for various applications.

Origin of microbial biomineralization and magnetotaxis during the Archean.

PubMed

Lin, Wei; Paterson, Greig A; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A; Zhu, Rixiang; Kirschvink, Joseph L; Pan, Yongxin

2017-02-28

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

Controlled cobalt doping of magnetosomes in vivo.

PubMed

Staniland, Sarah; Williams, Wyn; Telling, Neil; Van Der Laan, Gerrit; Harrison, Andrew; Ward, Bruce

2008-03-01

Magnetotactic bacteria biomineralize iron into magnetite (Fe3O4) nanoparticles that are surrounded by lipid vesicles. These 'magnetosomes' have considerable potential for use in bio- and nanotechnological applications because of their narrow size and shape distribution and inherent biocompatibility. The ability to tailor the magnetic properties of magnetosomes by chemical doping would greatly expand these applications; however, the controlled doping of magnetosomes has so far not been achieved. Here, we report controlled in vivo cobalt doping of magnetosomes in three strains of the bacterium Magnetospirillum. The presence of cobalt increases the coercive field of the magnetosomes--that is, the field necessary to reverse their magnetization--by 36-45%, depending on the strain and the cobalt content. With elemental analysis, X-ray absorption and magnetic circular dichroism, we estimate the cobalt content to be between 0.2 and 1.4%. These findings provide an important advance in designing biologically synthesized nanoparticles with useful highly tuned magnetic properties.

Fission and fusion scenarios for magnetic microswimmer clusters

DOE PAGES

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

2016-11-22

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethoramore » of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Lastly, our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria.« less

Metabolism in the Uncultivated Giant Sulfide-Oxidizing Bacterium Thiomargarita Namibiensis Assayed Using a Redox-Sensitive Dye

NASA Astrophysics Data System (ADS)

Bailey, J.; Flood, B.; Ricci, E.

2014-12-01

The colorless sulfur bacteria are non-photosynthetic chemolithotrophs that live at interfaces between nitrate, or oxygen, and hydrogen sulfide. In sulfidic settings such as cold seeps and oxygen minimum zones, these bacteria are thought to constitute a critical node in the geochemical cycling of carbon, sulfur, nitrogen, and phosphorous. Many of these bacteria remain uncultivated and their metabolisms and physiologies are incompletely understood. Thiomargarita namibiensis is the largest of these sulfur bacteria, with individual cells reaching millimetric diameters. Despite the current inability to maintain a Thiomargarita culture in the lab, their large size allows for individual cells to be followed in time course experiments. Here we report on the novel use of a tetrazolium-based dye that measures the flux of NADH production from catabolic pathways via a colorimetric response. Staining with this dye allows for metabolism to be detected, even in the absence of observable cell division. When coupled to microscopy, this approach also allows for metabolism in Thiomargaritato be differentiated from that of epibionts or contaminants in xenic samples. The results of our tetrazolium dye-based assay suggests that Thiomargarita is the most metabolically versatile under anoxic conditions where it appears capable of using acetate, succinate, formate, thiosulfate, citrate, thiotaurine, hydrogen sulfide, and perhaps hydrogen as electron donors. Under hypoxic conditions, staining results suggest the utilization of acetate, citrate, and hydrogen sulfide. Cells incubated under oxic conditions showed the weakest tetrazolium staining response, and then only to hydrogen sulfide and questionably succinate. These initial results using a redox sensitive dye suggest that Thiomargarita is most metabolically versatile under anaerobic and hypoxic conditions. The results of this assay can be further evaluated using molecular approaches such as transcriptomics, as well as provide cultivation strategies.

Molecular analysis of 16S rRNA genes identifies potentially periodontal pathogenic bacteria and archaea in the plaque of partially erupted third molars.

PubMed

Mansfield, J M; Campbell, J H; Bhandari, A R; Jesionowski, A M; Vickerman, M M

2012-07-01

Small subunit rRNA sequencing and phylogenetic analysis were used to identify cultivable and uncultivable microorganisms present in the dental plaque of symptomatic and asymptomatic partially erupted third molars to determine the prevalence of putative periodontal pathogens in pericoronal sites. Template DNA prepared from subgingival plaque collected from partially erupted symptomatic and asymptomatic mandibular third molars and healthy incisors was used in polymerase chain reaction with broad-range oligonucleotide primers to amplify 16S rRNA bacterial and archaeal genes. Amplicons were cloned, sequenced, and compared with known nucleotide sequences in online databases to identify the microorganisms present. Two thousand three hundred two clones from the plaque of 12 patients carried bacterial sequences from 63 genera belonging to 11 phyla, including members of the uncultivable TM7, SR1, and Chloroflexi, and difficult-to-cultivate Synergistetes and Spirochaetes. Dialister invisus, Filifactor alocis, Fusobacterium nucleatum, Porphyromonas endodontalis, Prevotella denticola, Tannerella forsythia, and Treponema denticola, which have been associated with periodontal disease, were found in significantly greater abundance in pericoronal compared with incisor sites. Dialister invisus and F nucleatum were found in greater abundance in sites exhibiting clinical symptoms. The archaeal species, Methanobrevibacter oralis, which has been associated with severe periodontitis, was found in 3 symptomatic patients. These findings have provided new insights into the complex microbiota of pericoronitis. Several bacterial and archaeal species implicated in periodontal disease were recovered in greater incidence and abundance from the plaque of partially erupted third molars compared with incisors, supporting the hypothesis that the pericoronal region may provide a favored niche for periodontal pathogens in otherwise healthy mouths. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Drought Impacts on Agricultural Production and Land Fallowing in California's Central Valley in 2015

NASA Technical Reports Server (NTRS)

Rosevelt, Carolyn; Melton, Forrest S.; Johnson, Lee; Guzman, Alberto; Verdin, James P.; Thenkabail, Prasad S.; Mueller, Rick; Jones, Jeanine; Willis, Patrick

2016-01-01

The ongoing drought in California substantially reduced surface water supplies for millions of acres of irrigated farmland in California's Central Valley. Rapid assessment of drought impacts on agricultural production can aid water managers in assessing mitigation options, and guide decision making with respect to mitigation of drought impacts. Satellite remote sensing offers an efficient way to provide quantitative assessments of drought impacts on agricultural production and increases in fallow acreage associated with reductions in water supply. A key advantage of satellite-based assessments is that they can provide a measure of land fallowing that is consistent across both space and time. We describe an approach for monthly and seasonal mapping of uncultivated agricultural acreage developed as part of a joint effort by USGS, USDA, NASA, and the California Department of Water Resources to provide timely assessments of land fallowing during drought events. This effort has used the Central Valley of California as a pilot region for development and testing of an operational approach. To provide quantitative measures of uncultivated agricultural acreage from satellite data early in the season, we developed a decision tree algorithm and applied it to time-series data from Landsat TM (Thematic Mapper), ETM+ (Enhanced Thematic Mapper Plus), OLI (Operational Land Imager), and MODIS (Moderate Resolution Imaging Spectroradiometer). Our effort has been focused on development of indicators of drought impacts in the March-August timeframe based on measures of crop development patterns relative to a reference period with average or above average rainfall. To assess the accuracy of the algorithms, monthly ground validation surveys were conducted across 650 fields from March-September in 2014 and 2015. We present the algorithm along with updated results from the accuracy assessment, and data and maps of land fallowing in the Central Valley in 2015.

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

PubMed Central

Chen, Tsute; Yu, Wen-Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

2010-01-01

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org PMID:20624719

Drought Impacts on Agricultural Production and Land Fallowing in California's Central Valley in 2015

NASA Astrophysics Data System (ADS)

Rosevelt, C.; Melton, F. S.; Johnson, L.; Guzman, A.; Verdin, J. P.; Thenkabail, P. S.; Mueller, R.; Jones, J.; Willis, P.

2015-12-01

The ongoing drought in California substantially reduced surface water supplies for millions of acres of irrigated farmland in California's Central Valley. Rapid assessment of drought impacts on agricultural production can aid water managers in assessing mitigation options, and guide decision making with respect to mitigation of drought impacts. Satellite remote sensing offers an efficient way to provide quantitative assessments of drought impacts on agricultural production and increases in fallow acreage associated with reductions in water supply. A key advantage of satellite-based assessments is that they can provide a measure of land fallowing that is consistent across both space and time. We describe an approach for monthly and seasonal mapping of uncultivated agricultural acreage developed as part of a joint effort by USGS, USDA, NASA, and the California Department of Water Resources to provide timely assessments of land fallowing during drought events. This effort has used the Central Valley of California as a pilot region for development and testing of an operational approach. To provide quantitative measures of uncultivated agricultural acreage from satellite data early in the season, we developed a decision tree algorithm and applied it to timeseries of data from Landsat TM, ETM+, OLI, and MODIS. Our effort has been focused on development of indicators of drought impacts in the March - August timeframe based on measures of crop development patterns relative to a reference period with average or above average rainfall. To assess the accuracy of the algorithms, monthly ground validation surveys were conducted across 650 fields from March - September in 2014 and 2015. We present the algorithm along with updated results from the accuracy assessment, and data and maps of land fallowing in the Central Valley in 2015.

Mapping Drought Impacts on Agricultural Production in California's Central Valley

NASA Astrophysics Data System (ADS)

Melton, F. S.; Guzman, A.; Johnson, L.; Rosevelt, C.; Verdin, J. P.; Dwyer, J. L.; Mueller, R.; Zakzeski, A.; Thenkabail, P. S.; Wallace, C.; Jones, J.; Windell, S.; Urness, J.; Teaby, A.; Hamblin, D.; Post, K. M.; Nemani, R. R.

2014-12-01

The ongoing drought in California has substantially reduced surface water supplies for millions of acres of irrigated farmland in California's Central Valley. Rapid assessment of drought impacts on agricultural production can aid water managers in assessing mitigation options, and guide decision making with respect to requests for local water transfers, county drought disaster designations, and allocation of emergency funds to mitigate drought impacts. Satellite remote sensing offers an efficient way to provide quantitative assessments of drought impacts on agricultural production and increases in idle acreage associated with reductions in water supply. A key advantage of satellite-based assessments is that they can provide a measure of land fallowing that is consistent across both space and time. We describe an approach for monthly and seasonal mapping of uncultivated agricultural acreage developed as part of a joint effort by USGS, USDA, NASA, and the California Department of Water Resources to provide timely assessments of land fallowing during drought events. This effort has used the Central Valley of California as a pilot region for development and testing of an operational approach. To provide quantitative measures of uncultivated agricultural acreage from satellite data early in the season, we developed a decision tree algorithm and applied it to timeseries of data from Landsat TM, ETM+, OLI, and MODIS. Our effort has been focused on development of indicators of drought impacts in the March - August timeframe based on measures of crop development patterns relative to a reference period with average or above average rainfall. To assess the accuracy of the algorithms, monthly ground validation surveys were conducted across 640 fields from March - September, 2014. We present the algorithm along with updated results from the accuracy assessment, and discuss potential applications to other regions.

Microbiologic Analysis of Complicated and Uncomplicated Acute Appendicitis.

PubMed

García-Marín, Andrés; Pérez-López, Mercedes; Martínez-Guerrero, Elena; Rodríguez-Cazalla, Lorena; Compañ-Rosique, Antonio

2018-01-01

Microbiologic studies suggest that complicated (CAA) and uncomplicated (UAA) acute appendicitis are different entities. Routine peritoneal fluid cultures continue to be controversially related to a low positive rate, found mainly in UAA; to isolation of typical micro-organisms with expected susceptibilities; and to a community-acquired intra-abdominal infection. The aim of this study was to describe microbiologic isolates in CAA and UAA and the usefulness of peritoneal fluid cultures to determine the susceptibilities to our antibiotic therapy guidelines. This study was a retrospective review of a prospective database collected at University San Juan Hospital (Spain) between June 2014 and June 2017. Complicated acute appendicitis was defined as gangrenous or perforated, whereas UAA was defined as phegmonous or suppurative. Our antibiotic recommendations are amoxicillin-clavulanic acid and in patients with β-lactam allergies, metronidazole plus aztreonam, and an aminoglycoside (gentamicin or tobramycin). Microbiologic cultures were performed in 264 patients, 157 with a CAA and 107 with a UAA. The positive culture rate was significantly higher in CAA (59%) than in UAA (24.3%). Gram-positive cocci (51.6% CAA; 23.1% UAA), including Streptococcus constellatus (29% CAA; 3.8% UAA), and anaerobes (67.7% CAA; 42.3% UAA) were significantly more common in CAA. The rates of antibiotic resistance were amoxicillin-clavulanic acid 14% (17.2% CAA; 3.8% UAA), gentamicin or tobramycin 8.4% (9.7% CAA; 3.8% UAA), ciprofloxacin 5.9% (6.5% CAA; 3.8% UAA), and ertapenem 10.9% (14% CAA; 0 UAA). The culture-positive rate was higher in CAA, with different isolates and susceptibilities than in UAA, identifying a higher frequency of gram-positive cocci (including S. constellatus) and anaerobes. We recommend obtaining peritoneal fluid cultures in CAA, which frequently will lead to a change in the antimicrobial drug therapy guidelines, creating specific recommendations in AA.

Modification of IgE binding to αS1-casein by proteolytic activity of Enterococcus faecium isolated from Iranian camel milk samples.

PubMed

Kordesedehi, Reihane; Taheri-Kafrani, Asghar; Rabbani-Khorasgani, Mohammad; Kazemi, Rezvan; Mutangadura, Daniel; Haertle, Thomas

2018-06-20

Milk is a perfect source of nutrients for neonates. When breast feeding cannot be done, an infant's alimentation is usually initiated to cow's milk, among the primary foods. It has been reported that about 2.5% of juveniles under the age of 3 years manifest allergic reactions to cow's milk proteins. Among the cow's milk proteins, casein fractions are considered as the strongest allergenic proteins. The proteolytic enzymes of lactic acid bacteria (LAB), during fermentation of dairy products, can break down milk proteins especially caseins and subsequently reduce the immune reactivity of allergenic proteins. In this research, raw bovine and camel milk samples were screened for cocci LAB strains and after isolation, their proteolytic activity against bovine milk caseins were evaluated by SDS-PAGE and RP-HPLC. The potential of cocci LAB strains on α S1 -casein degradation and their potential to break down the principle allergenic epitopes of this protein was detected using indirect competitive ELISA. Molecular identification of the best proteolytic strain was fulfilled by 16S rDNA fragment sequencing with universal primers. The obtained results demonstrated that Enterococcus faecium isolated from raw camel milk samples was the most efficient isolate in hydrolyzing Na-caseinate and α S1 -casein. Hydrolysated α S1 -casein by Enterococcus faecium was also less recognized by IgE of bovine milk allergic patients' sera in comparison with native α S1 -casein. It has been proposed that Enterococcus faecium could be an efficient strain in allergenicity reduction of cow's milk proteins. So it could be an excellent candidate to be potentially used in dairy industries. Copyright © 2018 Elsevier B.V. All rights reserved.

Misinterpretation of Gram Stain from the Stationary Growth Phase of Positive Blood Cultures for Brucella and Acinetobacter Species.

PubMed

Bazzi, Ali M; Al-Tawfiq, Jaffar A; Rabaan, Ali A

2017-01-01

Acinetobacter baumannii and Brucella species are Gram-negative organisms that are vulnerable to misinterpretation as Gram-positive or Gram-variable in blood cultures. We assess the random errors in gram stain interpretation to reduce the likelihood of such errors and therefore patient harm. Aerobic and anaerobic blood cultures from two patients in an acute care facility in Saudi Arabia were subjected to preliminary Gram-staining. In case 1, VITEK-2 Anaerobe Identification, repeat Gram staining from a blood agar plate, Remel BactiDrop™ Oxidase test, Urea Agar urease test and real-time PCR were used to confirm presence of Brucella and absence of Coryneform species. In case 2, repeat Gram- staining from the plate and the vials, VITEK-2 Gram-Negative Identification, real-time PCR and subculture on to Columbia agar, blood agar, and MacConkey agar were carried out to identify A. baumannii . In case 1, initially pleomorphic Gram-positive bacteria were identified. Coryneform species were suspected. Tiny growth was observed after 24 h on blood agar plates, and good growth by 48 h. Presence of Brucella species was ultimately confirmed. In case 2, preliminary Gram-stain results suggested giant Gram-positive oval cocci. Further testing over 18-24 h identified A. baumannii . Oxidase test from the plate and urease test from the culture vial is recommended after apparent identification of pleomorphic Gram-positive bacilli from blood culture, once tiny growth is observed, to distinguish Brucella from Corynebacterium species. If giant Gram-positive oval cocci are indicated by preliminary Gram-staining, it is recommended that the Gram stain be repeated from the plate after 4-6 h, or culture should be tested in Triple Sugar Iron (TSI) medium and the Gram stain repeated after 2-4 h incubation.

Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

DOE PAGES

Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; ...

2015-02-06

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n =more » 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.« less

Surgical Site Infections in Pediatric Spine Surgery: Comparative Microbiology of Patients with Idiopathic and Nonidiopathic Etiologies of Spine Deformity.

PubMed

Maesani, Matthieu; Doit, Catherine; Lorrot, Mathie; Vitoux, Christine; Hilly, Julie; Michelet, Daphné; Vidal, Christophe; Julien-Marsollier, Florence; Ilharreborde, Brice; Mazda, Keyvan; Bonacorsi, Stéphane; Dahmani, Souhayl

2016-01-01

Surgical site infections (SSIs) are a concern in pediatric spine surgery with unusually high rates for a clean surgery and especially for patients with deformity of nonidiopathic etiology. Microbiologic differences between etiologies of spine deformities have been poorly investigated. We reviewed all cases of SSI in spinal surgery between 2007 and 2011. Characteristics of cases and of bacteria according to the etiology of the spine disease were investigated. Of 496 surgeries, we identified 51 SSIs (10.3%) in 49 patients. Staphylococcus aureus was the most frequent pathogen whatever the etiology (n = 31, 61% of infection cases). The second most frequent pathogens vary according to the etiology of the spine deformity. It was Gram-negative bacilli (GNB) in nonidiopathic cases (n = 19, 45% of cases) and anaerobe in idiopathic cases (n = 8, 38% of cases), particularly Gram-positive anaerobic cocci (n = 5, 24% of cases). Infection rate was 6.8% in cases with idiopathic spine disease (n = 21) and 15.9% in cases with nonidiopathic spine disease (n = 30). Nonidiopathic cases were more frequently male with lower weight. American Society of Anesthesiologists score was more often greater than 2, they had more frequently sacral implants and postoperative intensive care unit stay. GNB were significantly associated with a nonidiopathic etiology, low weight, younger age and sacral fusion. SSIs were polymicrobial in 31% of cases with a mean of 1.4 species per infection cases. S. aureus is the first cause of SSI in pediatric spine surgery. However, Gram-positive anaerobic cocci should be taken into account in idiopathic patients and GNB in nonidiopathic patients when considering antibiotic prophylaxis and curative treatment.

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens

PubMed Central

Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.

2015-01-01

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci. PMID:25658760

Bactericidal Effects and Mechanism of Action of Olanexidine Gluconate, a New Antiseptic

PubMed Central

Iwata, Koushi; Nii, Takuya; Nakata, Hikaru; Tsubotani, Yoshie; Inoue, Yasuhide

2015-01-01

Olanexidine gluconate [1-(3,4-dichlorobenzyl)-5-octylbiguanide gluconate] (development code OPB-2045G) is a new monobiguanide compound with bactericidal activity. In this study, we assessed its spectrum of bactericidal activity and mechanism of action. The minimal bactericidal concentrations of the compound for 30-, 60-, and 180-s exposures were determined with the microdilution method using a neutralizer against 320 bacterial strains from culture collections and clinical isolates. Based on the results, the estimated bactericidal olanexidine concentrations with 180-s exposures were 869 μg/ml for Gram-positive cocci (155 strains), 109 μg/ml for Gram-positive bacilli (29 strains), and 434 μg/ml for Gram-negative bacteria (136 strains). Olanexidine was active against a wide range of bacteria, especially Gram-positive cocci, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, and had a spectrum of bactericidal activity comparable to that of commercial antiseptics, such as chlorhexidine and povidone-iodine. In vitro experiments exploring its mechanism of action indicated that olanexidine (i) interacts with the bacterial surface molecules, such as lipopolysaccharide and lipoteichoic acid, (ii) disrupts the cell membranes of liposomes, which are artificial bacterial membrane models, (iii) enhances the membrane permeability of Escherichia coli, (iv) disrupts the membrane integrity of S. aureus, and (v) denatures proteins at relatively high concentrations (≥160 μg/ml). These results indicate that olanexidine probably binds to the cell membrane, disrupts membrane integrity, and its bacteriostatic and bactericidal effects are caused by irreversible leakage of intracellular components. At relatively high concentrations, olanexidine aggregates cells by denaturing proteins. This mechanism differs slightly from that of a similar biguanide compound, chlorhexidine. PMID:25987609

Gram-Positive Anaerobic Cocci

PubMed Central

Murdoch, D. A.

1998-01-01

Gram-positive anaerobic cocci (GPAC) are a heterogeneous group of organisms defined by their morphological appearance and their inability to grow in the presence of oxygen; most clinical isolates are identified to species in the genus Peptostreptococcus. GPAC are part of the normal flora of all mucocutaneous surfaces and are often isolated from infections such as deep organ abscesses, obstetric and gynecological sepsis, and intraoral infections. They have been little studied for several reasons, which include an inadequate classification, difficulties with laboratory identification, and the mixed nature of the infections from which they are usually isolated. Nucleic acid studies indicate that the classification is in need of radical revision at the genus level. Several species of Peptostreptococcus have recently been described, but others still await formal recognition. Identification has been based on carbohydrate fermentation tests, but most GPAC are asaccharolytic and use the products of protein degradation for their metabolism; the introduction of commercially available preformed enzyme kits affords a physiologically more appropriate method of identification, which is simple and relatively rapid and can be used in routine diagnostic laboratories. Recent reports have documented the isolation in pure culture of several species, notably Peptostreptococcus magnus, from serious infections. Studies of P. magnus have elucidated several virulence factors which correlate with the site of infection, and reveal some similarities to Staphylococcus aureus. P. micros is a strongly proteolytic species; it is increasingly recognized as an important pathogen in intraoral infections, particularly periodontitis, and mixed anaerobic deep-organ abscesses. Comparison of antibiotic susceptibility patterns reveals major differences between species. Penicillins are the antibiotics of choice, although some strains of P. anaerobius show broad-spectrum β-lactam resistance. PMID:9457430

Bacteremia due to Streptococcus tigurinus: A case report and literature review.

PubMed

Hirai, Jun; Sakanashi, Daisuke; Hagihara, Mao; Haranaga, Shusaku; Uechi, Kohei; Kato, Hideo; Hamada, Hiroyuki; Nishiyama, Naoya; Koizumi, Yusuke; Suematsu, Hiroyuki; Yamagishi, Yuka; Fujita, Jiro; Mikamo, Hiroshige

2016-11-01

Gene sequence analysis methods, including 16S rRNA identification, allows accurate identification of Streptococcus species, which include phenotypically closely related species that are difficult to differentiate using conventional chemical methods. We report a case of bacteremia due to Streptococcus tigurinus, identified by 16S rRNA, in a 72-year-old woman with gastrointestinal cancer and ascites. She was hospitalized to undergo elective tumor-related surgery. Five days prior to undergoing surgery, she developed a fever with no obvious source of infection. Blood cultures identified gram-positive cocci. The patient's bacteremia was initially thought to be caused by an Enterococcus species, given her underlying gastrointestinal disease. However, alpha-hemolytic, mucoid, circular colonies were observed on sheep blood agar the following day. Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and biochemical testing suggested Streptococcus pneumoniae, we conducted further investigation to identify the bacterium, as the patient had no symptoms of infections usually related with S. pneumoniae such as pneumonia, meningitis, or sinusitis, and the bacteremia occurred 30 days after hospitalization. Finally, the gram-positive cocci were identified as S. tigurinus, assigned to the Streptococcus mitis group in 2012. Although the origin of infection was unclear, it was suspected that peritonitis or bacterial translocation from the gastrointestinal tract caused the bacteremia. This novel species was recently reported as being extremely pathogenic and different from other Streptococcus species. It has been reported to occur in cases of infectious endocarditis and bacteremia. In this article, we reviewed previous reports of S. tigurinus infection and summarized the clinical and pathogenetic features. Copyright © 2016 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Environmental history of Lake Hovsgul from physical interpretation of remanent magnetization endmember analysis

NASA Astrophysics Data System (ADS)

Kosareva, Lina; Fabian, Karl; Shcherbakov, Valera; Nurgaliev, Danis

2016-04-01

The environmental history of Lake Hovsgul (Mongolia) is studied based on magnetic measurements of the core KDP-01. The drill hole reached a maximum depth of 53 m, from which sediment cores with a total length of 48 m were recovered. Coring gaps are due to the applied drilling technology. Following the approach by Heslop and Dillon, 2007, we develop the way of decomposition of the total magnetic fraction of a sample into not virtual but real three distinctive mineralogical components. For this, we first apply the end-member non-negative matrix factorization (NMF) modeling for the unmixing magnetic remanence curves. Having these results in hands, we decompose the hysteresis loops, backfield and strong field thermomagnetic curves into the components which now can be interpreted as certain mineralogical fractions. The likely interpretation of the components obtained is as follows. The soft component is represented by a coarse grained magnetite fraction as it typically results from terrigenous influx via fluvial transport. The second component is presented by a sharply defined magnetite grain size fraction in the 30-100 nm range that in lake environments is related to magnetosome chains of magnetotactic bacteria. It apparently covaries with a diamagnetic mineral, most likely carbonate. This indicates a link to organic authigenic fractions and fits to biogenic magnetite from magnetotactic bacteria. The third component also has a very high coercivity around 85 mT and is identified as a mixture of biogenic and abiotic greigite common in suboxic/anoxic sediments. The results of such the combined study are used to infer information on paleoclimatic and paleogeography conditions around the lake Hovsgul's area for the period of the last million years. A correlation between the outbursts of biogenic magnetite and greigite content with warm periods is found. Within some parts of the core the dominance of greigite contribution into magnetic signal is observed which we link to onset of icy anoxic environmental conditions. The work was carried out according to the Russian Government's Program of Competitive Growth of Kazan Federal University, supported by the grant provided to the Kazan State University for performing the state program in the field of scientific research, and partially supported by the Russian Foundation for Basic research (grant №. 14_05_00785).

Deposition of pyromagnetically-enhanced Marlboro Clay offset from spherule peak at onset of CIE and Paleocene-Eocene boundary at the midshelf Millville core site (NJ Coastal Plain)

NASA Astrophysics Data System (ADS)

Kent, D. V.; Lanci, L.; Wang, H.; Wright, J.

2017-12-01

Wilson Lake B and Millville are the two core sites on the NJ Coastal Plain where an impact spherule layer was discovered at the base of the Marlboro Clay, coinciding with the onset of the carbon isotope excursion (CIE) that identifies the Paleocene-Eocene boundary (Schaller+2016 Science). At the more proximal Wilson Lake site ( 35 m paleowater depth, 20 km from the paleoshore), enhanced magnetization of the Marlboro Clay marked by a dramatic increase in concentration of submicron magnetic particles closely coincided with the sharp peak in abundance of the spherules (Kent+2017 EPSL). Discounting magnetotactic bacteria and impact plume condensate as significant sources of the magnetic nanoparticles that dominate the magnetization of the 10 m-thick Marlboro Clay, a pyrogenetic origin was postulated whereby a widespread and intense conflagration over the hinterlands, quite possibly impact-induced, produced magnetic nanoparticles in the heated soils, a process long known from wildfires and laboratory heating experiments. The pyromagnetically-enhanced kaolinite-rich soils would have been swept from the denuded landscape and deposited across the adjoining shelf, perhaps as mudwaves, to become the Marlboro Clay. The Millville site at double the paleowater depth and distance to the paleoshore compared to Wilson Lake (Makarova+2017 Paleoceanography) shows a similar enhancement in magnetization of the Marlboro Clay. However, the increase in magnetization in Millville starts well above ( 50 cm) the spherule peak and the onset of the CIE, which coincide with a sharp drop in what little carbonate content there is in the Marlboro Clay, resulting in a zone barren of foraminifers (Makarova+2017 op. cit.). The offset in deposition might be due to added barren zone or a longer transit of the soil muds to the more distant Millville site but would not be expected if the magnetic nanoparticles were produced in more direct response to the onset of the CIE, as from proliferation of magnetotactic bacteria. The pyromagnetic enhancement of soils and their (re)deposition can be viewed as local manifestations of a major event that triggered various global reverberations. For example, there is no counterpart of the Marlboro Clay in ODP Site 1051 on Blake Nose where a spherule layer was also found at the onset of the CIE (Schaller+2016 op. cit.).

[New methodological approaches to the detection and quantitative registration of Salmonella in the study of water objects].

PubMed

Aleshnia, V V; Panasovets, O P; Zhuravlev, P V; Sukhanova, S M; Golubenko, I A; Nedachin, A E; Talaeva, Iu G; Artemova, T Z; Gipp, E K; Butorina, N N; Zagaĭnova, A V; Shvager, M M; Mitrofanova, T V

2011-01-01

The paper gives data on the use of techniques to detect and register Salmonella in the water objects, by applying a new liquid nutrient medium. Experimental and field studies have shown its advantage over the accumulation media widely used in practical healthcare. It has been ascertained that the nutrient medium not only accumulates biomass, but also provides the restoration of the biological properties of uncultivated Salmonella species. The use of the nutrient medium at practical laboratories makes it possible to unify guidelines for the examination of water objects with varying degrees of biological pollution and to obtain the comparable results of analyses.

The role of ecological theory in microbial ecology.

PubMed

Prosser, James I; Bohannan, Brendan J M; Curtis, Tom P; Ellis, Richard J; Firestone, Mary K; Freckleton, Rob P; Green, Jessica L; Green, Laura E; Killham, Ken; Lennon, Jack J; Osborn, A Mark; Solan, Martin; van der Gast, Christopher J; Young, J Peter W

2007-05-01

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Postantibiotic effect of ceftaroline against gram-positive organisms.

PubMed

Pankuch, G A; Appelbaum, P C

2009-10-01

The postantibiotic effects (PAEs), postantibiotic sub-MIC effects (PA-SMEs), and sub-MIC effects (SMEs) of ceftaroline, a novel injectable cephalosporin, were determined for 15 gram-positive organisms. The pneumococcal, staphylococcal, and enterococcal PAEs were 0.8 to 1.8 h, 0.7 to 2.2 h, and 0.2 to 1.1 h, respectively. The corresponding PA-SMEs (0.4 times the MIC) were 2.5 to 6.7 h, 2.9 to >0.0 h, and 7.9 to >10.3 h, respectively. The PA-SMEs were longer than the PAEs, suggesting that sub-MIC levels extend the PAE of ceftaroline against gram-positive cocci.

Studies on the antibacterial activity of two new acylureidopenicillins, mezlocillin and azlocillin.

PubMed

Soares, L A; Trabulsi, L R

1979-01-01

The antimicrobial activity of 6-[(R)-2[3-methylsulfonyl-2-oxo-imidazolidine-1-carboxamido]-2-phenylacetamido]-penicillanic acid sodium salt (mezlocillin, Baypen) and 6-[(R)-2-(2-oxo-imidazolidine-1-carboxamido)-2-phenylacetamido-a1-penicillanic acid sodium salt (azlocillin, Securopen) was measured against 545 clinical isolates, including gram-negative rods, gram-positive cocci and Bacteroides. Mezlocillin was more effective than azlocillin against the majority of the strains studied, but azlocillin was more effective against Pseudomonas strains. The minimal bactericidal concentration was equal to the minimal inhibitory concentration for the strains tested, but it was twice or four-fold as high for Staphylococcus.

[Group A streptococcal meningitis: Streptococcus pneumoniae is not the only one to seep into the CSF fluid leak!].

PubMed

Zappella, N; Barrelet, A; Pangon, B; Laurent, V; Bruneel, F

2013-11-01

We reported a case of group A streptococcal meningitis in a patient with a CSF fluid leak. This case underlined several relevant points: (i) an unfrequent cause of bacterial meningitis; (ii) the main diagnosis to evoke when the direct examination of CSF shows Gram+ cocci with a negative pneumococcal antigen; (iii) that bacteria other than Streptococcus pneumoniae are possible in front of a meningitis associated with a CSF fluif leak. Copyright © 2013 Société française d’anesthésie et de réanimation (Sfar). Published by Elsevier SAS. All rights reserved.

[Osteomyelitis in tropical countries].

PubMed

Estel, S; Schönfelder, M

1991-01-01

A retrospective study was made of 13 patients admitted to the pediatric ward of Gondar College of Medical Sciences from October 1987 to May 1988. It was found that the disease occurs mainly in males. In the most cases there are clear clinical and radiological findings. The main reasons turned to be traumatic and spontaneous with unknown causes. Gram cocci takes the leading bacteries found on cultures taken from the discharging sinuses. Treatment was performed with appropriate antibiotics and surgical intervention when indicated. In regard to response to our treatment most of the patients showed good clinical improvement. With early treatment the course is found to be much more benign.

Postoperative infection in spine surgery: does the month matter?

PubMed

Durkin, Michael J; Dicks, Kristen V; Baker, Arthur W; Moehring, Rebekah W; Chen, Luke F; Sexton, Daniel J; Lewis, Sarah S; Anderson, Deverick J

2015-07-01

The relationship between time of year and surgical site infection (SSI) following neurosurgical procedures is poorly understood. Authors of previous reports have demonstrated that rates of SSI following neurosurgical procedures performed during the summer months were higher compared with rates during other seasons. It is unclear, however, if this difference was related to climatological changes or inexperienced medical trainees (the July effect). The aim of this study was to evaluate for seasonal variation of SSI following spine surgery in a network of nonteaching community hospitals. The authors analyzed 6 years of prospectively collected surveillance data (January 1, 2007, to December 31, 2012) from all laminectomies and spinal fusions from 20 hospitals in the Duke Infection Control Outreach Network of community hospitals. Surgical site infections were defined using National Healthcare Safety Network criteria and identified using standardized methods across study hospitals. Regression models were then constructed using Poisson distribution to evaluate for seasonal trends by month. Each analysis was first performed for all SSIs and then for SSIs caused by specific organisms or classes of organisms. Categorical analysis was performed using two separate definitions of summer: June through September (definition 1), and July through September (definition 2). The prevalence rate of SSIs during the summer was compared with the prevalence rate during the remainder of the year by calculating prevalence rate ratios and 95% confidence intervals. The authors identified 642 SSIs following 57,559 neurosurgical procedures (overall prevalence rate = 1.11/100 procedures); 215 occurred following 24,466 laminectomies (prevalence rate = 0.88/100 procedures), and 427 following 33,093 spinal fusions (prevalence rate = 1.29/100 procedures). Common causes of SSI were Staphylococcus aureus (n = 380; 59%), coagulase-negative staphylococci (n = 90; 14%), and Escherichia coli (n = 41; 6.4%). Poisson regression models demonstrated increases in the rates of SSI during each of the summer months for all SSIs and SSIs due to gram-positive cocci, S. aureus, and methicillin-sensitive S. aureus. Categorical analysis confirmed that the rate of SSI during the 4-month summer period was higher than the rate during the remainder of the year, regardless of which definition for summer was used (definition 1, p = 0.008; definition 2, p = 0.003). Similarly, the rates of SSI due to grampositive cocci and S. aureus were higher during the summer months than the remainder of the year regardless of which definition of summer was used. However, the rate of SSI due to gram-negative bacilli was not. The rate of SSI following fusion or spinal laminectomy/laminoplasty was higher during the summer in this network of community hospitals. The increase appears to be related to increases in SSIs caused by gram-positive cocci and, more specifically, S. aureus. Given the nonteaching nature of these hospitals, the findings demonstrate that increases in the rate of SSI during the summer are more likely related to ecological and/or environmental factors than the July effect.

Decree No. 2001, 28 September 1988.

PubMed

1988-01-01

This Decree regulates the establishment of indigenous reservations in Colombia. Under the Decree, an indigenous reservation is a legal institution constituted by the transfer to an indigenous community of title to the property where the community is situated or where it will be located. The property may be cultivated or uncultivated. The Decree sets forth the requirements for qualifying for the transfer of such land. Before the land is transferred, the Colombian Institute for Agricultural Reform is to monitor and review the proposed reservation. It is to undertake a socioeconomic and legal study of the indigenous community and to ascertain the community's origins, institutions, customs, and property claims. It is also to address the property claims of third parties. full text

Biosynthesis of Thermoresponsive Magnetic Nanoparticles by Magnetosome Display System.

PubMed

Yoshino, Tomoko; Shimada, Takumi; Ito, Yasuhito; Honda, Toru; Maeda, Yoshiaki; Matsunaga, Tadashi; Tanaka, Tsuyoshi

2018-05-16

Thermoresponsive magnetic nanoparticles (MNPs) were synthesized using a magnetosome display system. An elastin-like polypeptide decamer of VPGVG (ELP 10 ), which is hydrophobic above the transition temperature ( T t ) and can form an insoluble aggregation, was immobilized on biogenic MNPs in the magnetotactic bacterium, Magnetospirillum magneticum AMB-1. It was suggested that hydrophobicity of the MNP surface increased at 60 °C compared with 20 °C by the immobilization of ELP 10 . Size distribution analysis indicated that the immobilization of ELP 10 onto MNPs induced the increased hydrophobicity with increasing temperatures up to 60 °C, promoting aggregation of the particles by hydrophobic and magnetic interactions. These results suggest that the acceleration of magnetic collection at 60 °C was caused by particle aggregation promoted by hydrophobic interaction between ELP-MNPs. Furthermore, the immobilization of ELP on MNPs gave a quick magnetic collection at 60 °C by external magnetic field. The thermoresponsive properties will further expand the utility of biotechnological applications of biogenic MNPs.

Time-resolved 2-million-year-old supernova activity discovered in Earth’s microfossil record

PubMed Central

Ludwig, Peter; Bishop, Shawn; Egli, Ramon; Chernenko, Valentyna; Deneva, Boyana; Faestermann, Thomas; Famulok, Nicolai; Fimiani, Leticia; Gómez-Guzmán, José Manuel; Hain, Karin; Korschinek, Gunther; Hanzlik, Marianne; Merchel, Silke; Rugel, Georg

2016-01-01

Massive stars (M≳10 M⊙), which terminate their evolution as core-collapse supernovae, are theoretically predicted to eject >10−5M⊙ of the radioisotope 60Fe (half-life 2.61 Ma). If such an event occurs sufficiently close to our solar system, traces of the supernova debris could be deposited on Earth. Herein, we report a time-resolved 60Fe signal residing, at least partially, in a biogenic reservoir. Using accelerator mass spectrometry, this signal was found through the direct detection of live 60Fe atoms contained within secondary iron oxides, among which are magnetofossils, the fossilized chains of magnetite crystals produced by magnetotactic bacteria. The magnetofossils were chemically extracted from two Pacific Ocean sediment drill cores. Our results show that the 60Fe signal onset occurs around 2.6 Ma to 2.8 Ma, near the lower Pleistocene boundary, terminates around 1.7 Ma, and peaks at about 2.2 Ma. PMID:27503888

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

NASA Astrophysics Data System (ADS)

Deng, Zengqin; Wang, Qing; Liu, Zhao; Zhang, Manfeng; Machado, Ana Carolina Dantas; Chiu, Tsu-Pei; Feng, Chong; Zhang, Qi; Yu, Lin; Qi, Lei; Zheng, Jiangge; Wang, Xu; Huo, Xinmei; Qi, Xiaoxuan; Li, Xiaorong; Wu, Wei; Rohs, Remo; Li, Ying; Chen, Zhongzhou

2015-07-01

Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.

[Epidemiology of nosocomial infections in neonates].

PubMed

Lachassinne, E; Letamendia-Richard, E; Gaudelus, J

2004-03-01

Epidemiology of nosocomial infections in neonates has to be described according to our definitions (early onset GBS diseases excluded) and according to levels of care. Nosocomial risk exists in maternity departments (3% in postnatal beds), incidence rates are 7.5-12.7% or 1.3-8.5 per 1000 days in neonatal care units and 14.2% or 11.7 per 1000 days in neonatal intensive care units (NICU). Gram-positive cocci bloodstream infections are the most common nosocomial infections in NICU but viral gastroenteritis are more frequent in neonatal care units. Risk factors are low birthweight, small gestational age and intravascular catheter in NICU, and for viral nosocomial infections, visits and winter outbreaks.

Growth mechanics of bacterial cell wall and morphology of bacteria

NASA Astrophysics Data System (ADS)

Jiang, Hongyuan; Sun, Sean

2010-03-01

The peptidoglycan cell wall of bacteria is responsible for maintaining the cell shape and integrity. During the bacterial life cycle, the growth of the cell wall is affected by mechanical stress and osmotic pressure internal to the cell. We develop a theory to describe cell shape changes under the influence of mechanical forces. We find that the theory predicts a steady state size and shape for bacterial cells ranging from cocci to spirillum. Moreover, the theory suggest a mechanism by which bacterial cytoskeletal proteins such as MreB and crescentin can maintain the shape of the cell. The theory can also explain the several recent experiments on growing bacteria in micro-environments.

Systemic Staphylococcus pseudintermedius infection in an arctic fox (Vulpes lagopus) with severe multifocal suppurative meningoencephalitis and nephritis.

PubMed

Iwata, Kei; Kasuya, Kazufumi; Takayama, Kou; Nakahara, Yusuke; Kobayashi, Yoshifumi; Kato, Asako; Senba, Hironobu; Yanagisawa, Masae; Shibahara, Tomoyuki

2018-06-11

A 2-year-female arctic fox (Vulpes lagopus) developed anorexia, dehydration, and emaciation during the quarantine period for importation from Norway, and died 17 days later. At necropsy, a fistula was observed on the left gluteal region, and the left eye, left brain, and kidneys were discolored. Histologically, severe diffuse suppurative meningoencephalitis and renal abscesses were detected. Numerous Gram-positive cocci were detected in these lesions. Multidrug-susceptible Staphylococcus pseudintermedius were isolated from the lesions. These results suggest that S. pseudintermedius can cause severe multifocal suppurative meningoencephalitis and nephritis in foxes. This is the first report of multidrug-susceptible S. pseudintermedius meningoencephalitis and nephritis in a fox.

Microbiology of liver abscesses and the predictive value of abscess gram stain and associated blood cultures.

PubMed

Chemaly, Roy F; Hall, Gerri S; Keys, Thomas F; Procop, Gary W

2003-08-01

Although rare, pyogenic liver abscesses are potentially fatal. We evaluated the predictive value of Gram stain of liver abscess aspirates and temporally associated blood cultures. Gram stains detected bacteria in 79% of the liver abscesses tested. The sensitivity and specificity of Gram stain of the liver abscesses were 90% and 100% for Gram-positive cocci (GPC) and 52% and 94% for Gram-negative bacilli (GNB). The sensitivities of the blood cultures for any GPC and GNB present in the liver abscess were 30% and 39%, respectively. Although, Gram stains and blood cultures offer incomplete detection of the microbial contents of pyogenic liver abscesses, both tests should always accompany liver abscess cultures.

Physiology and phylogeny of the candidate phylum "Atribacteria" (formerly OP9/JS1) inferred from single-cell genomics and metagenomics

NASA Astrophysics Data System (ADS)

Dodsworth, J. A.; Murugapiran, S.; Blainey, P. C.; Nobu, M.; Rinke, C.; Schwientek, P.; Gies, E.; Webster, G.; Kille, P.; Weightman, A.; Liu, W. T.; Hallam, S.; Tsiamis, G.; Swingley, W.; Ross, C.; Tringe, S. G.; Chain, P. S.; Scholz, M. B.; Lo, C. C.; Raymond, J.; Quake, S. R.; Woyke, T.; Hedlund, B. P.

2014-12-01

Single-cell sequencing and metagenomics have extended the genomics revolution to yet-uncultivated microorganisms and provided insights into the coding potential of this so-called "microbial dark matter", including microbes belonging candidate phyla with no cultivated representatives. As more datasets emerge, comparison of individual genomes from different lineages and habitats can provide insight into the phylogeny, conserved features, and potential metabolic diversity of candidate phyla. The candidate bacterial phylum OP9 was originally found in Obsidian Pool, Yellowstone National Park, and it has since been detected in geothermal springs, petroleum reservoirs, and engineered thermal environments worldwide. JS1, another uncultivated bacterial lineage affiliated with OP9, is often abundant in marine sediments associated with methane hydrates, hydrocarbon seeps, and on continental margins and shelves, and is found in other non-thermal marine and subsurface environments. The phylogenetic relationship between OP9, JS1, and other Bacteria has not been fully resolved, and to date no axenic cultures from these lineages have been reported. Recently, 31 single amplified genomes (SAGs) from six distinct OP9 and JS1 lineages have been obtained using flow cytometric and microfluidic techniques. These SAGs were used to inform metagenome binning techniques that identified OP9/JS1 sequences in several metagenomes, extending genomic coverage in three of the OP9 and JS1 lineages. Phylogenomic analyses of these SAG and metagenome bin datasets suggest that OP9 and JS1 constitute a single, deeply branching phylum, for which the name "Atribacteria" has recently been proposed. Overall, members of the "Atribacteria" are predicted to be heterotrophic anaerobes without the capacity for respiration, with some lineages potentially specializing in secondary fermentation of organic acids. A set of signature "Atribacteria" genes was tentatively identified, including components of a bacterial microcompartments gene cluster that may be involved in carbohydrate catabolism. The "Atribacteria" may play important roles in biomass processing in anaerobic geothermal and subsurface environments.

Vertical and lateral distribution of fallout 137Cs and soil properties along representative toposequences of central Rif, Morocco.

PubMed

Mesrar, Haytam; Sadiki, Abdelhamid; Faleh, Ali; Quijano, Laura; Gaspar, Leticia; Navas, Ana

2017-04-01

The purpose of this study is to understand and quantify the relationships between current 137 Cs inventories and the soil properties and the physiographic characteristics. A total of 36 cores were taken in seven transects with different slopes, lithology and land use. The analysis focused on the 137 Cs mass activity as well as inventories and its relationship with soil properties as grain size and organic matter. The mass activity of 137 Cs and the inventories varied between 3.6 and 63.7 Bq kg -1 and between 521.7 and 3304.4 Bq m -2 , respectively. At uncultivated soils, high concentrations of 137 Cs are located in the top 10 cm and decreased exponentially in depth. Cultivated soils record disturbed and heterogeneous 137 Cs profiles with values of mass activity and inventories up to 38.7 Bq kg -1 and 2510.8 Bq m -2 , respectively. The 137 Cs inventories were significantly higher in uncultivated soils (mean: 2086.9 Bq m -2 ) compared to cultivated soils (mean: 1397.1 Bq m -2 ). The 137 Cs mass activity showed a significant positive correlation with organic matter, silt and clay, but it was negatively correlated with sand and pH respectively. High levels of 137 Cs were found at altitudes between 500 m and 640 m a.s.l, and at slopes from 8° to 11°, as well as in dense scrub land and Fersialitic soils. A principal component analysis showed that more than 86.7% of the variance in 137 Cs mass activity was explained by the organic matter content and the land use. The results of this study provide insights into the effects of soil properties and physiographic factors on the behaviour of 137 Cs in soils of Mediterranean environments of North Africa and strengthen the reliability of this radioisotope as an erosion tracer. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.

Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within themore » DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an archaeon from this phylum that is only 0.8 Mb in length and lacks almost all core biosynthetic pathways, but has genes encoding enzymes predicted to interact with bacterial cell walls, consistent with a symbiotic lifestyle. The second new phylum, for which we propose the name Pacearchaeota, was defined based on 46 newly sampled archaeal genomes. This phylum includes the first non-methanogen with an intermediate Type II/III RuBisCO. We also reconstructed a complete (1.24 Mb) genome for another DPANN archaeon, a member of the Diapherotrites phylum. Metabolic prediction and transcriptomic data indicate that this organism has a fermentation-based lifestyle. In fact, genomic analyses consistently indicate lack of recognizable pathways for sulfur, nitrogen, methane, oxygen, and metal cycling, and suggest that symbiotic and fermentation-based lifestyles are widespread across the DPANN superphylum. Thus, as for a recently identified superphylum of bacteria with small genomes and no cultivated representatives, the biogeochemical impacts of this major radiation of archaea are primarily through anaerobic carbon and hydrogen cycling.« less

The Domestication Syndrome in Phoenix dactylifera Seeds: Toward the Identification of Wild Date Palm Populations

PubMed Central

Gros-Balthazard, Muriel; Newton, Claire; Ivorra, Sarah; Pierre, Marie-Hélène; Terral, Jean-Frédéric

2016-01-01

Investigating crop origins is a priority to understand the evolution of plants under domestication, develop strategies for conservation and valorization of agrobiodiversity and acquire fundamental knowledge for cultivar improvement. The date palm (Phoenix dactylifera L.) belongs to the genus Phoenix, which comprises 14 species morphologically very close, sometimes hardly distinguishable. It has been cultivated for millennia in the Middle East and in North Africa and constitutes the keystone of oasis agriculture. Yet, its origins remain poorly understood as no wild populations are identified. Uncultivated populations have been described but they might represent feral, i.e. formerly cultivated, abandoned forms rather than truly wild populations. In this context, this study based on morphometrics applied to 1625 Phoenix seeds aims to (1) differentiate Phoenix species and (2) depict the domestication syndrome observed in cultivated date palm seeds using other Phoenix species as a “wild” reference. This will help discriminate truly wild from feral forms, thus providing new insights into the evolutionary history of this species. Seed size was evaluated using four parameters: length, width, thickness and dorsal view surface. Seed shape was quantified using outline analyses based on the Elliptic Fourier Transform method. The size and shape of seeds allowed an accurate differentiation of Phoenix species. The cultivated date palm shows distinctive size and shape features, compared to other Phoenix species: seeds are longer and elongated. This morphological shift may be interpreted as a domestication syndrome, resulting from the long-term history of cultivation, selection and human-mediated dispersion. Based on seed attributes, some uncultivated date palms from Oman may be identified as wild. This opens new prospects regarding the possible existence and characterization of relict wild populations and consequently for the understanding of the date palm origins. Finally, we here describe a pipeline for the identification of the domestication syndrome in seeds that could be used in other crops. PMID:27010707

Human exposure to lead and other potentially harmful elements associated with galena mining at New Zurak, central Nigeria

NASA Astrophysics Data System (ADS)

Lar, U. A.; Ngozi-Chika, C. S.; Ashano, E. C.

2013-08-01

Galena mining in New Zurak, central Nigeria is currently increasing in intensity, with widespread artisanal mining taking place alongside mechanised mining. These activities are causing immeasurable damage to the environment. The prolonged human exposure and ingestion of Pb and other potentially harmful elements (PHEs) such as U, Cd, Se, Zn and As that are released from ores during these (mining) activities is a cause of great concern to populations that live in the vicinity of these mine fields. Many of the communities make their living from subsistence farming, growing food from the surroundings, and obtaining drinking water from nearby surface and sub-surface water resources. An overall assessment of the degree of contamination or toxicity of Pb and other PHEs was carried out using the indices of geoaccumulation (Igeo) and contamination factors (CFs), in the different media sampled - farmland soils, uncultivated lands, mine tailings/dumps, natural waters and vegetables. Results reveal that the mine tailings and dumps are highly contaminated with Pb and other PHEs followed in decreasing degree of contamination by the uncultivated lands, farmlands and natural waters. These findings suggest that release of Pb and other PHEs from the galena mining activity has contributed significantly to the enrichment of these elements in the surrounding environment, including the natural water bodies, and are disposed to subsequent entry into the human body through the food chain. As such these PHE accumulations pose significant risks to the environment and human health, especially of children and pregnant women who are the most vulnerable groups in the area. In order to forestall a reoccurrence of the Zamfara Pb poisoning episode in northwestern Nigeria in 2010, where more than 400 children died, the authorities concerned should ensure that mining in New Zurak is done in a more environmentally friendly manner, ensuring the maintenance of an environmental quality adequate for good health and well-being of the surrounding mining communities.

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

DOE PAGES

Hiras, Jennifer; Wu, Yu-Wei; Eichorst, Stephanie A.; ...

2015-09-01

Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a larger lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided amore » consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome ( > 95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.« less

The distribution and dynamics of chromium and nickel in cultivated and uncultivated semi-arid soils from Nigeria.

PubMed

Agbenin, John O

2002-12-02

Growing concern about heavy metal contamination of agricultural lands under long-term application of inorganic fertilizers and organic wastes makes periodic risk assessment of heavy metal accumulation in arable lands imperative. As a part of a much larger study to systematically document the status of heavy metals in savanna soils this study investigated the distribution and dynamics of Cr and Ni in a savanna soil after 50 years of continuous cultivation and application of inorganic fertilizers and organic manures. The cultivated fields were fertilized with inorganic fertilizers (NPK), farmyard manure (FYM), FYM+NPK for 50 years and a control plot under continuous cultivation for 50 years but did not receive either FYM or NPK. Two uncultivated or natural sites were sampled as reference conditions for assessing the dynamics of Cr and Ni induced by cultivation and management practices. The distribution of Cr and Ni in the soil profiles exhibited eluvial-illuvial patterns. Sand and clay fractions explained between 62 and 90% of the variance in Cr and Ni concentration and distribution in the soil profiles. Mean Cr concentrations ranged from 17 to 59 mg kg(-1), while Ni varied from <1 mg kg(-1) in the topsoil to 16 mg kg(-1) in the subsoil. Mass balance calculations showed a loss of 10% Cr and 17% Ni in the FYM field, and approximately 4% Cr and 11% Ni in the NPK field compared to the natural site after 50 years of cultivation. The control and FYM + NPK field had, however, a positive balance of Cr and Ni. In general, it was concluded that existing soil management practices in this region are unlikely to lead to Cr and Ni build-up probably because of low rates of application of inorganic fertilizers, farmyard manure and other organic wastes to the soils.

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.

PubMed

Hiras, Jennifer; Wu, Yu-Wei; Eichorst, Stephanie A; Simmons, Blake A; Singer, Steven W

2016-04-01

Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.

The Domestication Syndrome in Phoenix dactylifera Seeds: Toward the Identification of Wild Date Palm Populations.

PubMed

Gros-Balthazard, Muriel; Newton, Claire; Ivorra, Sarah; Pierre, Marie-Hélène; Pintaud, Jean-Christophe; Terral, Jean-Frédéric

2016-01-01

Investigating crop origins is a priority to understand the evolution of plants under domestication, develop strategies for conservation and valorization of agrobiodiversity and acquire fundamental knowledge for cultivar improvement. The date palm (Phoenix dactylifera L.) belongs to the genus Phoenix, which comprises 14 species morphologically very close, sometimes hardly distinguishable. It has been cultivated for millennia in the Middle East and in North Africa and constitutes the keystone of oasis agriculture. Yet, its origins remain poorly understood as no wild populations are identified. Uncultivated populations have been described but they might represent feral, i.e. formerly cultivated, abandoned forms rather than truly wild populations. In this context, this study based on morphometrics applied to 1625 Phoenix seeds aims to (1) differentiate Phoenix species and (2) depict the domestication syndrome observed in cultivated date palm seeds using other Phoenix species as a "wild" reference. This will help discriminate truly wild from feral forms, thus providing new insights into the evolutionary history of this species. Seed size was evaluated using four parameters: length, width, thickness and dorsal view surface. Seed shape was quantified using outline analyses based on the Elliptic Fourier Transform method. The size and shape of seeds allowed an accurate differentiation of Phoenix species. The cultivated date palm shows distinctive size and shape features, compared to other Phoenix species: seeds are longer and elongated. This morphological shift may be interpreted as a domestication syndrome, resulting from the long-term history of cultivation, selection and human-mediated dispersion. Based on seed attributes, some uncultivated date palms from Oman may be identified as wild. This opens new prospects regarding the possible existence and characterization of relict wild populations and consequently for the understanding of the date palm origins. Finally, we here describe a pipeline for the identification of the domestication syndrome in seeds that could be used in other crops.

Occurrence, characteristics and sources of polycyclic aromatic hydrocarbons in arable soils of Beijing, China.

PubMed

Liu, Hang; Yu, Xiaolu; Liu, Zirui; Sun, Ying

2018-05-04

This study investigated the occurrence and sources of polycyclic aromatic hydrocarbons (PAHs) from arable soils in Beijing and compared them with 4 other types of soils: soil from uncultivated land, an incineration plant, a suburb and a woodland. The total concentrations of PAHs ranged from 189.3 to 888.7 μg/kg (mean: 518.2 μg/kg for greenhouses and 455.2 μg/kg for fields). The seven carcinogenic PAHs accounted for 11.2-81.3% of Σ15PAHs in arable soils. Benzo[a]pyrene toxic equivalent (BaP eq ) concentrations were 82.8 μg/kg and 85.4 μg/kg in greenhouses and fields, respectively. Greenhouses and fields were both dominated by PAHs with 3 and 4 rings. Acenaphthene (ACE), indeno[1,2,3-cd] pyrene (IcdP) and benzo[ghi]perylene (BghiP) were the major compounds. These results showed that there was insignificant difference between the soil from greenhouses and fields and both had low carcinogenic potential risk. The diagnostic ratios suggested that the arable soils were mainly contaminated by coal/biomass combustion. Based on a positive matrix factorization (PMF) model, six sources were identified including coal combustion, waste incineration, tar, diesel combustion, biomass burning and gasoline combustion. Coal and gasoline combustion contributed over 40% of the measured PAHs in arable soils. Diesel combustion, tar and waste incineration were the main sources of pollution for soil from the uncultivated land, woodland and incineration plant/suburban. It was concluded that PMF was effective in determining the source apportionment. Urbanization and the evolution of human activities have caused PAH sources to become more complicated in industrial areas compared to regions with little human disturbance. Because of this, various factors need to be considered to control the PAH contamination in arable soils. Copyright © 2018 Elsevier Inc. All rights reserved.

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.

PubMed

Thomas, Pious; Sekhar, Aparna Chandra

2017-05-01

The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.

Amplification and sequence analysis of partial bacterial 16S ribosomal RNA gene in gallbladder bile from patients with primary biliary cirrhosis.

PubMed

Hiramatsu, K; Harada, K; Tsuneyama, K; Sasaki, M; Fujita, S; Hashimoto, T; Kaneko, S; Kobayashi, K; Nakanuma, Y

2000-07-01

The etiopathogenesis of bile duct lesion in primary biliary cirrhosis is unknown, though the participation of bacteria and/or their components and products is suspected. In this study, we tried to detect and identify bacteria in the bile of patients with primary biliary cirrhosis by polymerase chain reaction using universal bacterial primers of the 16S ribosomal RNA gene. Gallbladder bile samples from 15 patients with primary biliary cirrhosis, 5 with primary sclerosing cholangitis, 5 with hepatitis C virus-related liver cirrhosis, 11 with cholecystolithiasis, and from 12 normal adult gallbladders were used. In addition to the culture study, partial bacterial 16S ribosomal RNA gene was amplified by polymerase chain reaction (PCR) taking advantage of universal primers that can amplify the gene of almost all bacterial species, and the amplicons were cloned and sequenced. Sequence homology with specific bacterial species was analyzed by database research. Bacterial contamination at every step of the bile sampling, DNA extraction and PCR study was avoided. Furthermore, to confirm whether bacterial DNA is detectable in liver explants, the same analysis was performed using 10 liver explants of patients with primary biliary cirrhosis. In primary biliary cirrhosis, 75% (p<0.0001) of 100 clones were identified as so-called gram-positive cocci while these cocci were positive in only 5% in cholecystolithiasis (p<0.0001). In cholecystolithiasis gram-negative rods were predominant instead. One bacterial species detected in a normal adult was not related to those detected in primary biliary cirrhosis and cholecystolithiasis patients. No bacterial DNA was detected by PCR amplification in 10 liver explants of patients with primary biliary cirrhosis. The present results raise several possible roles of gram-positive bacteria in bile in the etiopathogenesis of primary biliary cirrhosis. However, these results could also reflect an epiphenomenon due to decreased bile flow in the patients with primary biliary cirrhosis at an advanced stage.

In vitro activity of RP 59500, a semisynthetic injectable pristinamycin, against staphylococci, streptococci, and enterococci.

PubMed Central

Fass, R J

1991-01-01

The in vitro activity of RP 59500, a semisynthetic pristinamycin, was compared with the activities of vancomycin, oxacillin, ampicillin, gentamicin, ciprofloxacin, and rifampin against five Staphylococcus species, five Streptococcus species, and four Enterococcus species. For staphylococci, MICs were 0.13 to 1 microgram/ml and the MICs for 90% of the strains tested (MIC90s) were 0.13 to 0.5 microgram/ml; there were no differences between oxacillin-susceptible and -resistant strains. For streptococci, MICs were 0.03 to 4 micrograms/ml and MIC90s were 0.25 to 2 micrograms/ml; viridans group streptococci were the least susceptible streptococci. For enterococci, MICs were 0.25 to 32 micrograms/ml and MIC90s were 2 to 4 micrograms/ml; Enterococcus faecalis was the least susceptible. Vancomycin was the only comparative drug with consistent activity against all species of gram-positive cocci. With RP 59500, raising the inoculum 100-fold, lowering the pH of cation-adjusted Mueller-Hinton broth to 5.5, or omitting cation supplementation had little effect on MICs, but 50% serum increased MICs 2 to 4 dilution steps. The differences between MBCs and MICs were greater for staphylococci and enterococci than for streptococci. Time-kill studies with 24 strains indicated that RP 59500 concentrations 2-, 4-, and 16-fold greater than the MICs usually killed bacteria of each species at similar rates; reductions in CFU per milliliter were less than those observed with oxacillin or vancomycin against staphylococci and less than those observed with ampicillin against enterococci. RP 59500 antagonized the bactericidal activities of oxacillin and gentamicin against Staphylococcus aureus ATCC 29213 and that of ampicillin against E. faecalis ATCC 29212. Against the latter, combination with gentamicin was indifferent. RP 59500 has a broad spectrum of in vitro activity against gram-positive cocci; combining it with other drugs is not advantageous. PMID:1903912

Identity and ecophysiology of uncultured actinobacterial polyphosphate-accumulating organisms in full-scale enhanced biological phosphorus removal plants.

PubMed

Kong, Yunhong; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

2005-07-01

Microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) was used to screen for potential polyphosphate-accumulating organisms (PAO) in a full-scale enhanced biological phosphorus removal (EBPR) plant. The results showed that, in addition to uncultured Rhodocyclus-related PAO, two morphotypes hybridizing with gene probes for the gram-positive Actinobacteria were also actively involved in uptake of orthophosphate (Pi). Clone library analysis and further investigations by MAR-FISH using two new oligonucleotide probes revealed that both morphotypes, cocci in clusters of tetrads and short rods in clumps, were relatively closely related to the genus Tetrasphaera within the family Intrasporangiaceae of the Actinobacteria (93 to 98% similarity in their 16S rRNA genes). FISH analysis of the community biomass in the treatment plant investigated showed that the short rods (targeted by probe Actino-658) were the most abundant (12% of all Bacteria hybridizing with general bacterial probes), while the cocci in tetrads (targeted by probe Actino-221) made up 7%. Both morphotypes took up P(i) aerobically only if, in a previous anaerobic phase, they had taken up organic matter from wastewater or a mixture of amino acids. They could not take up short-chain fatty acids (e.g., acetate), glucose, or ethanol under anaerobic or aerobic conditions. The storage compound produced during the anaerobic period was not polyhydroxyalkanoates, as for Rhodocyclus-related PAO, and its identity is still unknown. Growth and uptake of Pi took place in the presence of oxygen and nitrate but not nitrite, indicating a lack of denitrifying ability. A survey of the occurrence of these actinobacterial PAO in 10 full-scale EBPR plants revealed that both morphotypes were widely present, and in several plants more abundant than the Rhodocyclus-related PAO, thus playing a very important role in the EBPR process.

In Vitro Evaluation of CBR-2092, a Novel Rifamycin-Quinolone Hybrid Antibiotic: Microbiology Profiling Studies with Staphylococci and Streptococci ▿

PubMed Central

Robertson, Gregory T.; Bonventre, Eric J.; Doyle, Timothy B.; Du, Qun; Duncan, Leonard; Morris, Timothy W.; Roche, Eric D.; Yan, Dalai; Lynch, A. Simon

2008-01-01

We present data from antimicrobial assays performed in vitro that pertain to the potential clinical utility of a novel rifamycin-quinolone hybrid antibiotic, CBR-2092, for the treatment of infections mediated by gram-positive cocci. The MIC90s for CBR-2092 against 300 clinical isolates of staphylococci and streptococci ranged from 0.008 to 0.5 μg/ml. Against Staphylococcus aureus, CBR-2092 exhibited prolonged postantibiotic effects (PAEs) and sub-MIC effects (SMEs), with values of 3.2, 6.5, and >8.5 h determined for the PAE (3× MIC), SME (0.12× MIC), and PAE-SME (3× MIC/0.12× MIC) periods, respectively. Studies of genetically defined mutants of S. aureus indicate that CBR-2092 is not a substrate for the NorA or MepA efflux pumps. In minimal bactericidal concentration and time-kill studies, CBR-2092 exhibited bactericidal activity against staphylococci that was retained against rifampin- or intermediate quinolone-resistant strains, with apparent paradoxical cidal characteristics against rifampin-resistant strains. In spontaneous resistance studies, CBR-2092 exhibited activity consistent with balanced contributions from its composite pharmacophores, with a mutant prevention concentration of 0.12 μg/ml and a resistance frequency of <10−12 determined at 1 μg/ml in agar for S. aureus. Similarly, CBR-2092 suppressed the emergence of preexisting rifamycin resistance in time-kill studies undertaken at a high cell density. In studies of the intracellular killing of S. aureus, CBR-2092 exhibited prolonged bactericidal activity that was superior to the activities of moxifloxacin, rifampin, and a cocktail of moxifloxacin and rifampin. Overall, CBR-2092 exhibited promising activity in a range of antimicrobial assays performed in vitro that pertain to properties relevant to the effective treatment of serious infections mediated by gram-positive cocci. PMID:18443106

Microbiological Etiologies of Pneumonia Complicating Stroke: A Systematic Review.

PubMed

Kishore, Amit K; Vail, Andy; Jeans, Adam R; Chamorro, Angel; Di Napoli, Mario; Kalra, Lalit; Langhorne, Peter; Roffe, Christine; Westendorp, Willeke; Nederkoorn, Paul J; Garau, Javier; van de Beek, Diederik; Montaner, Joan; Woodhead, Mark; Meisel, Andreas; Smith, Craig J

2018-06-18

Identifying the causal pathogens of pneumonia complicating stroke is challenging, and antibiotics used are often broad spectrum, without recourse to the microbiological cause. We aimed to review existing literature to identify organisms responsible for pneumonia complicating stroke, before developing a consensus-based approach to antibiotic treatment. A systematic literature review of multiple electronic databases using predefined search criteria was undertaken, in accordance with Cochrane and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidance. Published studies of hospitalized adults with ischemic stroke, intracerebral hemorrhage, or both, which identified microbiological etiologies for pneumonia complicating stroke up to January 1, 2017, were considered. Analysis included summary statistics and random-effects meta-analysis where appropriate. Fifteen studies (40% ischemic stroke, 60% ischemic stroke and intracerebral hemorrhage) involving 7968 patients were included. Reported occurrence of pneumonia varied considerably between studies (2%-63%) with a pooled frequency of 23% (95% confidence interval, 14%-34%; I 2 =99%). Where reported (60%), the majority of pneumonia occurred within 1 week of stroke (78%). Reported frequency of positive culture data (15%-88%) varied widely. When isolated, aerobic Gram-negative bacilli (38%) and Gram-positive cocci (16%) were most frequently cultured; commonly isolated organisms included Enterobacteriaceae (21.8%: Klebsiella pneumoniae , 12.8% and Escherichia coli, 9%), Staphylococcus aureus (10.1%), Pseudomonas aeruginosa (6%), Acinetobacter baumanii (4.6%), and Streptococcus pneumoniae (3.5%). Sputum was most commonly used to identify pathogens, in isolation (40%) or in conjunction with tracheal aspirate (15%) or blood culture (20%). Although the analysis was limited by small and heterogeneous study populations, limiting determination of microbiological causality, this review suggests aerobic Gram-negative bacilli and Gram-positive cocci are frequently associated with pneumonia complicating stroke. This supports the need for appropriately designed studies to determine microbial cause and a consensus-based approach in antibiotic usage and further targeted antibiotic treatment trials for enhanced antibiotic stewardship. © 2018 American Heart Association, Inc.

Bacterial infection of the lower respiratory tract in 34 horses.

PubMed

Racklyeft, D J; Love, D N

2000-08-01

To investigate associations between the bacteriology and aspects of history, clinical presentation, outcome and pathology of lower respiratory tract disease of 34 horses. Detailed aerobic and anaerobic bacteriological investigations were performed on clinical specimens from horses with pneumonia, lung abscessation and necrotic pneumonia with or without pleurisy in an attempt to identify those bacteria that might contribute to the initiation and progression of infection. Bacteria were cultured from 33 of the 34 horses. In ten cases, only aerobic/facultatively anaerobic isolates were cultured while aerobic/facultatively anaerobic bacteria and obligately anaerobic bacteria were isolated in the other 23 cases. Moderate to large numbers of anaerobic bacteria were isolated only when the estimated duration of illness was at least five days. Bacteria were not cultured from 12 of the pleural fluid samples but were always cultured from pulmonary samples (either transtracheal aspirates from live horses or pulmonary lesions at necropsy). Streptococcus equi subsp zooepidemicus was isolated in the three cases where only one bacterial species was cultured. In the other 30 cases, multiple species were isolated. These included most often and in greatest numbers, Streptococcus equi subsp zooepidemicus, Pasteurellaceae, Escherichia coli, anaerobic cocci, Eubacterium fossor, Bacteroides tectum, Prevotella heparinolytica, Fusobacterium spp, and pigmented members of the genera Prevotella and Porphyromonas. Aerobic/facultatively anaerobic organisms were isolated from 97% of horses, while obligately anaerobic organisms were cultured from 68% of horses. There was no association between the isolation of any specific bacterium and the outcome of disease. However, obligately anaerobic bacteria (such as anaerobic cocci, Bacteroides tectum, P heparinolytica and Fusobacterium spp) and the facultatively anaerobic species Escherichia coli, were recovered more commonly from horses that died or were euthanased than from those that survived. There was an association between failure of horses to recover from pleuropneumonia and delay in diagnosis and initiation of treatment.

Physical impaction injury effects on bacterial cells during spread plating influenced by cell characteristics of the organisms.

PubMed

Thomas, P; Mujawar, M M; Sekhar, A C; Upreti, R

2014-04-01

To understand the factors that contribute to the variations in colony-forming units (CFU) in different bacteria during spread plating. Employing a mix culture of vegetative cells of ten organisms varying in cell characteristics (Gram reaction, cell shape and cell size), spread plating to the extent of just drying the agar surface (50-60 s) was tested in comparison with the alternate spotting-and-tilt-spreading (SATS) approach where 100 μl inoculum was distributed by mere tilting of plate after spotting as 20-25 microdrops. The former imparted a significant reduction in CFU by 20% over the spreader-independent SATS approach. Extending the testing to single organisms, Gram-negative proteobacteria with relatively larger cells (Escherichia, Enterobacter, Agrobacterium, Ralstonia, Pantoea, Pseudomonas and Sphingomonas spp.) showed significant CFU reduction with spread plating except for slow-growing Methylobacterium sp., while those with small rods (Xenophilus sp.) and cocci (Acinetobacter sp.) were less affected. Among Gram-positive nonspore formers, Staphylococcus epidermidis showed significant CFU reduction while Staphylococcus haemolyticus and actinobacteria (Microbacterium, Cellulosimicrobium and Brachybacterium spp.) with small rods/cocci were unaffected. Vegetative cells of Bacillus pumilus and B. subtilis were generally unaffected while others with larger rods (B. thuringiensis, Brevibacillus, Lysinibacillus and Paenibacillus spp.) were significantly affected. A simulated plating study coupled with live-dead bacterial staining endorsed the chances of cell disruption with spreader impaction in afflicted organisms. Significant reduction in CFU could occur during spread plating due to physical impaction injury to bacterial cells depending on the spreader usage and the variable effects on different organisms are determined by Gram reaction, cell size and cell shape. The inoculum spreader could impart physical disruption of vegetative cells against a hard surface. Possibility of CFU reduction in sensitive organisms and the skewed selection of hardier organisms during spread plating, and the recommendation of SATS as an easier and safer alternative for CFU enumerations. © 2013 The Society for Applied Microbiology.

Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Alatoom, Adnan A; Cunningham, Scott A; Ihde, Sherry M; Mandrekar, Jayawant; Patel, Robin

2011-08-01

We evaluated Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 305 clinical isolates of staphylococci, streptococci, and related genera by comparing direct colony testing with preparatory extraction. Isolates were previously identified by use of phenotypic testing and/or 16S rRNA gene sequencing. Manufacturer-specified score cutoffs for genus- and species-level identification were used. After excluding 7 isolates not present in the Biotyper library, the Biotyper correctly identified 284 (95%) and 207 (69%) isolates to the genus and species levels, respectively, using extraction. By using direct colony testing, the Biotyper identified 168 (56%) and 60 (20%) isolates to the genus and species levels, respectively. Overall, more isolates were identified to the genus and species levels with preparatory extraction than with direct colony testing (P < 0.0001). The analysis was repeated after dividing the isolates into two subgroups, staphylococci, streptococci, and enterococci (n = 217) and "related genera" (n = 81). For the former subgroup, the extraction method resulted in the identification of 213 (98%) and 171 (79%) isolates to the genus and species levels, respectively, whereas the direct colony method identified 136 (63%) and 56 (26%) isolates to the genus and species levels, respectively. In contrast, for the subgroup of related genera, the extraction method identified 71 (88%) and 36 (44%) isolates to the genus and species levels, respectively, while the direct colony method identified 32 (40%) and 4 (5%) isolates to the genus and species levels, respectively. For both subgroups, preparatory extraction was superior to direct colony testing for the identification of isolates to the genus and species levels (P < 0.0001). Preparatory extraction is needed for the identification of a substantial proportion of Gram-positive cocci using the Biotyper method according to manufacturer-specified score cutoffs.

Pederin-type pathways of uncultivated bacterial symbionts: analysis of o-methyltransferases and generation of a biosynthetic hybrid.

PubMed

Zimmermann, Katrin; Engeser, Marianne; Blunt, John W; Munro, Murray H G; Piel, Jörn

2009-03-04

The complex polyketide pederin is a potent antitumor agent isolated from Paederus spp. rove beetles. We have previously isolated a set of genes from a bacterial endosymbiont that are good candidates for pederin biosynthesis. To biochemically study this pathway, we expressed three methyltransferases from the putative pederin pathway and used the partially unmethylated analogue mycalamide A from the marine sponge Mycale hentscheli as test substrate. Analysis by high-resolution MS/MS and NMR revealed that PedO regiospecifically methylates the marine compound to generate the nonnatural hybrid compound 18-O-methylmycalamide A with increased cytotoxicity. To our knowledge, this is the first biochemical evidence that invertebrates can obtain defensive complex polyketides from bacterial symbionts.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea

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

Tolar, Bradley B.; Herrmann, Jonathan; Bargar, John R.

In this paper, knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowlede of key N-cycling enzymes from ecologically-relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, though (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) andmore » nitrite reductase (NirK).« less

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea

DOE PAGES

Tolar, Bradley B.; Herrmann, Jonathan; Bargar, John R.; ...

2017-07-05

In this paper, knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowlede of key N-cycling enzymes from ecologically-relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, though (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) andmore » nitrite reductase (NirK).« less

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

PubMed

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

PubMed

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Development and use of species-specific oligonucleotide probes for differentiation of Streptococcus uberis and Streptococcus parauberis.

PubMed Central

Bentley, R W; Leigh, J A; Collins, M D

1993-01-01

Oligonucleotide probes specific for 16S rRNA and capable of differentiating Streptococcus uberis and S. parauberis from each other and other esculin-hydrolyzing streptococci were developed. Use of a mini-RNA extraction technique for gram-positive cocci associated with bovine mastitis has allowed the probes to be used for identification of esculin-hydrolyzing streptococci from two dairy herds at the Institute for Animal Health, Compton, United Kingdom. One hundred seventy-nine of 206 isolates were identified as S. uberis, 3 were identified as S. parauberis, and 24 were not identified. Isolates not identified by the probes were tested biochemically and found to be mainly Enterococcus faecium, E. faecalis, or S. bovis. Images PMID:8417033

Pancreatic Abscess in a cat due to Staphylococcus aureus infection.

PubMed

Nemoto, Yuki; Haraguchi, Tomoya; Shimokawa Miyama, Takako; Kobayashi, Kosuke; Hama, Kaori; Kurogouchi, Yosuke; Fujiki, Noriyuki; Baba, Kenji; Okuda, Masaru; Mizuno, Takuya

2017-07-07

A 16-year-old spayed female American Shorthair cat was presented with lethargy, anorexia, and wamble. Physical and blood examination did not reveal any remarkable findings. Abdominal ultrasonography identified the presence of a localized anechoic structure with a thick wall in contact with the small intestine and adjacent to the liver. Ultrasound-guided fine-needle aspiration of the structure revealed fluid containing numerous cocci and neutrophils. Two days after antibiotic treatment, exploratory laparotomy was performed and the content of the structure was removed before multiple lavages. The pathological and bacteriological examination results supported a confirmatory diagnosis of pancreatic abscess due to Staphylococcus aureus infection, making this the first such report in a cat. The cat remained healthy thereafter with no disease recurrence.

Evaluation of urine culture screening by light-scatter photometry

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

Hale, D.C.; Thrupp, L.D.; Matsen, J.M.

1981-08-01

Urine screening for bacteriuria by light-scatter photometry (Autobac) was evaluated for accuracy and compared with a colony count by the calibrated loop method. Incubation time, inoculum size, precision, and interference of particulate matter were evaluated in an effort to standardize the screening procedure. Results showed that urines could be accurately screened for Enterobacteriaceae by inoculating a single Autobac cuvette chamber with 0.1 or 0.2 ml of urine and determining the voltage change after four hours. A change of greater than or equal to 0.2 units indicates significant bacteriuria. Decreased accuracy was noted for urines having greater than 10(5) cfu/ml ofmore » Pseudomonas species or gram-positive cocci, possibly because these organisms grow more slowly.« less

Early formation of dental plaque on platic films. 1. Light microscopic observations.

PubMed

Rönström, A; Attström, R; Egelberg, J

1975-02-01

In human subjects with healthy gingiva thin transparent plastic films were applied to the buccal surfaces of premolars in the upper and lower jaws. The films were left in place for peiods of 15, 30, 60, 120 and 240 minutes. The presence of coccoid bacteria, leukocytes and epithelial cells was investigated in an area adjacent to the gingival margin. The results showed that by 15 minutes coccoid bacteria had become attached to the artificial tooth surface. The number of microorganisms gradually increased during the time of the study. Large numbers of cocci and the formation of micro-colonies were observed after 120 and 240 minutes. Increasing numbers of leukocytes and epithelial cells were also found during the period of observation.

Clinical characteristics of Staphylococcus epidermidis: a systematic review

PubMed Central

Namvar, Amirmorteza Ebrahimzadeh; Bastarahang, Sara; Abbasi, Niloufar; Ghehi, Ghazaleh Sheikhi; Farhadbakhtiarian, Sara; Arezi, Parastoo; Hosseini, Mahsa; Baravati, Sholeh Zaeemi; Jokar, Zahra; Chermahin, Sara Ganji

2014-01-01

Staphylococci are known as clustering Gram-positive cocci, nonmotile, non-spore forming facultatively anaerobic that classified in two main groups, coagulase-positive and coagulase-negative. Staphylococcus epidermidis with the highest percentage has the prominent role among coagulase-negative Staphylococci that is the most important reason of clinical infections. Due to various virulence factors and unique features, this microorganism is respected as a common cause of nosocomial infections. Because of potential ability in biofilm formation and colonization in different surfaces, also using of medical implant devices in immunocompromised and hospitalized patients the related infections have been increased. In recent decades the clinical importance and the emergence of methicillin-resistant Staphylococcus epidermidis strains have created many challenges in the treatment process. PMID:25285267

Characterization of Staphylococcus spp. and Micrococcus spp. isolated from Iberian ham throughout the ripening process.

PubMed

Rodríguez, M; Núñez, F; Córdoba, J J; Sanabria, C; Bermúdez, E; Asensio, M A

1994-12-01

The Iberian dry cured ham is an uncooked meat product highly appreciated because of its characteristic flavour. This product is obtained from highly marbled Iberian pig hindlegs after 18-24 months of maturation under natural environmental conditions. The role of Micrococcaceae in the development of the aroma characteristics of this products remains unclear. Identification of Gram-positive, catalase-positive cocci isolated from Mannitol Salt Agar plates showed that Staphylococcus xylosus followed by Staphylococcus equorum are the predominant organisms, even after 16 months of maturing. A remarkable variety of types of both staphylococci and micrococci are detected at any sampling time. The metabolic activities of these organisms could contribute to the characteristics of the final product.

Micrococcus species-related peritonitis in patients receiving peritoneal dialysis.

PubMed

Kao, Chih-Chin; Chiang, Chih-Kang; Huang, Jenq-Wen

2014-01-01

Peritonitis is a major complication of peritoneal dialysis (PD) and remains the most common cause of PD failure. Micrococci are catalase-positive, coagulase-negative, and gram-positive cocci that are spherical, often found in tetrad, and belong to the family Micrococcaceae. Micrococcus species are commonly found in the environment, and it is now recognized that Micrococcus species can be opportunistic pathogens in immunocompromised patients. The only consistent predisposing factor for Micrococcus infection is an immunocompromised state. We report three cases of Micrococcus PD peritonitis. Improper practice of PD may have been the causative factor. Although Micrococcus species are low-virulence pathogens, infection could result in refractory peritonitis and subsequent PD failure. Intraperitoneal administration of vancomycin for at least 2 weeks is recommended for Micrococcus peritonitis.

Printing 1D Assembly Array of Single Particle Resolution for Magnetosensing.

PubMed

Gao, Meng; Kuang, Minxuan; Li, Lihong; Liu, Meijin; Wang, Libin; Song, Yanlin

2018-05-01

Magnetosensing is a ubiquitous ability for many organism species in nature. 1D assembly, especially that arranged in single-particle-resolution regulation, is able to sense the direction of magnetic field depending on the enhanced dipolar interaction in the linear orientation. Inspired by the magnetosome structure in magnetotactic bacteria, a 1D assembly array of single particle resolution with controlled length and well-behaved configuration is prepared via inkjet printing method assisted with magnetic guiding. In the fabrication process, chains in a "tip-to-tip" regulation with the desired number of particles are prepared in a confined tiny inkjet-printed droplet. By adjusting the receding angle of the substrate, the assembled 1D morphology is kept/deteriorated depending on the pinning/depinning behavior during ink evaporation, which leads to the formation of well-behaved 1D assembly/aggregated dot assembly. Owing to the high-aspect-ratio characteristic of the assembled structure, the as-prepared 1D arrays can be used for magnetic field sensing with anisotropic magnetization M // /M ⊥ up to 6.03. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metamorphosis of Magnetospirillum magneticum AMB-1 cells

NASA Astrophysics Data System (ADS)

Zhang, Fengli; Yu-Zhang, Kui; Zhao, Sanjun; Xiao, Tian; Denis, Michel; Wu, Longfei

2010-03-01

Magnetospirillum magneticum strain AMB-1 belongs to the family of magnetotactic bacteria. It possesses a magnetosome chain aligning, with the assistance of cytoskeleton filaments MamK, along the long axis of the spiral cells. Most fresh M. magneticum AMB-1 cells exhibit spiral morphology. In addition, other cell shapes such as curved and spherical were also observed in this organism. Interestingly, the spherical cell shape increased steadily with prolonged incubation time. As the actin-like cytoskeleton protein MreB is involved in maintenance of cell shapes in rod-shaped bacteria such as Escherichia coli and Bacillus subtilis, the correlation between MreB protein levels and cell shape was investigated in this study. Immunoblotting analysis showed that the quantity of MreB decreased when the cell shape changed along with incubation time. As an internal control, the quantity of MamA was not obviously changed under the same conditions. Cell shape directs cell-wall synthesis during growth and division. MreB is required for maintaining the cell shape. Thus, MreB might play an essential role in maintaining the spiral shape of M. magneticum AMB-1 cells.

Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions

NASA Astrophysics Data System (ADS)

Felfoul, Ouajdi; Mohammadi, Mahmood; Taherkhani, Samira; de Lanauze, Dominic; Zhong Xu, Yong; Loghin, Dumitru; Essa, Sherief; Jancik, Sylwia; Houle, Daniel; Lafleur, Michel; Gaboury, Louis; Tabrizian, Maryam; Kaou, Neila; Atkin, Michael; Vuong, Té; Batist, Gerald; Beauchemin, Nicole; Radzioch, Danuta; Martel, Sylvain

2016-11-01

Oxygen-depleted hypoxic regions in the tumour are generally resistant to therapies. Although nanocarriers have been used to deliver drugs, the targeting ratios have been very low. Here, we show that the magneto-aerotactic migration behaviour of magnetotactic bacteria, Magnetococcus marinus strain MC-1 (ref. 4), can be used to transport drug-loaded nanoliposomes into hypoxic regions of the tumour. In their natural environment, MC-1 cells, each containing a chain of magnetic iron-oxide nanocrystals, tend to swim along local magnetic field lines and towards low oxygen concentrations based on a two-state aerotactic sensing system. We show that when MC-1 cells bearing covalently bound drug-containing nanoliposomes were injected near the tumour in severe combined immunodeficient beige mice and magnetically guided, up to 55% of MC-1 cells penetrated into hypoxic regions of HCT116 colorectal xenografts. Approximately 70 drug-loaded nanoliposomes were attached to each MC-1 cell. Our results suggest that harnessing swarms of microorganisms exhibiting magneto-aerotactic behaviour can significantly improve the therapeutic index of various nanocarriers in tumour hypoxic regions.

Tuning Bacterial Hydrodynamics with Magnetic Fields: A Path to Bacterial Robotics

NASA Astrophysics Data System (ADS)

Pierce, Christopher; Mumper, Eric; Brangham, Jack; Wijesinghe, Hiran; Lower, Stephen; Lower, Brian; Yang, Fengyuan; Sooryakumar, Ratnasingham

Magnetotactic Bacteria (MTB) are a group of motile prokaryotes that synthesize chains of lipid-bound, magnetic nano-particles. In this study, the innate magnetism of these flagellated swimmers is exploited to explore their hydrodynamics near confining surfaces, using the magnetic field as a tuning parameter. With weak (Gauss), uniform, external, magnetic ?elds and the field gradients arising from micro-magnetic surface patterns, the relative strength of hydrodynamic, magnetic and ?agellar force components is tuned through magnetic control of the bacteria's orientation and position. In addition to direct measurement of several hydrodynamic quantities related to the motility of individual cells, their tunable dynamics reveal a number of novel, highly controllable swimming behaviors with potential value in micro-robotics applications. Specifically, the experiments permit the MTB cells to be directed along parallel or divergent trajectories, suppress their flagellar forces through magnetic means, and induce transitions between planar, circulating trajectories and drifting, vertically oriented ``top-like'' motion. The implications of the work for fundamental hydrodynamics research as well as bacterially driven robotics applications will be discussed.

Genetic manipulation of iron biomineralization enhances MR relaxivity in a ferritin-M6A chimeric complex.

PubMed

Radoul, Marina; Lewin, Limor; Cohen, Batya; Oren, Roni; Popov, Stanislav; Davidov, Geula; Vandsburger, Moriel H; Harmelin, Alon; Bitton, Ronit; Greneche, Jean-Marc; Neeman, Michal; Zarivach, Raz

2016-05-23

Ferritin has gained significant attention as a potential reporter gene for in vivo imaging by magnetic resonance imaging (MRI). However, due to the ferritin ferrihydrite core, the relaxivity and sensitivity for detection of native ferritin is relatively low. We report here on a novel chimeric magneto-ferritin reporter gene - ferritin-M6A - in which the magnetite binding peptide from the magnetotactic bacteria magnetosome-associated Mms6 protein was fused to the C-terminal of murine h-ferritin. Biophysical experiments showed that purified ferritin-M6A assembled into a stable protein cage with the M6A protruding into the cage core, enabling magnetite biomineralisation. Ferritin-M6A-expressing C6-glioma cells showed enhanced (per iron) r2 relaxivity. MRI in vivo studies of ferritin-M6A-expressing tumour xenografts showed enhanced R2 relaxation rate in the central hypoxic region of the tumours. Such enhanced relaxivity would increase the sensitivity of ferritin as a reporter gene for non-invasive in vivo MRI-monitoring of cell delivery and differentiation in cellular or gene-based therapies.

N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species

USGS Publications Warehouse

Bazylinski, D.A.; Dean, A.J.; Schuler, D.; Phillips, E.J.P.; Lovley, D.R.

2000-01-01

Cells of Geobacter metallireducens, Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2-dependent growth, the first anaerobically with Fe(lll) as the electron acceptor, and the latter three species micro-aerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5 ?? 5.9nmol C2H4 produced min-1 mg-1 cell protein) while growing with Fe(lll) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.

Truncated Hexa-Octahedral Magnetite Crystals in Martian Meteorite ALH84001: Evidence of Biogenic Activity on Early Mars

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K.; Clemett, S. J.; Schwartz, C.; McIntosh, J. R.; Bazylinski, D. A.; Kirschvink, J.; McKay, D. S.; Gibson, E. K.; Vali, H.; Romanek, C. S.

2004-01-01

The landmark paper by McKay et al. [1] cited four lines of evidence associated with the Martian meteorite ALH84001 to support the hypothesis that life existed on Mars approximately 4 Ga ago. Now, more than five years later, attention has focused on the ALH84001 magnetite grains embedded within carbonate globules in the ALH84001 meteorite. We have suggested that up to approx.25% of the ALH84001 magnetite crystals are products of biological activity [e.g., 2]. The remaining magnetites lack sufficient characteristics to constrain their origin. The papers of Thomas Keprta et al. were criticized arguing that the three dimensional structure of ALH84001 magnetite crystals can only be unambiguously determined using electron tomographic techniques. Clemett et al. [3] confirmed that magnetites produced by magnetotactic bacteria strain MV-I display a truncated hexa-octahedral geometry using electron tomography and validated the use of the multi-tilt classical transmission microscopy technique used by [2]. Recently the geometry of the purported martian biogenic magnetites was shown be identical to that for MV-1 magnetites using electron tomography [6].

Toxic fungi.

PubMed

Lampe, K F

1979-01-01

Much progress in the areas of identification of active components and elucidation of the toxic mechanisms for the principal poisonous mushrooms has been made in the past decade. This affords a more rational approach to therapeutic management which has consequently resulted in a decrease in the morbidity and mortality associated with these species. However, the effectiveness of a large number of adjuvants for Amanita phalloides poisoning still needs critical laboratory evaluation. The current status of knowledge concerning the toxic potential and contituents of many mushroom species, including the gastroenteric irritants, is inadequate. The problem of geographic variation or genetic strain in the concentration of toxins of many species also requires further investigation. The recent awareness and interest in the pharmacology and toxicology of uncultivated mushrooms in North America and Great Britain should encourage continued active research.

Consumption of Camembert cheese stimulates commensal enterococci in healthy human intestinal microbiota.

PubMed

Firmesse, Olivier; Rabot, Sylvie; Bermúdez-Humarán, Luis G; Corthier, Gérard; Furet, Jean-Pierre

2007-11-01

Enterococci are natural inhabitants of the human gastrointestinal tract and the main Gram-positive and facultative anaerobic cocci recovered in human faeces. They are also present in a variety of fermented dairy and meat products, and some rare isolates are responsible for severe infections such as endocarditis and meningitis. The aim of the present study was to evaluate the effect of Camembert cheese consumption by healthy human volunteers on the faecal enterococcal population. A highly specific real-time quantitative PCR approach was designed and used to type enterococcal species in human faeces. Two species were found, Enterococcus faecalis and Enterococcus faecium, and only the Enterococcus faecalis population was significantly enhanced after Camembert cheese consumption, whereas Escherichia coli population and the dominant microbiota remained unaffected throughout the trial.

[Antimicrobial sensitivity of the environmental microbiota in the intensive care units of a peruvian hospital].

PubMed

Díaz-Tello, José; Rojas-Jaimes, Jesús; Ibarra-Trujillo, Jimmy; Tárraga-Gonzales, Delza

2017-01-01

The objective was to detect Gram-negative bacilli and Gram-positive cocci isolated from the environmental microbiota of the Intensive Care Unit (ICU) departments of Neonatology, Pediatrics, and Transplants (kidney, liver, and general) in a Lima hospital and determine their antimicrobial sensitivity. Eighty samples were obtained from inanimate surfaces using a wet swab. A total of 61 bacterial strains were identified, including Staphylococcus epidermis (46.0%), Alcaligenes sp. (21.3%), Pseudomonas aeruginosa (16.4%), Acinetobacter sp. (13.1%), Staphylococcus aureus (1.6%), and Staphylococcus haemolyticus (1.6%). Acinetobacter sp. and P. aeruginosa showed a heightened sensitivity to the antibiotics assessed, while Alcaligenes sp. and S. epidermidis presented the highest antimicrobial resistance. It is recommended that sustained asepsis and monitoring methods be used in ICUs.

[Stroke due to infective endocarditis diagnosed by the retrieved thrombus: a case report].

PubMed

Nakanishi, Kaoru; Kawano, Hiroyuki; Amano, Tatsuo; Omori, Yoshihiko; Kanma, Hiroshi; Hirano, Teruyuki

2018-01-26

A 80-years-old woman suddenly presented with aphasia, right hemiparesis, and dysesthesia. MRA showed the left middle cerebral artery occlusion. She was diagnosed as hyperacute ischemic stroke. She was treated with intravenous recombinant tissue plasminogen activator and underwent endovascular thrombectomy. On admission, she had a fever and high C reactive protein, and was treated with antibiotic therapy. The pathological diagnosis of the retrieved thrombus revealed the cluster of the gram positive cocci. The blood culture was negative and thransthoracic echocardiogram did not detect the vegetation. She was finally diagnosed as cardioembolic stroke due to infective endocarditis based on the pathological diagnosis of the retrieved thrombus. The pathological diagnosis of the retrieved thrombus was quite important to clarify the cause of ischemic stroke.

An Appalachian Amazon? Magnetofossil evidence for the development of a tropical river-like system in the mid-Atlantic United States during the Paleocene-Eocene Thermal Maximum

NASA Astrophysics Data System (ADS)

Kopp, R. E.; Schumann, D.; Raub, T. D.; Powars, D. S.; Godfrey, L. V.; Swanson-Hysell, N.; Maloof, A. C.; Vali, H.

2009-12-01

The Paleocene-Eocene Thermal Maximum is preserved within the mid-Atlantic Coastal Plain as a unique clay deposited in the Salisbury Embayment, a tectonic downwarp that stretches from southeastern Virginia to central New Jersey. The mostly massive and kaolinite-rich clay is distinct from the glauconitic sediments that otherwise characterize regional Paleocene and lower Eocene deposits. It contains abundant magnetite produced by magnetotactic bacteria and by larger, presumptively eukaryotic microorganisms not yet known from any other locality. Because most magnetotactic bacteria live within a specific, narrow redox environment -- the suboxic zone of a water column or sediments, where both oxygen and sulfide concentrations are low and iron concentrations relatively high -- their biominerals can be used as a paleoenvironmental tracer. High iron bioavailability indicates a relatively thick suboxic zone. The preservation of iron biominerals suggests that this zone was located in sediments, rather than in the water column, as water column suboxia is associated with high sedimentary organic carbon concentrations, which promote magnetite dissolution. The thickest modern, sedimentary, high-iron suboxic zones occur in tropical river-dominated shelves, such as the Amazon Shelf. These zones result from the combination of a moderately high input of reactive Fe (produced by tropical weathering conditions) with a high-energy environment (produced by tides, frontal-zone currents, and surface waves) that promotes the regular physical reworking of the sediments, thus allowing the re-oxidation of reduced Fe and increasing the availability of Fe as an electron acceptor. To test the "Appalachian Amazon" hypothesis, we mapped the distribution of magnetofossils throughout the Salisbury Embayment using ferromagnetic resonance spectroscopy and electron microscopy, supplemented by organic carbon isotope data. We find three magnetic facies in the clay: Facies 1, characterized by a mix of detrital particles and magnetofossils; Facies 2, with a higher magnetofossil-to-detrital ratio; and Facies 3, with only transient magnetofossils. Facies 1 occurs in inner-middle neritic deposits of central Maryland and northern Virginia, near where the modern Potomac crosses the Fall Line. Facies 2 occurs throughout the middle neritic deposits of eastern Maryland and Virginia and of southern New Jersey. Facies 3 occurs in the outer neritic deposits of eastern New Jersey and on the northern and southern flanks of the embayment. Consistent with the hypothesis, this distribution suggests a link between the magnetofossil distribution and a river system with an outlet in the vicinity of Facies 1. The development of such a river system may have been linked to a combination of more intense weathering, higher precipitation, and increased storminess.

Experimental determination of the magnetic dipole moment of candidate magnetoreceptor cells in trout

NASA Astrophysics Data System (ADS)

Winklhofer, M.; Eder, S.; Cadioiu, H.; McNaughton, P. A.; Kirschvink, J. L.

2011-12-01

Based on histological, physiological, and physical evidence, Walker et al (1997) and Diebel et al (2000) have identified distinctive cells in the olfactory epithelium of the rainbow trout (Onchorynchus mykiss) that contain magnetite and are closely associated with neurons that respond to changes in magnetic field. To put biophysical constraints on the possible transduction mechanism of magnetic signals, and in particular, to find out if the intracellular magnet is free to rotate or rather firmly anchored within the cell body, we have studied the magneto-mechanical response of isolated candidate receptor cells in suspension using a light microscope equipped with two pairs of Helmholtz coils. From the characteristic re-orientation time of suspended cells after a change in magnetic field direction, we have determined the magnitude of the magnetic dipole moment of the cells in function of the external field strength (0.4 mT to 3.2 mT) in order to find out whether or not the natural magnetic moment is remanence-based or induced (i.e., single-domain vs. superparamagnetic/multi-domain). Results: 1) The mechanical response of isolated cells to a change in magnetic field direction was always immediate, irrespective of the direction of change, which implies that the intracellular magnet is not free to rotate in the cell, but rather rigidly attached, probably to the plasma membrane, which is also suggested by our confocal fluorescence-microscope studies. 2) The cellular dipole moment turned out to be independent of the external field strength. Thus, the natural magnetic dipole moment is based on magnetic remanence, which points to single-domain particles and corroborates the results by Diebel et al (2000), who obtained switching fields consistent with single-domain magnetite. 3). The magnetic dipole moment is found to be of the order of several tens of fAm2, which greatly exceeds previous estimates (0.5 fAm2), and thus is similar to values reported for the most strongly magnetic types of magnetotactic bacteria (Hanzlik et al. 2002). Our results demonstrate that the magnetically identified cells clearly meet the physical requirements for a magnetoreceptor capable of rapidly detecting small changes in the external magnetic field. Diebel, C.E., Proksch, R., Green, C.R., Neilson, P. & Walker, M.M. (2000) Magnetite defines a vertebrate magnetoreceptor. Nature 406, 299-302. Hanzlik, M., Winklhofer, M., Petersen, N. (2002) Pulsed-field-remanence measurements on individual magnetotactic bacteria, J. Magn. Magn. Mater., 248(2), 258-267. Walker, M.M., Diebel, C.E., Haugh, C.V., Pankhurst, P.M., Montgomery, J.C. & Green, C.R. (1997) Structure and function of the vertebrate magnetic sense. Nature 390, 371-376.

Soil Organic Matter Stability and Soil Carbon Storage with Changes in Land Use Intensity in Uganda

NASA Astrophysics Data System (ADS)

Tiemann, L. K.; Grandy, S.; Hartter, J.

2014-12-01

As the foundation of soil fertility, soil organic matter (SOM) formation and break-down is a critical factor of agroecosystem sustainability. In tropical systems where soils are quickly weathered, the link between SOM and soil fertility is particularly strong; however, the mechanisms controlling the stabilization and destabilization of SOM are not well characterized in tropical soils. In western Uganda, we collected soil samples under different levels of land use intensity including maize fields, banana plantations and inside an un-cultivated native tropical forest, Kibale National Park (KNP). To better understand the link between land use intensity and SOM stability we measured total soil C and N, and respiration rates during a 369 d soil incubation. In addition, we separated soils into particle size fractions, and mineral adsorbed SOM in the silt (2-50 μm ) and clay (< 2 μm) fractions was dissociated, purified and chemically characterized via pyrolysis-GC/MS. Cultivated soil C and N have declined by 22 and 48%, respectively, in comparison to uncultivated KNP soils. Incubation data indicate that over the last decade, relatively accessible and labile soil organic carbon (SOC) pools have been depleted by 55-59% in cultivated soils. As a result of this depletion, the chemical composition of SOM has been altered such that clay and silt associated SOM differed significantly between agricultural fields and KNP. In particular, nitrogen containing compounds were in lower abundance in agricultural compared to KNP soils. This suggests that N depletion due to agriculture has advanced to pools of mineral associated organic N that are typically protected from break-down. In areas where land use intensity is relatively greater, increases in polysaccharides and lipids in maize fields compared to KNP indicate increases in microbial residues and decomposition by-products as microbes mine SOM for organic N. Chemical characterization of post-incubation SOM will help us better understand how microbes preferentially break-down SOM. Agricultural intensification over the past decade in western Uganda has depleted SOC, on average, by 1427 g m-2. In addition, depletion of organic nitrogen reserves in stable SOM pools corresponds with reported declines in crop yields and productivity in this region.

Identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms

PubMed Central

2010-01-01

Background Fumarase catalyzes the reversible hydration of fumarate to L-malate and is a key enzyme in the tricarboxylic acid (TCA) cycle and in amino acid metabolism. Fumarase is also used for the industrial production of L-malate from the substrate fumarate. Thermostable and high-activity fumarases from organisms that inhabit extreme environments may have great potential in industry, biotechnology, and basic research. The marine environment is highly complex and considered one of the main reservoirs of microbial diversity on the planet. However, most of the microorganisms are inaccessible in nature and are not easily cultivated in the laboratory. Metagenomic approaches provide a powerful tool to isolate and identify enzymes with novel biocatalytic activities for various biotechnological applications. Results A plasmid metagenomic library was constructed from uncultivated marine microorganisms within marine water samples. Through sequence-based screening of the DNA library, a gene encoding a novel fumarase (named FumF) was isolated. Amino acid sequence analysis revealed that the FumF protein shared the greatest homology with Class II fumarate hydratases from Bacteroides sp. 2_1_33B and Parabacteroides distasonis ATCC 8503 (26% identical and 43% similar). The putative fumarase gene was subcloned into pETBlue-2 vector and expressed in E. coli BL21(DE3)pLysS. The recombinant protein was purified to homogeneity. Functional characterization by high performance liquid chromatography confirmed that the recombinant FumF protein catalyzed the hydration of fumarate to form L-malate. The maximum activity for FumF protein occurred at pH 8.5 and 55°C in 5 mM Mg2+. The enzyme showed higher affinity and catalytic efficiency under optimal reaction conditions: Km= 0.48 mM, Vmax = 827 μM/min/mg, and kcat/Km = 1900 mM/s. Conclusions We isolated a novel fumarase gene, fumF, from a sequence-based screen of a plasmid metagenomic library from uncultivated marine microorganisms. The properties of FumF protein may be ideal for the industrial production of L-malate under higher temperature conditions. The identification of FumF underscores the potential of marine metagenome screening for novel biomolecules. PMID:21092234

VirSorter: mining viral signal from microbial genomic data.

PubMed

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L; Sullivan, Matthew B

2015-01-01

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter's prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in "reverse" to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.

VirSorter: mining viral signal from microbial genomic data

PubMed Central

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.

2015-01-01

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems. PMID:26038737

Klamath River Water Quality Data from Link River Dam to Keno Dam, Oregon, 2008

USGS Publications Warehouse

Sullivan, Annett B.; Deas, Michael L.; Asbill, Jessica; Kirshtein, Julie D.; Butler, Kenna D.; Vaughn, Jennifer

2009-01-01

This report documents sampling and analytical methods and presents field data from a second year of an ongoing study on the Klamath River from Link River Dam to Keno Dam in south central Oregon; this dataset will form the basis of a hydrodynamic and water quality model. Water quality was sampled weekly at six mainstem and two tributary sites from early April through early November, 2008. Constituents reported herein include field-measured water-column parameters (water temperature, pH, dissolved oxygen concentration, specific conductance); total nitrogen and phosphorus; particulate carbon and nitrogen; total iron; filtered orthophosphate, nitrite, nitrite plus nitrate, ammonia, organic carbon, and iron; specific UV absorbance at 254 nanometers; chlorophyll a; phytoplankton and zooplankton enumeration and species identification; and bacterial abundance and morphological subgroups. Sampling program results indicated: *Most nutrient and carbon concentrations were lowest in spring, increased starting in mid-June, remained elevated in the summer, and decreased in fall. Dissolved nitrite plus nitrate had a different seasonal cycle and was below detection or at low concentration in summer. *Although total nitrogen and total phosphorus concentrations did not show large differences from upstream to downstream, filtered ammonia and orthophosphate concentrations increased in the downstream direction and particulate carbon and particulate nitrogen generally decreased in the downstream direction. *Large bacterial cells made up most of the bacteria biovolume, though cocci were the most numerous bacteria type. Cocci, with diameters of 0.1 to 0.2 micrometers, were smaller than the filter pore sizes used to separate dissolved from particulate matter. *Phytoplankton biovolumes were dominated by diatoms in spring and by the blue-green alga Aphanizomenon flos-aquae after mid-June. Another blue-green, Anabaena flos-aquae, was noted in samples from late May to late June. Phytoplankton biovolumes generally were highest at the upstream Link River and Railroad Bridge sites and decreased in the downstream direction. *Zooplankton densities were largest in late April. Populations were dominated by rotifers and copepods in early spring, and by rotifers and cladocerans in summer, with cladocerans most common at the most upstream site.

Female genital tract bacterial coisolates with Candida albicans in patients without clinical vaginitis.

PubMed Central

Monif, G R; Carson, H J

1998-01-01

OBJECTIVE: In vitro, Candida albicans has demonstrated the ability to inhibit replication of selected bacteria. Little information exists on the impact of C. albicans on the vaginal bacterial flora in vivo. The purpose of this study is to identify the coexisting bacterial flora when C. albicans is isolated from vaginal cultures submitted to a hospital-based testing facility for reasons other than vulvovaginitis. METHODOLOGY: All specimens (240) received from ambulatory care clinics over a six-month period were cultured for aerobic and anaerobic bacteria and Candida species. Those specimens submitted for cervicitis, vaginitis, or vaginal discharge and those from which yeasts other than C. albicans were isolated were eliminated. To control for sample biases, a subgroup composed of all pregnant women for whom cultures were done as screening procedures was similarly studied. Chi-square analyses, comparing the prevalence of individual bacteria isolated with and without the presence of C. albicans, were done for all study populations using SPSS for Windows software (1994). RESULTS: Two hundred and forty consecutive specimens were bacteriologically analyzed. Of the 220 vaginal samples used in the study, C. albicans was isolated in 44 instances (20%). Neither the presence of the lactobacilli nor the presence of Gardnerella vaginalis markedly influenced the isolation rate of C. albicans. The group B streptococci had a greater probability of coisolation when C. albicans was present (27.3% verses 16%), but this was not statistically significant (P < 0.8). Dissociation between the presence of C. albicans and the coisolation of Peptostreptococcus species and anaerobic gram-positive cocci and/or bacilli was noted (P < 0.0819), while the incidence of gram-positive aerobic bacilli was reduced in the presence of C. albicans (30/176 [17.1%] versus 6/44 [13.6%]), this reduced incidence was not statistically significant. Isolation data of the subgroup of pregnant women supported these observations. CONCLUSION: Within the limitations of the study, statistically, the data suggests that an inverse relationship exists between the presence of C. albicans and recovery of Peptostreptococcus and anaerobic gram-positive cocci and bacilli. PMID:9702585

Female genital tract bacterial coisolates with Candida albicans in patients without clinical vaginitis.

PubMed

Monif, G R; Carson, H J

1998-01-01

In vitro, Candida albicans has demonstrated the ability to inhibit replication of selected bacteria. Little information exists on the impact of C. albicans on the vaginal bacterial flora in vivo. The purpose of this study is to identify the coexisting bacterial flora when C. albicans is isolated from vaginal cultures submitted to a hospital-based testing facility for reasons other than vulvovaginitis. All specimens (240) received from ambulatory care clinics over a six-month period were cultured for aerobic and anaerobic bacteria and Candida species. Those specimens submitted for cervicitis, vaginitis, or vaginal discharge and those from which yeasts other than C. albicans were isolated were eliminated. To control for sample biases, a subgroup composed of all pregnant women for whom cultures were done as screening procedures was similarly studied. Chi-square analyses, comparing the prevalence of individual bacteria isolated with and without the presence of C. albicans, were done for all study populations using SPSS for Windows software (1994). Two hundred and forty consecutive specimens were bacteriologically analyzed. Of the 220 vaginal samples used in the study, C. albicans was isolated in 44 instances (20%). Neither the presence of the lactobacilli nor the presence of Gardnerella vaginalis markedly influenced the isolation rate of C. albicans. The group B streptococci had a greater probability of coisolation when C. albicans was present (27.3% verses 16%), but this was not statistically significant (P < 0.8). Dissociation between the presence of C. albicans and the coisolation of Peptostreptococcus species and anaerobic gram-positive cocci and/or bacilli was noted (P < 0.0819), while the incidence of gram-positive aerobic bacilli was reduced in the presence of C. albicans (30/176 [17.1%] versus 6/44 [13.6%]), this reduced incidence was not statistically significant. Isolation data of the subgroup of pregnant women supported these observations. Within the limitations of the study, statistically, the data suggests that an inverse relationship exists between the presence of C. albicans and recovery of Peptostreptococcus and anaerobic gram-positive cocci and bacilli.

Comparison of antral tap with endoscopically directed nasal culture.

PubMed

Casiano, R R; Cohn, S; Villasuso, E; Brown, M; Memari, F; Barquist, E; Namias, N

2001-08-01

The diagnosis of acute bacterial rhinosinusitis continues to generate controversy in critically ill patients. The efficacy of endoscopically directed cultures in these patients is unknown. We compared antral tap (AT) with endoscopic tissue culture (ETC) of the osteomeatal complex in an intensive care unit (ICU) setting. Twenty patients admitted to a surgical/trauma ICU were evaluated by AT and ENB for the presence of rhinosinusitis. All patients had 1) a fever of unknown origin without resolution on empiric antibiotic therapy for > or =48 hrs; 2) other sources of fever ruled out; 3) computed tomography scan evidence of mucoperiosteal thickening +/- sinus air/fluid levels; and 4) attempt at conservative treatment with topical decongestants and removal of all nasal intubation. Microbiologic data were collected and analyzed for any statistical difference between groups. A total of 29 sides underwent simultaneous tap and endoscopically directed tissue culture. The mean age was 40 years (range, 23-77 y) with 85% being males. Fifteen of 20 (75%) patients in the AT group were culture-positive. Of the 49 isolates from the AT, 55% yielded Gram-negative bacilli (Acinetobacter sp. 37%) and 45% yielded Gram-positive cocci. The ETC group was culture-positive in 18 of 20 (90%) patients. Of the 52 isolates from the ETC, Gram-negative bacilli were found in 58% (Acinetobacter sp. 33%) and 42% yielded Gram-positive cocci. The ETCs were culture-positive in all but 1 patient with positive taps. There appeared to be a concordance between AT and ETC in 60% of the patients. In five instances (25%), results of the AT or ETC changed ICU management. Two patients ultimately required sinus surgery. Sinus taps and/or endoscopically directed tissue cultures led to a change in ICU care in 25% of ICU patients studied. In patients with fever of unknown origin and computed tomography evidence of sinusitis, an antral tap continues to provide important information concerning maxillary sinusitis. However, ETC may give as good a representation of the microbiology and secondary inflammatory changes responsible for bacterial ICU rhinosinusitis causing fever of unknown origin. Further study on a larger group of patients is needed.

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05.

PubMed

Perin, Luana Martins; Dal Bello, Barbara; Belviso, Simona; Zeppa, Giuseppe; Carvalho, Antônio Fernandes de; Cocolin, Luca; Nero, Luís Augusto

2015-12-02

Minas cheese is a popular dairy product in Brazil that is traditionally produced using raw or pasteurized cow milk. This study proposed an alternative production of Minas cheese using raw goat milk added of a nisin producer Lactococcus lactis subsp. lactis GLc05. An in situ investigation was carried on to evaluate the interactions between the L. lactis subsp. lactis GLc05 and the autochthonous microbiota of a Minas cheese during the ripening; production of biogenic amines (BAs) was assessed as a safety aspect. Minas cheese was produced in two treatments (A, by adding L. lactis subsp. lactis GLc05, and B, without adding this strain), in three independent repetitions (R1, R2, and R3). Culture dependent (direct plating) and independent (rep-PCR and PCR-DGGE) methods were employed to characterize the microbiota and to assess the possible interferences caused by L. lactis subsp. lactis GLc05. BA amounts were measured using HPLC. A significant decrease in coagulase-positive cocci was observed in the cheeses produced by adding L. lactis subsp. lactis GLc05 (cheese A). The rep-PCR and PCR-DGGE highlighted the differences in the microbiota of both cheeses, separating them into two different clusters. Lactococcus sp. was found as the main microorganism in both cheeses, and the microbiota of cheese A presented a higher number of species. High concentrations of tyramine were found in both cheeses and, at specific ripening times, the BA amounts in cheese B were significantly higher than in cheese A (p<0.05). The interaction of nisin producer L. lactis subsp. lactis GLc05 was demonstrated in situ, by demonstration of its influence in the complex microbiota naturally present in a raw goat milk cheese and by controlling the growth of coagulase-positive cocci. L. lactis subsp. lactis GLc05 influenced also the production of BA determining that their amounts in the cheeses were maintained at acceptable levels for human consumption. Copyright © 2015 Elsevier B.V. All rights reserved.

High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.

PubMed

Turaev, Dmitrij; Rattei, Thomas

2016-06-01

The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data. In this review, we pinpoint the most promising current developments in metagenomics. They facilitate microbial systems biology towards a systemic understanding of mechanisms in microbial communities with scopes of application in many areas of our daily life. Copyright © 2016 Elsevier Ltd. All rights reserved.

In Vitro Activity of Delafloxacin against Contemporary Bacterial Pathogens from the United States and Europe, 2014

PubMed Central

Pfaller, M. A.; Sader, H. S.; Rhomberg, P. R.

2017-01-01

ABSTRACT The in vitro activities of delafloxacin and comparator antimicrobial agents against 6,485 bacterial isolates collected from medical centers in Europe and the United States in 2014 were tested. Delafloxacin was the most potent agent tested against methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus, Streptococcus pneumoniae, viridans group streptococci, and beta-hemolytic streptococci and had activity similar to that of ciprofloxacin and levofloxacin against certain members of the Enterobacteriaceae. Overall, the broadest coverage of the tested pathogens (Gram-positive cocci and Gram-negative bacilli) was observed with meropenem and tigecycline in both Europe and the United States. Delafloxacin was shown to be active against organisms that may be encountered in acute bacterial skin and skin structure infections, respiratory infections, and urinary tract infections. PMID:28167542

In Vitro Activity of Delafloxacin against Contemporary Bacterial Pathogens from the United States and Europe, 2014.

PubMed

Pfaller, M A; Sader, H S; Rhomberg, P R; Flamm, R K

2017-04-01

The in vitro activities of delafloxacin and comparator antimicrobial agents against 6,485 bacterial isolates collected from medical centers in Europe and the United States in 2014 were tested. Delafloxacin was the most potent agent tested against methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus , Streptococcus pneumoniae , viridans group streptococci, and beta-hemolytic streptococci and had activity similar to that of ciprofloxacin and levofloxacin against certain members of the Enterobacteriaceae Overall, the broadest coverage of the tested pathogens (Gram-positive cocci and Gram-negative bacilli) was observed with meropenem and tigecycline in both Europe and the United States. Delafloxacin was shown to be active against organisms that may be encountered in acute bacterial skin and skin structure infections, respiratory infections, and urinary tract infections. Copyright © 2017 Pfaller et al.

Chemical composition and antibacterial activity of propolis collected by three different races of honeybees in the same region.

PubMed

Silici, Sibel; Kutluca, Semiramis

2005-05-13

The chemical analysis and antibacterial activity of three types of propolis collected three different races of Apis mellifera bee in the same apiary were investigated. Propolis samples were investigated by GC/MS, 48 compounds were identified 32 being new for propolis. The compounds identified indicated that the main plant sources of propolis were Populus alba, Populus tremuloides and Salix alba. The antimicrobial activity against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Candida albicans was evaluated. Ethanolic extracts of propolis samples showed high antibacterial activity against Gram-positive cocci (Staphylococcus aureus), but had a weak activity against Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and yeast (Candida albicans). Propolis sample collected by Apis mellifera caucasica showed a higher antibacterial activity than collected by Apis mellifera anatolica and Apis mellifera carnica.

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

PubMed

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

2017-05-04

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

Isolation, identification and sensitivity pattern of microorganisms isolated from the urine of pregnant women.

PubMed

Karim, S; Khan, K I

1994-01-01

The present studies were conducted to detect and identify the microorganism from the urine of pregnant women having urinary tract infection. The antibiotic susceptibility of these isolated microorganisms was also determined. The microorganisms found responsible for the infection were bacteria, fungi, yeast and protozoa. Among the bacteria two were identified as Gram-positive cocci i.e. Staphylococcus aureus and S. epidermidis, the remaining two were Gram-negative bacilli which were Escherichia coil and Pseudomonas aeruginosa. The fungus was identified as AspelEillus niger and the yeast like fungus Candida albican. The only protozoan found in some of the urine samples was Trichomonas vaginalis. These isolated and identified microorganisms were more susceptible to Norfloxacin, Velosef, Minocin, Nitrofurantoin, Malidixic acid and Metronidazole whereas antibiotics Penbritin and Cefaloridine were least effective against these microorganisms.

In Vitro Antimicrobial Activity of Razupenem (SMP-601, PTZ601) against Anaerobic Bacteria▿

PubMed Central

Tran, Chau Minh; Tanaka, Kaori; Yamagishi, Yuka; Goto, Takatsugu; Mikamo, Hiroshige; Watanabe, Kunitomo

2011-01-01

We evaluated the in vitro antianaerobic activity of razupenem (SMP-601, PTZ601), a new parenterally administered carbapenem, against 70 reference strains and 323 clinical isolates. Razupenem exhibited broad-spectrum activity against anaerobes, inhibiting most of the reference strains when used at a concentration of ≤1 μg/ml. Furthermore, it exhibited strong activity, comparable to those of other carbapenems (meropenem and doripenem), against clinically isolated non-fragilis Bacteroides spp. (MIC90s of 2 μg/ml), with MIC90 values of 0.06, 0.03, and 0.5 μg/ml against Prevotella spp., Porphyromonas spp., and Fusobacterium spp., respectively. Clinical isolates of anaerobic Gram-positive cocci, Eggerthella spp., and Clostridium spp. were highly susceptible to razupenem (MIC90s, 0.03 to 1 μg/ml). PMID:21343447

Curvularia keratomycosis in a dog.

PubMed

Ben-Shlomo, Gil; Plummer, Caryn; Barrie, Kathleen; Brooks, Dennis

2010-03-01

A 10-year-old, spayed female Bichon Frise was referred to the Veterinary Medical Center of the University of Florida with a 6-week history of blepharospasm and a nonhealing ulcer of the left eye. Ophthalmic examination revealed a 3-4 mm diameter corneal ulcer with faint edema at the lesion edge, and a raised grayish area on the paraxial cornea near the 2 o'clock position. Cytological testing revealed fungal hyphae and extracellular cocci. Culture of the lesion found heavy growth of Enterococcus faecalis and Curvularia spp. Treatment with a combination of topical antibiotics (polymyxin B, sulfate/trimetoprim, and 10% sulfacetamide sodium), 1% miconazole, autologous serum, and 5% hypertonic saline was instituted. After 8 days of medical therapy, an improvement of clinical signs was noted, and 15 days after initiation of treatment, the ulcer was healed with minimal corneal scarring.

Synthesis and antibacterial activity of bis-[2-hydroxy-3-(1,7,8,9,10-pentamethyl-3,5-dioxo-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-en-4-yloxy)-propyl]-dimethyl-ammonium chloride.

PubMed

Struga, Marta; Kossakowski, Jerzy; Stefańska, Joanna; Zimniak, Andrzej; Koziol, Anna E

2008-06-01

A new quaternary ammonium compound, bis-[2-hydroxy-3-(1,7,8,9,10-pentamethyl-3,5-dioxo-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-en-4-yloxy)-propyl]-dimethyl-ammonium chloride (4), was synthesized. The compound was investigated for antibacterial activity, including Gram-positive cocci and Gram-negative rods, and antifungal activity. Compound 4 showed significant inhibition against Staphylococcus aureus. Research was carried out over 4 standard strains and 40 hospital strains. Elementary analysis and/or MS, (1)H NMR and (13)C NMR spectra confirmed the identity of the products. The molecular structure of 3 was determined by an X-ray analysis.

Species identification and susceptibility to 17 antibiotics of coagulase-negative staphylococci isolated from clinical specimens.

PubMed

Marsik, F J; Brake, S

1982-04-01

A total of 299 isolates of gram-positive, catalase-positive, coagulase-negative cocci were isolated from a variety of specimens collected from patients at a large university hospital, and 281 (94%) were identified as staphylococci by established methods. Using the scheme of Kloos and Schleifer, we determined the species of the coagulase-negative staphylococci. Staphylococcus epidermidis was the cause of all bacteremias and the most commonly isolated species from bone, joint, and wound infections. Staphylococcus haemolyticus was the second most common isolate from wound infections, and Staphylococcus saprophyticus was the most commonly isolated species from urinary tract infections. Antibiograms to 17 antimicrobial agents were performed by a microdilution technique, and the results revealed that S. epidermidis was resistant to a water spectrum of antimicrobial agents than the other species of staphylococci were.

Species identification and susceptibility to 17 antibiotics of coagulase-negative staphylococci isolated from clinical specimens.

PubMed Central

Marsik, F J; Brake, S

1982-01-01

A total of 299 isolates of gram-positive, catalase-positive, coagulase-negative cocci were isolated from a variety of specimens collected from patients at a large university hospital, and 281 (94%) were identified as staphylococci by established methods. Using the scheme of Kloos and Schleifer, we determined the species of the coagulase-negative staphylococci. Staphylococcus epidermidis was the cause of all bacteremias and the most commonly isolated species from bone, joint, and wound infections. Staphylococcus haemolyticus was the second most common isolate from wound infections, and Staphylococcus saprophyticus was the most commonly isolated species from urinary tract infections. Antibiograms to 17 antimicrobial agents were performed by a microdilution technique, and the results revealed that S. epidermidis was resistant to a water spectrum of antimicrobial agents than the other species of staphylococci were. PMID:7068839

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment

PubMed Central

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

2015-01-01

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

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment.

PubMed

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

2015-01-01

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

Truncated hexa-octahedral magnetite crystals in ALH84001: Presumptive biosignatures

PubMed Central

Thomas-Keprta, Kathie L.; Clemett, Simon J.; Bazylinski, Dennis A.; Kirschvink, Joseph L.; McKay, David S.; Wentworth, Susan J.; Vali, Hojatollah; Gibson, Everett K.; McKay, Mary Fae; Romanek, Christopher S.

2001-01-01

McKay et al. [(1996) Science 273, 924–930] suggested that carbonate globules in the meteorite ALH84001 contained the fossil remains of Martian microbes. We have characterized a subpopulation of magnetite (Fe3O4) crystals present in abundance within the Fe-rich rims of these carbonate globules. We find these Martian magnetites to be both chemically and physically identical to terrestrial, biogenically precipitated, intracellular magnetites produced by magnetotactic bacteria strain MV-1. Specifically, both magnetite populations are single-domain and chemically pure, and exhibit a unique crystal habit we describe as truncated hexa-octahedral. There are no known reports of inorganic processes to explain the observation of truncated hexa-octahedral magnetites in a terrestrial sample. In bacteria strain MV-1 their presence is therefore likely a product of Natural Selection. Unless there is an unknown and unexplained inorganic process on Mars that is conspicuously absent on the Earth and forms truncated hexa-octahedral magnetites, we suggest that these magnetite crystals in the Martian meteorite ALH84001 were likely produced by a biogenic process. As such, these crystals are interpreted as Martian magnetofossils and constitute evidence of the oldest life yet found. PMID:11226210

Truncated hexa-octahedral magnetite crystals in ALH84001: presumptive biosignatures

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; Clemett, S. J.; Bazylinski, D. A.; Kirschvink, J. L.; McKay, D. S.; Wentworth, S. J.; Vali, H.; Gibson, E. K. Jr; McKay, M. F.; Romanek, C. S.

2001-01-01

McKay et al. [(1996) Science 273, 924-930] suggested that carbonate globules in the meteorite ALH84001 contained the fossil remains of Martian microbes. We have characterized a subpopulation of magnetite (Fe(3)O(4)) crystals present in abundance within the Fe-rich rims of these carbonate globules. We find these Martian magnetites to be both chemically and physically identical to terrestrial, biogenically precipitated, intracellular magnetites produced by magnetotactic bacteria strain MV-1. Specifically, both magnetite populations are single-domain and chemically pure, and exhibit a unique crystal habit we describe as truncated hexa-octahedral. There are no known reports of inorganic processes to explain the observation of truncated hexa-octahedral magnetites in a terrestrial sample. In bacteria strain MV-1 their presence is therefore likely a product of Natural Selection. Unless there is an unknown and unexplained inorganic process on Mars that is conspicuously absent on the Earth and forms truncated hexa-octahedral magnetites, we suggest that these magnetite crystals in the Martian meteorite ALH84001 were likely produced by a biogenic process. As such, these crystals are interpreted as Martian magnetofossils and constitute evidence of the oldest life yet found.

Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance

PubMed Central

Barber-Zucker, Shiran; Uebe, René; Davidov, Geula; Navon, Yotam; Sherf, Dror; Chill, Jordan H.; Kass, Itamar; Bitton, Ronit; Schüler, Dirk; Zarivach, Raz

2016-01-01

Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human. PMID:27550551

Bacterially synthesized ferrite nanoparticles for magnetic hyperthermia applications.

PubMed

Céspedes, Eva; Byrne, James M; Farrow, Neil; Moise, Sandhya; Coker, Victoria S; Bencsik, Martin; Lloyd, Jonathan R; Telling, Neil D

2014-11-07

Magnetic hyperthermia uses AC stimulation of magnetic nanoparticles to generate heat for cancer cell destruction. Whilst nanoparticles produced inside magnetotactic bacteria have shown amongst the highest reported heating to date, these particles are magnetically blocked so that strong heating occurs only for mobile particles, unless magnetic field parameters are far outside clinical limits. Here, nanoparticles extracellularly produced by the bacteria Geobacter sulfurreducens are investigated that contain Co or Zn dopants to tune the magnetic anisotropy, saturation magnetization and nanoparticle sizes, enabling heating within clinical field constraints. The heating mechanisms specific to either Co or Zn doping are determined from frequency dependent specific absorption rate (SAR) measurements and innovative AC susceptometry simulations that use a realistic model concerning clusters of polydisperse nanoparticles in suspension. Whilst both particle types undergo magnetization relaxation and show heating effects in water under low AC frequency and field, only Zn doped particles maintain relaxation combined with hysteresis losses even when immobilized. This magnetic heating process could prove important in the biological environment where nanoparticle mobility may not be possible. Obtained SARs are discussed regarding clinical conditions which, together with their enhanced MRI contrast, indicate that biogenic Zn doped particles are promising for combined diagnostics and cancer therapy.

Evaluation of the Influence That Was Produced by Phytoremediation of Soil Microorganisms at Oil Showings

NASA Astrophysics Data System (ADS)

Kaimi, Etsuko; Kawakita, Morikazu; Mukaidani, Tsukasa; Fujiwara, Kazuhiro; Okada, Shin-Ichi; Yasuda, Yoshio

Phytoremediation has been identified as a potentially environmentally friendly and cost effective technique for the treatment of contaminated soil. However, phytoremediation has an unknown mechanism. In this study, we focus on the effects of the cultivation of Italian ryegrass on the soil microbes collected at oil showings, which were expected to have a variety of crude oil degradable microorganisms. We evaluated the number of crude oil degradable microorganism, microbial activity, microflora using the PCR-DGGE method and the change in the concentration of crude oil in the soil. The results indicated that the microflora was affected by the cultivation of Itarian ryegrass, and that the microbial activity and the number of crude oil degradable microorganisms were also improved by the cultivation. Moreover, the concentration of crude oil in the rhizosphere soil decreased significantly when compared to the uncultivated soil. These results suggested that cultivation could regulate microflora selectively, which degraded crude oil.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

PubMed Central

Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry; Gurevich, Alexey A.; Dvorkin, Mikhail; Kulikov, Alexander S.; Lesin, Valery M.; Nikolenko, Sergey I.; Pham, Son; Prjibelski, Andrey D.; Pyshkin, Alexey V.; Sirotkin, Alexander V.; Vyahhi, Nikolay; Tesler, Glenn; Pevzner, Pavel A.

2012-01-01

Abstract The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. PMID:22506599

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

Walsh, David A.; Zaikova, Elena; Howes, Charles L.

Oxygen minimum zones (OMZs), also known as oceanic"dead zones", are widespread oceanographic features currently expanding due to global warming and coastal eutrophication. Although inhospitable to metazoan life, OMZs support a thriving but cryptic microbiota whose combined metabolic activity is intimately connected to nutrient and trace gas cycling within the global ocean. Here we report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur-oxidation and nitrate respiration responsive to a wide rangemore » of water column redox states. Thus, SUP05 plays integral roles in shaping nutrient and energy flow within oxygen-deficient oceanic waters via carbon sequestration, sulfide detoxification and biological nitrogen loss with important implications for marine productivity and atmospheric greenhouse control.« less

A New Era of the Vaginal Microbiome: Advances using Next-Generation Sequencing

PubMed Central

Fettweis, Jennifer M.; Serrano, Myrna G.; Girerd, Philippe H.; Jefferson, Kimberly K.

2012-01-01

Until recently, bacterial species that inhabit the human vagina have been primarily studied using organism-centric approaches. Understanding how these bacterial species interact with each other and the host vaginal epithelium is essential for a more complete understanding of vaginal health. Molecular approaches have already led to the identification of uncultivated bacterial taxa associated with bacterial vaginosis. Here, we review recent studies of the vaginal microbiome and discuss how culture-independent approaches, such as applications of next-generation sequencing, are advancing the field and shifting our understanding of how vaginal health is defined. This work may to lead to improved diagnostic tools and treatments for women who suffer from, or are at risk for, vaginal imbalances, pregnancy complications, and sexually acquired infections. These approaches may also transform our understanding of how host genetic factors, physiological conditions (e.g. menopause) and environmental exposures (e.g. smoking, antibiotic usage) influence the vaginal microbiome. PMID:22589096

PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts

PubMed Central

Lim, Shaun W.; Lance, Shea T.; Stedman, Kenneth M.; Abate, Adam R.

2017-01-01

Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the “gold standard” of virus enumeration, the plaque assay. PMID:28042018

PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts.

PubMed

Lim, Shaun W; Lance, Shea T; Stedman, Kenneth M; Abate, Adam R

2017-04-01

Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the "gold standard" of virus enumeration, the plaque assay. Copyright © 2017 Elsevier B.V. All rights reserved.

Widespread occurrence of structurally diverse tetraether membrane lipids: Evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles

PubMed Central

Schouten, Stefan; Hopmans, Ellen C.; Pancost, Richard D.; Damsté, Jaap S. Sinninghe

2000-01-01

Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) and branched glycerol dialkyl diethers are main membrane constituents of cultured hyperthermophilic archaea and eubacteria, respectively, and are found in environments with temperatures >60°C. Recently, we developed a new technique for the analysis of intact core tetraether lipids in cell material and sediments. The application of this technique to recent sediments shows that known and newly identified isoprenoid and branched GDGTs are widespread in low-temperature environments (<20°C) and are structurally far more diverse than previously thought. Their distribution indicates the ubiquitous environmental presence of as yet uncultivated, nonthermophilic organisms that may have independently evolved from hyperthermophilic archaea and eubacteria. The structures of some of the new GDGTs point to the hybridization of both typical archaeal and eubacterial biosynthetic pathways in single organisms. PMID:11121044

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

PubMed Central

Ma, Liang; Wei Huang, Da; Khil, Pavel P.; Dekker, John P.; Kutty, Geetha; Bishop, Lisa; Liu, Yueqin; Deng, Xilong; Pagni, Marco; Hirsch, Vanessa; Lempicki, Richard A.

2018-01-01

ABSTRACT Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro. Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals. PMID:29739910

Molecular Typing of Borrelia burgdorferi

PubMed Central

Wang, Guiqing; Liveris, Dionysios; Mukherjee, Priyanka; Jungnick, Sabrina; Margos, Gabriele; Schwartz, Ira

2015-01-01

Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens. PMID:25082003

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the oceanic crust deep biosphere

NASA Astrophysics Data System (ADS)

Carr, S. A.; Jungbluth, S.; Rappe, M. S.; Orcutt, B.

2017-12-01

The marine sedimentary and crustal subsurface biospheres harbor many uncultured microorganisms, including those belonging to Hydrothermarchaeota, formerly known as Marine Benthic Group E. SSU rRNA sequences of Hydrothermarchaeota have been identified in marine sediments across the globe, often in low abundance. Recently, crustal fluids from two subseafloor borehole observatories located on the eastern flank of the Juan de Fuca Ridge (i.e., CORKs at IODP Holes U1362A and U1362B), were collected for single-cell and metagenomic analyses. Both techniques revealed Hydrothermarchaeota to be prevalent in this system. Collectively, single-cell amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) depict Hydrothermarchaeota as opportunists, potentially capable of dissimilative and assimilative carboxydotrophy, sulfate reduction, thiosulfate reduction, nitrate reduction, chemotaxis, and motility. We propose that this diverse suit of metabolic potential may be advantageous for the hydrologically and geochemically dynamic subsurface crustal aquifer, an environment thought to be energy and nutrient limited.

Discovery of a novel methanogen prevalent in thawing permafrost.

PubMed

Mondav, Rhiannon; Woodcroft, Ben J; Kim, Eun-Hae; McCalley, Carmody K; Hodgkins, Suzanne B; Crill, Patrick M; Chanton, Jeffrey; Hurst, Gregory B; VerBerkmoes, Nathan C; Saleska, Scott R; Hugenholtz, Philip; Rich, Virginia I; Tyson, Gene W

2014-01-01

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

What band rocks the MTB? (Invited)

NASA Astrophysics Data System (ADS)

Kind, J.; García-Rubio, I.; Gehring, A. U.

2013-12-01

Magnetotactic bacteria (MTB) are a polyphyletic group of bacteria that have been found in marine and lacustrine environments and soils [e.g. 1]. The hallmark of MTB is their intracellular formation of magnetosomes, single-domain ferrimagnetic particles that are aligned in chains. The chain configuration generates a strong magnetic dipole, which is used as magnetic compass to move the MTB into their favorable habit. The term band corresponds to a frequency window of microwaves in the gigahertz (GHz) range. Ferromagnetic resonance (FMR) spectroscopy uses the microwave absorption in a magnetic field to analyze the anisotropy properties and the domain state of magnetic materials. Specific microwave frequency causes absorption in a characteristic magnetic field range. For the investigation of MTB we use S-band (4.02 GHz), X-band (9.47 GHz), and Q-band (34.16 GHz). Experiments on cultured MTB and on sediment samples of Holocene age showed that absorption in X- and Q-band occurs when the sample is in a saturated or nearly saturated state [2, 3]. By contrast, absorption in the S-band appears in lower magnetic fields, where the sample is far from saturation. All FMR spectra show two distinct low-field features that can be assigned to magnetite particles in chains, aligned parallel and perpendicular to the external magnetic field. The detailed separation of the parallel and perpendicular components in the bulk samples is hampered, because of the random orientation of the chains in the sample. The comparison of S-, X-, and Q-band shows that the lower the frequency the better the separation of the components. In the S-band FMR spectroscopy, the separation of chains parallel to the external magnetic field is supported by the internal field of the sample. This field is caused by the remanence that contributes to the external magnetic field to fulfill the resonance condition [3,4]. Considering the different FMR responses, it can be postulated that a lower microwave frequency generally leads to a better resolution of the chain configuration. Finally, for the investigation of geological samples, the application of S-band can be a powerful tool to complement the commonly used X-band FMR spectroscopy, i.e. multiple band rock the MTB. [1] Blakemore R.P., 1975, Magnetotactic bacteria, Science, 190, 377-379 [2] Mastogiacomo G., Fischer H., Garcia-Rubio I., and Gehring A. U., 2010, Ferromagnetic resonance spectroscopic response of magnetic chains in a biological matrix, J. Magn. Magn. Matter, 322, 661-663, doi: 10.1016/j.jmmm.2009.10.035 [3] Gehring A. U., Kind. J., Charilaou M., Garcia-Rubio I., 2011, S-band ferromagnetic resonance spectroscopy and the detection of magnetofossils, J. R. Soc. Interface, 10(80), doi: 10.1098/rsif.2012.0790 [4] Kind J., van Raden U., Garcia-Rubio I., and Gehring A. U., 2012, Rock magnetic techniques complemented by ferromagnetic resonance spectroscopy to analyse a sediment record, Geophys. J. Int., 191, 51-61, doi: 10.1111/j.1365-246X.2012.05620.x

Quantifying Glosair™ 400 efficacy for surface disinfection of American Type Culture Collection strains and micro-organisms recently isolated from intensive care unit patients.

PubMed

Herruzo, R; Vizcaíno, M J; Herruzo, I

2014-07-01

Microbial contamination of hospital surfaces may be a source of infection for hospitalized patients. We evaluated the efficacy of Glosair™ 400 against two American Type Culture Collection strains and 18 clinical isolates, placed on glass germ-carriers. Carriers were left to air-dry for 60 min and then exposed to a cycle before detection of any surviving micro-organisms. Antibiotic-susceptible Gram-negative bacilli were less susceptible (although not significantly) to this technique than resistant Gram-negative bacilli or Gram-positive cocci and yeasts (3, 3.4 and 4.6 log10 reduction, respectively). In conclusion, in areas that had not been cleaned, aerosolized hydrogen peroxide obtained >3 log10 mean destruction of patients' micro-organisms. Copyright © 2014 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Recently described clinically important anaerobic bacteria: medical aspects.

PubMed

Finegold, S M; Jousimies-Somer, H

1997-09-01

There is still inadequate information on the role of certain newly described or reclassified anaerobes in disease processes, on their normal sites of carriage, and on their antimicrobial susceptibilities. Herein, we summarize this information (most of the literature reviewed is from the past 5 years, but a few of the articles are approximately 10 years old). Porphyromonas species had seemed to be relatively nonpathogenic, but recent work indicates that this belief is incorrect. P. gingivalis, P levii-like organisms, and P. endodontalis-like organisms have been recovered from a variety of oral and extraoral infections. P. macacae has been recovered from infected cat bite wounds. Sutterella wadsworthensis, recently differentiated from Campylobacter gracilis, has been found in a variety of infections. Bilophila wadsworthia has also been recovered from a wide variety of infections. Newly described anaerobic cocci, gram-positive nonsporeforming rods, and clostridia have also been isolated from various infections.

Report of two paediatric cases of central line infections caused by species of the genus Kocuria

PubMed Central

Hamula, Camille L.; Dingle, Tanis C.

2016-01-01

Introduction: Species of the genus Kocuria are Gram-positive cocci of the family Micrococcacceae that are ubiquitous in the environment and part of the normal skin and oral flora in humans. A paucity of cases have been reported of Kocuria as human pathogens and there are currently no evidence-based guidelines for managing these uncommon infections. Case presentation: We present two paediatric cases of central line infections with species of the genus Kocuria that required line removal despite antimicrobial therapy. Conclusion: Species of the genus Kocuria are uncommon human pathogens that have rarely been reported to cause opportunistic infections in both adult and paediatric populations. The cases presented here add to the growing body of literature documenting the pathogenicity of these organisms and the possible need for line removal to achieve clinical cure in central line-associated bacteraemia caused by species of the genus Kocuria. PMID:28348760

Staphylococcal dermatitis in quail with a parakeratotic hyperkeratotic dermatosis suggestive of pantothenic acid deficiency.

PubMed

Raidal, S R

1995-09-01

This report describes an outbreak of Staphylococcal dermatitis which occurred in commercial Japanese quail (Coturnix coturnix japonica) with a history and clinico-pathological evidence suggestive of pantothenic acid deficiency. The flock had a low hatchability rate (40 to 43%) and a high percentage (50%) of dead-in-shell embryos. Approximately 5 to 15% of the grower flock developed crusty facial scabs and conjunctivitis from 4 days of age. Culture of eyelid skin yielded pure growths of non-haemolytic, coagulase-negative Staphylococcus spp. Histological examination revealed a generalised hyperkeratosis and parakeratosis of feathers, feather follicles and non-follicular skin. There was invasion of feather follicles by cocci and focal areas of suppurative exudative dermatitis and subcutaneous abscesses particularly in the eyelids and commissures of the beak. Clinical signs were alleviated by treatment with amoxycillin and a change in ration formulation.

[Diagnosis and treatment of suppurative processes caused by non-clostridial anaerobic microflora].

PubMed

Ofanesian, S S

1989-06-01

One hundred and fifty patients suffering from various purulent diseases (60 persons) and postoperative purulent complications (90 persons) caused by nonclostridial anaerobes were examined. Nonclostridial anaerobic bacteria were isolated most frequently in acute mastitis, paraproctitis, and postinfectious abscesses among patients of the first group and after appendectomy and resection of the large intestine among those of the second group. The character of the wound discharge, the location of the focus of infection, the tendency of the purulent process to form a great number of cavities and fistules, bacterioscopy of the native material, etc. help in establishing the diagnosis (before the results of bacteriological tests are obtained). Purulent processes caused by a combination of anaerobic cocci and aerobic flora take a particularly unfavourable course. Antibiotic therapy should consists of high doses of one or two antibiotics combined with metronidazole and nystatin.

Wide distribution of virulence genes among Enterococcus faecium and Enterococcus faecalis clinical isolates.

PubMed

Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasanthakumari; Sadeghifard, Nourkhoda; Ramli, Ramliza; Hamat, Rukman Awang

2014-01-01

Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%), and the extended temperatures between 5(°)C and 65(°)C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species.

Wide Distribution of Virulence Genes among Enterococcus faecium and Enterococcus faecalis Clinical Isolates

PubMed Central

Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasanthakumari; Sadeghifard, Nourkhoda; Ramli, Ramliza; Hamat, Rukman Awang

2014-01-01

Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%), and the extended temperatures between 5°C and 65°C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species. PMID:25147855

Use of Antibody to Membrane Adenosine Triphosphatase in the Study of Bacterial Relationships1

PubMed Central

Whiteside, Theresa L.; De Siervo, August J.; Salton, Milton R. J.

1971-01-01

An antiserum to Ca2+-activated adenosine triphosphatase from membranes of Micrococcus lysodeikticus cross-reacted in agar gels with membrane adenosine triphosphatases from other pigmented micrococci and related species. Species of Micrococcus and Sarcina showed different levels of inhibition of adenosine triphosphatase activities in heterologous reactions with antiserum. Inter- and intraspecific relationships based on the inhibition reaction were compared with an independent parameter, namely the quantitative and qualitative composition of the bacterial membrane phospholipids and fatty acids. The guanine plus cytosine contents in the deoxyribonucleic acid of the species studied correlated well with the serological cross-reactivity of adenosine triphosphatases from their membranes. The types of cross-bridges found in the peptidoglycans of these cocci were also compared with the other properties. The results suggest that an antiserum specific for a major membrane protein may be a reliable and most useful adjunct in studying bacterial serotaxonomy. Images PMID:4323299

Use of antibody to membrane adenosine triphosphatase in the study of bacterial relatioships.

PubMed

Whiteside, T L; De Siervo, A J; Salton, M R

1971-03-01

An antiserum to Ca(2+)-activated adenosine triphosphatase from membranes of Micrococcus lysodeikticus cross-reacted in agar gels with membrane adenosine triphosphatases from other pigmented micrococci and related species. Species of Micrococcus and Sarcina showed different levels of inhibition of adenosine triphosphatase activities in heterologous reactions with antiserum. Inter- and intraspecific relationships based on the inhibition reaction were compared with an independent parameter, namely the quantitative and qualitative composition of the bacterial membrane phospholipids and fatty acids. The guanine plus cytosine contents in the deoxyribonucleic acid of the species studied correlated well with the serological cross-reactivity of adenosine triphosphatases from their membranes. The types of cross-bridges found in the peptidoglycans of these cocci were also compared with the other properties. The results suggest that an antiserum specific for a major membrane protein may be a reliable and most useful adjunct in studying bacterial serotaxonomy.

Vaginal lactobacilli inhibiting growth of Gardnerella vaginalis, Mobiluncus and other bacterial species cultured from vaginal content of women with bacterial vaginosis.

PubMed

Skarin, A; Sylwan, J

1986-12-01

On a solid agar medium the growth-inhibitory effect of 9 Lactobacillus strains cultured from vaginal content was tested on bacteria cultured from vaginal content of women with bacterial vaginosis: Mobiluncus, Gardnerella vaginalis, Bacteroides and anaerobic cocci. Inhibition zones were observed in the growth of all of the strains isolated from women with bacterial vaginosis around all lactobacilli. The inhibitory effect of the lactobacilli was further tested on various anaerobic and facultatively anaerobic species, both type strains and fresh extragenitally cultured strains. Four Bacteroides fragilis strains as well as 2 out of 4 Staphylococcus aureus strains were clearly inhibited by the lactobacilli. The inhibition zones were generally wider at pH 5.5 than at 6.0. For all inhibited strains, (the S. aureus excepted) a low pH on the agar around the lactobacilli correlated to wider growth-inhibition zones.

Case of pacemaker pocket infection caused by Finegoldia magna.

PubMed

Hosseini Dehkordi, Seyed Hamed; Osorio, Georgina

2017-10-01

Finegoldia magna (formerly called Peptostreptococcus magnus) is a Gram-positive anaerobic coccus which is increasingly recognized as an opportunistic pathogen. We present a case of F. magna associated non-valvular cardiovascular device-related infection in an 83 year-old male who received a permanent pacemaker for sick sinus syndrome seven weeks prior to his presentation. Five weeks after the implantation, the pacemaker and leads were explanted because of clinical evidence of pacemaker pocket infection. He was initially treated with sulfamethoxazole-trimethoprim based on the Gram stain results from the removed pacemaker. However, two weeks later, he was readmitted with sepsis and was successfully treated with ampicillin-sulbactam. Culture results from the pacemaker and pocket as well as blood cultures grew F. magna. Clinicians should be aware of the possibility of F. magna infection when initial gram stain results show "gram positive cocci". Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization by volatile compounds of microbial deep spoilage in Iberian dry-cured ham.

PubMed

Martín, Alberto; Benito, María J; Aranda, Emilio; Ruiz-Moyano, Santiago; Córdoba, Juan J; Córdoba, María G

2010-08-01

In the present study, volatile compounds of spoiled dry-cured Iberian ham with deep spoilage or "bone taint" were analyzed and correlated with level of spoilage and the microorganisms detected. Volatile compounds extracted by a solid phase micro-extraction technique were assayed by gas chromatography/mass spectrometry. The spoiled hams were evaluated sensorially, and the correlations among volatile compounds, spoilage level, and microbial counts were studied. The spoiled hams had higher concentrations of hydrocarbons, alcohols, acids, esters, pyrazines, sulfur compounds, and other minor volatile compounds than unspoiled hams. The sensorial analysis showed that the spoilage level of hams correlated with several volatile compounds, most of them associated with Gram-positive catalase positive cocci and Enterobacteriaceae counts. Cyclic compounds such as cyclohexanone, some ethers, and pyrazines should be considered as indicators to monitor incipient microbial deep spoilage in the elaboration of this meat product.

Cavity Forming Pneumonia Due to Staphylococcus aureus Following Dengue Fever.

PubMed

Miyata, Nobuyuki; Yoshimura, Yukihiro; Tachikawa, Natsuo; Amano, Yuichiro; Sakamoto, Yohei; Kosuge, Youko

2015-11-01

While visiting Malaysia, a 22-year-old previously healthy Japanese man developed myalgia, headache, and fever, leading to a diagnosis of classical dengue fever. After improvement and returning to Japan after a five day hospitalization, he developed productive cough several days after defervescing from dengue. Computed tomography (CT) thorax scan showed multiple lung cavities. A sputum smear revealed leukocytes with phagocytized gram-positive cocci in clusters, and grew an isolate Staphylococcus aureus sensitive to semi-synthetic penicillin; he was treated successfully with ceftriaxone and cephalexin. This second reported case of pneumonia due to S. aureus occurring after dengue fever, was associated both with nosocomial exposure and might have been associated with dengue-associated immunosuppression. Clinicians should pay systematic attention to bacterial pneumonia following dengue fever to establish whether such a connection is causally associated. © The American Society of Tropical Medicine and Hygiene.

Effects of soils and grazing on breeding birds of uncultivated upland grasslands of the Northern Great Plains

USGS Publications Warehouse

Kantrud, H.A.; Kologiski, R.L.

1982-01-01

The principal use of uncultivated upland grasslands in the northern Great Plains is for livestock production. However, on lands set aside for wildlife or for scientific or recreational use, grazing by livestock may be used as a management measure to enhance populations of game species or to create conditions that increase the diversity of plant or animal species. To determine the effects of grazing on the avifauna of various types of Great Plains grasslands, we conducted bird censuses and plant surveys during 1974-78 on 615 plots of lightly, moderately, or heavily grazed native rangeland.Numbers of horned lark (Eremophila alpestris), western meadowlark (Sturnella neglecta), lark bunting (Calamospiza melanocorys), and chestnut-collared longspur (Calcarius ornatus) accounted for 65-75% of the total bird population, regardless of grazing intensity. For the entire area sampled (600,000 km2), horned lark, western meadowlark, and chestnut-collared longspur were the dominant birds. Major differences in composition of the dominant species and species richness occurred among the major soils. Increased mean annual soil temperature seemingly had a greater negative influence on avian species richness than did decreased soil moisture or organic matter content. Differences in total bird density were not significant among soils and among grazing intensities within most soils. For the area as a whole, light or moderate grazing resulted in increased species richness. Of the 29 species studied, 2 responded significantly to grazing for the area as a whole and 6 others to grazing on the soil in which peak densities occurred. Response of several other species to grazing effects evidently varied among strata.A list of plants with mean cover values of more than 1% in any of the 18 combinations of soils and grazing intensities contained less than 25 species, attesting to the relative simplicity of the grassland vegetation in the northern Great Plains. Agropyron spp. and Bouteloua gracilis were the dominant plants that provided greater than average cover on the best habitat for the most bird species. Optimum habitat for each bird species is given in terms of grazing, soils, and dominant plant species. Increased soil temperature probably had a negative effect on plant species richness, especially among soils with a high organic matter content that supported perennial grasses and other mesophytes.

Microbial diversity within Juan de Fuca ridge basement fluids sampled from oceanic borehole observatories

NASA Astrophysics Data System (ADS)

Jungbluth, S.; Bowers, R.; Lin, H.; Hsieh, C.; Cowen, J. P.; Rappé, M.

2012-12-01

Three generations of sampling and instrumentation platforms known as Circulation Obviation Retrofit Kit (CORK) observatories affixed to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) boreholes are providing unrivaled access to fluids originating from 1.2-3.5 million-years (Myr) old basaltic crust of the eastern flank of the Juan de Fuca ridge. Borehole fluid samples obtained via a custom seafloor fluid pumping and sampling system coupled to CORK continuous fluid delivery lines are yielding critical insights into the biogeochemistry and nature of microbial life inhabiting the sediment-covered basement environment. Direct microscopic enumeration revealed microbial cell abundances that are 2-41% of overlying bottom seawater. Snapshots of basement fluid microbial diversity and community structure have been obtained through small subunit ribosomal RNA (SSU rRNA) gene cloning and sequencing from five boreholes that access a range of basement ages and temperatures at the sediment-basement interface. SSU rRNA gene clones were derived from four different CORK installations (1026B, 1301A, 1362A, and 1362B) accessing relatively warmer (65°C) and older (3.5 Myr) ridge flank, and one location (1025C) accessing relatively cooler (39°C) and younger (1.2 Myr) ridge flank, revealing that warmer basement fluids had higher microbial diversity. A sampling time-series collected from borehole 1301A has revealed a microbial community that is temporally variable, with the dominant lineages changing between years. Each of the five boreholes sampled contained a unique microbial assemblage, however, common members are found from both cultivated and uncultivated lineages within the archaeal and bacterial domains, including meso- and thermophilic microbial lineages involved with sulfur cycling (e.g Thiomicrospira, Sulfurimonas, Desulfocapsa, Desulfobulbus). In addition, borehole fluid environmental gene clones were also closely related to uncultivated lineages recovered from both terrestrial and marine hydrothermal systems (e.g. Candidatus Desulforudis, Candidate Phylum OP8) as well as globally distributed marine sediments (e.g. Miscellaneous Crenarchaeotic Group, JTB35). This analysis provides a framework for future research investigating the evolutionary and functional diversity, population genetics, and activity of the poorly understood habitat. These ongoing sampling expeditions greatly benefit from improvements to both CORK observatories and evolving sampling equipment including microbiologically-friendly materials and dependable access to pristine fluids from the ocean crust.

In situ Culturing with Isolation-chip Technology in Hydrogeothermal Springs

NASA Astrophysics Data System (ADS)

Cantrell, T.; Sutton, S. A.; Tan, G.; Duca, Z. A.; Balayan, V.; Rajesh, N.; Rennie, V.; Haneda, S.; Matsuura, K.; Thiel, V.; Stockton, A. M.

2017-12-01

An estimated 99% of the world's microbial species are uncultivable by traditional laboratory procedures; however, when microbes can be cultured, valuable phenotypic, metabolic and extracellular information can be attained due to increased sample mass and purity [1,2]. Recent attempts to culture the uncultivable microbial "dark matter" have included co-culturing and culturing in situ [3,4]. An emerging microfluidic in situ culturing platform, the isolation chip (iChip), is based on agarose gel microbial trapping. Samples are taken, diluted and inoculated into the agarose matrix, and followed by emplacement back in the site of origin, where nutrients are accessible from the environment. We tested these devices in hydrothermal fields in 2015 in Iceland, followed by additional field campaigns in Japan and Iceland in 2016. The Japan field campaign, described here, was conducted in the Japanese Alps in the Negano prefecture. The site was monitored over a ten-day period, during which temperature, conductivity and dissolved oxygen were recorded. Fluorescent confocal microscopy was used to visualize the morphologies of 56 sample plugs. A majority of the growth occurred within 50 microns of the plug surface, and a majority of the observed morphologies were documented. Amplification and sequencing of the 16s rRNA region (V3-V4) indicated that of the 26 samples selected, 4 samples were isolated extremophile monocultures. Two members of the genus Anoxybacillus were identified in a chip which had incubated under green mats and in high levels of dissolved oxygen in the bulk fluid, which may indicate culturing selectivity. This work represents the novel application of an emerging microfluidic technology to provide pure monoclonal samples of extremophile organisms, potentially enabling study via molecular techniques that would otherwise be inaccessible. [1] Amador, E. S. et al. Planetary and Space Science 106, 1-10, doi:10.1016/j.pss.2014.11.006 (2015). [2] Lombard, N., Prestat, E., van Elsas, J. D. & Simonet, P. FEMS Microbiol. Ecol. 78, 31-49, doi:10.1111/j.1574-6941.2011.01140.x (2011). [3] Epstein, S. S. Curr. Opin. Microbiol. 16, 636-642, doi:10.1016/j.mib.2013.08.003 (2013). [4] Stewart, E. J. J. Bacteriol. 194, 4151-4160, doi:10.1128/jb.00345-12 (2012).

Vadose zone processes delay groundwater nitrate reduction response to BMP implementation as observed in paired cultivated vs. uncultivated potato rotation fields

NASA Astrophysics Data System (ADS)

Jiang, Y.; Nyiraneza, J.; Murray, B. J.; Chapman, S.; Malenica, A.; Parker, B.

2017-12-01

Nitrate leaching from crop production contributes to groundwater contamination and subsequent eutrophication of the receiving surface water. A study was conducted in a 7-ha potato-grain-forages rotation field in Prince Edward Island (PEI), Canada during 2011-2016 to link potato rotation practices and groundwater quality. The field consists of fine sandy loam soil and is underlain by 7-9 m of glacial till, which overlies the regional fractured ;red-bed; sandstone aquifer. The water table is generally located in overburden close to the bedrock interface. Field treatments included one field zone taken out of production in 2011 with the remaining zones kept under a conventional potato rotation. Agronomy data including crop tissue, soil, and tile-drain water quality were collected. Hydrogeology data including multilevel monitoring of groundwater nitrate and hydraulic head and data from rock coring for nitrate distribution in overburden and bedrock matrix were also collected. A significant amount of nitrate leached below the soil profile after potato plant kill (referred to as topkill) in 2011, most of it from fertilizer N. A high level of nitrate was also detected in the till vadose zone through coring in December 2012 and through multilevel groundwater sampling from January to May 2014 in both cultivated and uncultivated field zones. Groundwater nitrate concentrations increased for about 2.5 years after the overlying potato field was removed from production. Pressure-driven uniform flow processes dominate water and nitrate transport in the vadose zone, producing an apparently instant water table response but a delayed groundwater quality response to nitrate leaching events. These data suggest that the uniform flow dominated vadose zone in agricultural landscapes can cause the accumulation of a significant amount of nitrate originated from previous farming activities, and the long travel time of this legacy nitrate in the vadose zone can result in substantially delayed responses of groundwater quality to field management adjustments. The delayed effects should also apply to the transport of other contaminants. This study also suggests that management practices should be optimized to reduce soil nitrate build-up during the non-growing season (when plant N uptake is diminishing and the soil contains excessive moisture, for example, after the potato harvest period in PEI) in order to protect groundwater quality.

Organic matter and soil structure in the Everglades Agricultural Area

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

Wright, Alan L.; Hanlon, Edward A.

This publication pertains to management of organic soils (Histosols) in the Everglades Agricultural Area (EAA). These former wetland soils are a major resource for efficient agricultural production and are important globally for their high organic matter content. Recognition of global warming has led to considerable interest in soils as a repository for carbon. Soils rich in organic matter essentially sequester or retain carbon in the profile and can contribute directly to keeping that sequestered carbon from entering the atmosphere. Identification and utilization of management practices that minimize the loss of carbon from organic soils to the atmosphere can minimize effectsmore » on global warming and increase the longevity of subsiding Histosols for agricultural use. Understanding and predicting how these muck soils will respond to current and changing land uses will help to manage soil carbon. The objectives of this document are to: a. Discuss organic soil oxidation relative to storing or releasing carbon and nitrogen b. Evaluate effects of cultivation (compare structure for sugarcane vs. uncultivated soil) Based upon the findings from the land-use comparison (sugarcane or uncultivated), organic carbon was higher with cultivation in the lower depths. There is considerable potential for minimum tillage and residue management to further enhance carbon sequestration in the sugarcane system. Carbon sequestration is improved and soil subsidence is slowed with sugarcane production, and both of these are positive outcomes. Taking action to increase or maintain carbon sequestration appears to be appropriate but may introduce some risk to farming operations. Additional management methods are needed to reduce this risk. For both the longevity of these organic soils and from a global perspective, slowing subsidence through BMP implementation makes sense. Since these BMPs also have considerable societal benefit, it remains to be seen if society will help to offset a part or all of the additional risk through some form of cost-sharing program or carbon credits trading. In general, the subsidence throughout the EAA has been slowed because of higher water table management and implementation of other selected BMPs. In addition, the comparison of soil with different land uses shows that the humification rate, conversion of organic matter from peat to humus, has changed. Another likely factor is a relative increase in the mineral content of soil as the organic constituents are lost through subsidence.« less

Biofuels on the landscape: Is "land sharing" preferable to "land sparing"?

NASA Astrophysics Data System (ADS)

DeLucia, E. H.; Anderson-Teixeira, K. J.; Duval, B. D.; Long, S. P.

2012-12-01

Widespread land use changes—and ensuing effects on biodiversity and ecosystem services—are expected as a result of expanding bioenergy production. Although almost all US production of ethanol today is from corn, it is envisaged that future ethanol production will also draw from cellulosic sources such as perennial grasses. In selecting optimal bioenergy crops, there is debate as to whether it is preferable from an environmental standpoint to cultivate bioenergy crops with high ecosystem services (a "land sharing" strategy) or to grow crops with lower ecosystem services but higher yield, thereby requiring less land to meet bioenergy demand (a "land sparing" strategy). Here, we develop a simple model to address this question. Assuming that bioenergy crops are competing with uncultivated land, our model calculates land requirements to meet a given bioenergy demand intensity based upon the yields of bioenergy crops and combines fractional land cover of each ecosystem type with its associated ecosystem services to determine whether land sharing or land sparing strategies maximize ecosystem services at the landscape level. We apply this model to a case in which climate protection through GHG regulation—an ecosystem's greenhouse gas value (GHGV)—is the ecosystem service of interest. We consider five bioenergy crops competing for land area with five unfarmed ecosystem types in the central and eastern US. Our results show that the relative advantages of land sparing and land sharing depend upon the type of ecosystem with which the bioenergy crop is competing for land; as the GHGV value of the unfarmed land increases, the preferable strategy shifts from land sharing to land sparing. This implies that, while it may be preferable to replace ecologically degraded land with high-GHGV, lower yielding bioenergy crops, average landscape GHGV will most often be maximized through high yielding bioenergy crops that leave more land for uncultivated, high-GHGV ecosystems. While our case study focuses on GHGV, the same principles will be generally applicable to any ecosystem service whose value does not depend upon the spatial configuration of the landscape. Whenever bioenergy crops have substantially lower ecosystem services than the ecosystems with which they are competing for land, the most effective strategy for meeting bioenergy demand while maximizing ecosystem services on a landscape level is one of land sparing—that is, focusing simultaneously on maximizing the yield of bioenergy crops while preserving or restoring natural ecosystems.

Radiation resistence of microorganisms from radiation sterilization processing environments

NASA Astrophysics Data System (ADS)

Sabovljev, Svetlana A.; Žunić, Zora S.

The radiation resistance of microorganisms was examined on the samples of dust collected from the radiation sterilization processing environments including assembly, storage, and sterilization plant areas. The isolation of radiation resistant strains was performed by irradiation with screening doses ranging from 10 to 35 kGy and test pieces containing 10 6 to 10 8 CFU in dried serum-broth, representing 100 to 5000 colonies of primary cultures of microorganisms from 7 different sites. In an examination of 16900 colonies of aerobic microorganisms from 3 hygienically controlled production sites and 4 uncontrolled ones, 30 strains of bacteria were isolated. Of those 15 were classified as genus Bacillus, 9 as Micrococcus and 6 as Sarcina. All of the 15 strains of Gram positive sporeforming aerobic rods exhibited an exponential decrease in the surviving fraction as a function of dose, indicating that the inactivation of spores of aerobic rods is a consequence of a single energy deposition into the target. All strains were found to be moderately resistant to radiation with D-6 values (dose required to reduce survival to 6 log cycles) between 18 and 26 kGy. All of the isolated Gram positive cocci showed inactivation curves having a shoulder, indicating that different processes are involved in the inactivation of these cells, e.g. accumulation of sublethal lesions, or final repair capacity of potential lethal lesions. Moderate radiation resistance was observed in 13 strains with D-6 values between 16 to 30 kGy. Two slow-growing, red pigmented strains tentatively classified as genus Micrococcus isolated from uncontrolled sites (human dwellings) were exceptionally resistant with D-6 more than 45 kGy. For hygienically controlled sites, Gram positive spereforming rods composed two thirds of the resistant microflora, while Gram positive cocci comprised one third. For hygienically uncontrolled sites this ratio was reversed. An assumption is made that one isolated strain has grown up from one CFU in the original microflora. In the light of the observed proportion of radiation resistant bacteria in microflora from hygienically controlled radiation sterilization processing environments, and assuming an initial contamination of 50 CFU per product unit, there is no more than one chance of a contaminated item remaining within a population of 10 7 items subjected to sterilization by exposure to a radiation dose of 25 kGy.

X-Ray Absorption Spectroscopy As a Probe of Microbial Sulfur Biochemistry: the Nature of Bacterial Sulfur Globules Revisited

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

George, G.N.; Gnida, M.; Bazylinski, D.A.

2009-05-18

The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions andmore » that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question--the chemical nature of bacterial sulfur. We examine isolated sulfur globules of Allochromatium vinosum and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S{sub 8}.« less

Targeted thermal therapy with genetically engineered magnetite magnetosomes@RGD: Photothermia is far more efficient than magnetic hyperthermia.

PubMed

Plan Sangnier, Anouchka; Preveral, Sandra; Curcio, Alberto; K A Silva, Amanda; Lefèvre, Chistopher T; Pignol, David; Lalatonne, Yoann; Wilhelm, Claire

2018-06-10

Providing appropriate means for heat generation by low intratumoral nanoparticle concentrations is a major challenge for cancer nanotherapy. Here we propose RGD-tagged magnetosomes (magnetosomes@RGD) as a biogenic, genetically engineered, inorganic platform for multivalent thermal cancer treatment. Magnetosomes@RGD are biomagnetite nanoparticles synthesized by genetically modified magnetotactic bacteria thanks to a translational fusion of the RGD peptide with the magnetosomal protein MamC. Magnetosomes@RGD thus combine the high crystallinity of their magnetite core with efficient surface functionalization. The specific affinity of RGD was first quantified by single-cell magnetophoresis with a variety of cell types, including immune, muscle, endothelial, stem and cancer cells. The highest affinity and cellular uptake was observed with PC3 prostatic and HeLa uterine cancer cells. The efficiency of photothermia and magnetic hyperthermia was then compared on PC3 cells. Unexpectedly, photothermia was far more efficient than magnetic hyperthermia, which was almost totally inhibited by the cellular environment. RGD targeting was then assessed in vivo at tumor site, in mice bearing PC3 tumors. As a result, we demonstrate that targeted magnetic nanoparticles could generate heat on a therapeutic level after systemic administration, but only under laser excitation, and successfully inhibit tumor progression. Copyright © 2018 Elsevier B.V. All rights reserved.

Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

DOE PAGES

Zhang, Honghu; Liu, Xunpei; Feng, Shuren; ...

2015-02-10

In this study, magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence ofmore » hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.« less

Exposure of magnetic bacteria to simulated mobile phone-type RF radiation has no impact on mortality.

PubMed

Cranfield, Charles G; Wieser, Heinz Gregor; Dobson, Jon

2003-09-01

The interaction of mobile phone RF emissions with biogenic magnetite in the human brain has been proposed as a potential mechanism for mobile phone bioeffects. This is of particular interest in light of the discovery of magnetite in human brain tissue. Previous experiments using magnetite-containing bacteria exposed directly to emissions from a mobile phone have indicated that these emissions might be causing greater levels of cell death in these bacterial populations when compared to sham exposures. A repeat of these experiments examining only the radio frequency (RF) global system for mobile communication (GSM) component of the mobile phone signal in a well-defined waveguide system (REFLEX), shows no significant change in cell mortality compared to sham exposures. A nonmagnetite containing bacterial cell strain (CC-26) with similar genotype and phenotype to the magnetotactic bacteria was used as a control. These also showed no significant change in cell mortality between RF and sham exposed samples. Results indicate that the RF components of mobile phone exposure do not appear to be responsible for previous findings indicating cell mortality as a result of direct mobile phone exposure. A further mobile phone emission component that should be investigated is the 2-Hz magnetic field pulse generated by battery currents during periods of discontinuous transmission.

Microeukaryotic diversity in marine environments, an analysis of surface layer sediments from the East Sea.

PubMed

Park, Soo-Je; Park, Byoung-Joon; Pham, Vinh Hoa; Yoon, Dae-No; Kim, Si-Kwan; Rhee, Sung-Keun

2008-06-01

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.

Morphology as a basis for taxonomy of large spirochetes symbiotic in wood-eating cockroaches and termites: Pillotina gen. nov., nom. rev.; Pillotina calotermitidis sp. nov., nom. rev.; Diplocalyx gen. nov., nom. rev.; Diplocalyx calotermitidis sp. nov., nom. rev.; Hollandina gen. nov., nom.[TRUNCATED

NASA Technical Reports Server (NTRS)

Bermudes, D.; Chase, D.; Margulis, L.

1988-01-01

The purposes of this paper are (i) to present a framework for the morphometric analysis of large uncultivable spirochetes that are symbiotic in wood-eating cockroaches and termites; (ii) to revive, in accordance with the rules of the International Code of Nomenclature of Bacteria, the names of three genera (Pillotina, Diplocalyx, and Hollandina) and three species (Pillotina calotermitidis, Diplocalyx calotermitidis, and Hollandina pterotermitidis) for the same organisms to which the names were originally applied, because these names were not included on the 1980 Approved Lists of Bacterial Names; and (iii) to formally propose the name Clevelandina reticulitermitidis for a new genus and species of spirochetes from the termite Reticulitermes tibialis. None of these genera and species has been cultivated either axenically or in mixed culture; hence, all are based on type-descriptive material.

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE PAGES

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG; ...

2012-11-29

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

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

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Environmental Behavior of Chlorpyrifos and Endosulfan in a Tropical Soil in Central Brazil.

PubMed

Dores, Eliana F G C; Spadotto, Claudio A; Weber, Oscarlina L S; Dalla Villa, Ricardo; Vecchiato, Antonio B; Pinto, Alicio A

2016-05-25

The environmental behavior of chlorpyrifos and endosulfan in soil was studied in the central-western region of Brazil by means of a field experiment. Sorption was evaluated in laboratory batch experiments. Chlorpyrifos and endosulfan were applied to experimental plots on uncultivated soil and the following processes were studied: leaching, runoff, and dissipation in top soil. Field dissipation of chlorpyrifos and endosulfan was more rapid than reported in temperate climates. Despite the high Koc of the studied pesticides, the two endosulfan isomers and endosulfan sulfate as well as chlorpyrifos were detected in percolated water. In runoff water and sediment, both endosulfan isomers and endosulfan sulfate were detected throughout the period of study. Observed losses of endosulfan by leaching (below a depth of 50 cm) and runoff were 0.0013 and 1.04% of the applied amount, whereas chlorpyrifos losses were 0.003 and 0.032%, respectively. Leaching of these highly adsorbed pesticides was attributed to preferential flow.

Factors affecting HCH and DDT in soils around watersheds of Beijing reservoirs, China.

PubMed

Hu, Wenyou; Lu, Yonglong; Wang, Tieyu; Luo, Wei; Zhang, Xiang; Geng, Jing; Wang, Guang; Shi, Yajuan; Jiao, Wentao; Chen, Chunli

2010-04-01

The factors that influence the dynamics of hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) in soils around the watersheds of Beijing reservoirs were examined. Compared with other studies on HCH and DDT in soils and established reference values, the concentrations of HCH and DDT in soils around our study area were relatively low. The relationships between HCH and DDT concentrations and land use, soil texture, and soil properties were discussed. HCH and DDT concentrations were higher in arable soils than those in uncultivated fallow soils. Although land use was the most important factor affecting HCH and DDT residues, additional factors such as soil texture and soil total organic carbon were also involved in pesticide retention in soils. The results indicated that the historical agricultural applications of HCH and DDT were the major source of their residues. Atmospheric deposition, as well as long-distance transportation and inputs from surrounding weathered agricultural soils may also serve as important sources of HCH and DDT residues in the watersheds.

Case Report: Molecular Confirmation of Lobomycosis in an Italian Traveler Acquired in the Amazon Region of Venezuela.

PubMed

Beltrame, Anna; Danesi, Patrizia; Farina, Claudio; Orza, Pierantonio; Perandin, Francesca; Zanardello, Claudia; Rodari, Paola; Staffolani, Silvia; Bisoffi, Zeno

2017-12-01

Lobomycosis is a chronic skin mycosis endemic in Amazon regions characterized by chronic nodular or keloidal lesions caused by Lacazia loboi , an uncultivable fungus. Imported cases in nonendemic countries are rare and diagnosed after years. We describe a case of lobomycosis in a healthy 55-year-old Italian traveler who had acquired the infection during 5-day-honeymoon in the Amazon region of Venezuela in 1999. Several weeks after return, he recalled pruritus and papular skin lesions on the left lower limb, subsequently evolving to a plaque-like lesion. Blastomycosis and cryptococcosis were hypothesized based on microscopic morphology of yeast-like bodies found in three consecutive biopsies, although fungal cultures were always negative. In 2016, exfoliative cytology and a biopsy specimen examination showed round yeast-like organisms (6-12 μm), isolated or in a chain, connected by short tubular projections fulfilling the morphologic diagnostic criteria of Lacazia spp. The microscopic diagnosis was confirmed by molecular identification.

Horizontal transfer of potential mobile units in phytoplasmas

PubMed Central

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2013-01-01

Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches’ broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution. PMID:24251068

Applicability of 239Pu as a tracer for soil erosion in the wet-dry tropics of northern Australia

NASA Astrophysics Data System (ADS)

Lal, R.; Tims, S. G.; Fifield, L. K.; Wasson, R. J.; Howe, D.

2013-01-01

The technique of accelerator mass spectroscopy (AMS) has been employed to determine modern soil loss rates through the analysis of 239Pu profiles in soil cores from the Daly basin in Northern Territory, Australia. In areas in which soil conservation banks were not present or were only added recently (<25a) and which had a history of grazing and cultivation the measured soil loss rates over the past ∼50 years were 7.5-19.5 t ha-1 a-1. The measured rates are up to 5 times higher compared to agricultural and uncultivated areas within soil conservation banks in other parts of the catchment. High intensity seasonal rainfall combined with reduction in land cover due to grazing and episodic bush fires are primary factors influencing erosion although other impacts on the landscape such as tillage generated runoff and land clearing seem to be responsible for accelerated sediment production.

Reduced body condition and enzymatic alterations in frogs inhabiting intensive crop production areas.

PubMed

Brodeur, Julie C; Suarez, Romina P; Natale, Guillermo S; Ronco, Alicia E; Elena Zaccagnini, Maria

2011-07-01

Parameters indicative of general condition and health were compared amongst adult frogs inhabiting uncultivated lands and fields subjected to agricultural practices typical of the humid pampas of Argentina. Whereas no significant differences existed in the parasite load and external malformations prevalence rate of adult frogs from either environments, a reduced condition factor was clearly demonstrated in frogs from agricultural lands. This conclusion was reached for four frog species of different life habits: the terrestrial fossorial Rhinella fernandezae, the terrestrial Leptodactylus latinasus, the semi-aquatic Leptodactylus ocellatus, and the arborescent Hypsiboas pulchellus. A distinct pattern of enzymatic modifications was furthermore observed in L. ocellatus and H. pulchellus from agricultural lands, including elevated hepatic activities of catalase and cholinesterase, and an inhibition of liver GST activity. Further studies should investigate the causes and consequences of the systematically low condition factor observed in frogs from agricultural fields of the humid pampas of Argentina. Copyright © 2011 Elsevier Inc. All rights reserved.

Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method.

PubMed

Sharma, Nandita; Tanksale, Himgouri; Kapley, Atya; Purohit, Hemant J

2012-12-01

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.

An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease.

PubMed

Fettweis, Jennifer M; Serrano, Myrna G; Huang, Bernice; Brooks, J Paul; Glascock, Abigail L; Sheth, Nihar U; Strauss, Jerome F; Jefferson, Kimberly K; Buck, Gregory A

2014-01-01

Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly associated with trichomoniasis that was previously known by its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease. The genomes of four strains of this species were reconstructed using metagenome sequencing and assembly of DNA from four discrete mid-vaginal samples, one of which was obtained from a pregnant woman with trichomoniasis who delivered prematurely. These bacteria harbor several putative virulence factors and display unique metabolic strategies. Genes encoding proteins with high similarity to potential virulence factors include two collagenases, a hemolysin, an O-sialoglycoprotein endopeptidase and a feoB-type ferrous iron transport system. We propose the name "Candidatus Mycoplasma girerdii" for this potential new pathogen.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

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

Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.

The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here, we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning amore » single sample as well as comparing the microbial community composition between different sampling environments. Availability and implementation: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license. Supplementary information: Supplementary data are available at Bioinformatics online.« less

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

PubMed Central

Dodsworth, Jeremy A.; Blainey, Paul C.; Murugapiran, Senthil K.; Swingley, Wesley D.; Ross, Christian A.; Tringe, Susannah G.; Chain, Patrick S. G.; Scholz, Matthew B.; Lo, Chien-Chi; Raymond, Jason; Quake, Stephen R.; Hedlund, Brian P.

2013-01-01

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters, and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly-complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden-Meyerhof glycolysis with production of hydrogen, acetate, and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’. PMID:23673639

Dereplication, Aggregation and Scoring Tool (DAS Tool) v1.0

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

SIEBER, CHRISTIAN

Communities of uncultivated microbes are critical to ecosystem function and microorganism health, and a key objective of metagenomic studies is to analyze organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of genes to genomes, yet existing binning methods often fail to predict a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotypes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tools applied to a constructedmore » community generated more accurate bins than any automated method. Further, when applied to samples of different complexity, including soil, natural oil seeps, and the human gut, DAS Tool recovered substantially more near-complete genomes than any single binning method alone. Included were three genomes from a novel lineage . The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.« less

A rain splash transport equation assimilating field and laboratory measurements

USGS Publications Warehouse

Dunne, T.; Malmon, D.V.; Mudd, S.M.

2010-01-01

Process-based models of hillslope evolution require transport equations relating sediment flux to its major controls. An equation for rain splash transport in the absence of overland flow was constructed by modifying an approach developed by Reeve (1982) and parameterizing it with measurements from single-drop laboratory experiments and simulated rainfall on a grassland in East Africa. The equation relates rain splash to hillslope gradient, the median raindrop diameter of a storm, and ground cover density; the effect of soil texture on detachability can be incorporated from other published results. The spatial and temporal applicability of such an equation for rain splash transport in the absence of overland flow on uncultivated hillslopes can be estimated from hydrological calculations. The predicted transport is lower than landscape-averaged geologic erosion rates from Kenya but is large enough to modify short, slowly eroding natural hillslopes as well as microtopographic interrill surfaces between which overland flow transports the mobilized sediment. Copyright 2010 by the American Geophysical Union. Copyright 2010 by the American Geophysical Union.

Horizontal transfer of potential mobile units in phytoplasmas.

PubMed

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2013-09-01

Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches' broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution.

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance.

PubMed

Nakagawa, Satoshi; Takai, Ken

2008-07-01

Deep-sea vents support productive ecosystems driven primarily by chemoautotrophs. Chemoautotrophs are organisms that are able to fix inorganic carbon using a chemical energy obtained through the oxidation of reduced compounds. Following the discovery of deep-sea vent ecosystems in 1977, there has been an increasing knowledge that deep-sea vent chemoautotrophs display remarkable physiological and phylogenetic diversity. Cultivation-dependent and -independent studies have led to an emerging view that the majority of deep-sea vent chemoautotrophs have the ability to derive energy from a variety of redox couples other than the conventional sulfur-oxygen couple, and fix inorganic carbon via the reductive tricarboxylic acid cycle. In addition, recent genomic, metagenomic and postgenomic studies have considerably accelerated the comprehensive understanding of molecular mechanisms of deep-sea vent chemoautotrophy, even in yet uncultivable endosymbionts of vent fauna. Genomic analysis also suggested that there are previously unrecognized evolutionary links between deep-sea vent chemoautotrophs and important human/animal pathogens. This review summarizes chemoautotrophy in deep-sea vents, highlighting recent biochemical and genomic discoveries.

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

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1.

PubMed

Charpentier, Elena; Garnaud, Cécile; Wintenberger, Claire; Bailly, Sébastien; Murat, Jean-Benjamin; Rendu, John; Pavese, Patricia; Drouet, Thibault; Augier, Caroline; Malvezzi, Paolo; Thiébaut-Bertrand, Anne; Mallaret, Marie-Reine; Epaulard, Olivier; Cornet, Muriel; Larrat, Sylvie; Maubon, Danièle

2017-08-01

Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus.

Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1

PubMed Central

Charpentier, Elena; Garnaud, Cécile; Wintenberger, Claire; Bailly, Sébastien; Murat, Jean-Benjamin; Rendu, John; Pavese, Patricia; Drouet, Thibault; Augier, Caroline; Malvezzi, Paolo; Thiébaut-Bertrand, Anne; Mallaret, Marie-Reine; Epaulard, Olivier; Cornet, Muriel; Larrat, Sylvie

2017-01-01

Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus. PMID:28726611

Geometeorological data collected by the USGS Desert Winds Project at Gold Spring, Great Basin desert, northeastern Arizona, 1979-1992

USGS Publications Warehouse

Helm, P.J.; Breed, C.S.; Tigges, R.K.; Garcia, P.A.

1995-01-01

The primary purpose of the Desert Winds Project (DWP) is to obtain high-resolution meteorological data and related surface geological and vegetation data for natural (e.g., uncultivated) desert sites where wind is or has been a major erosive or depositional force. The objectives are twofold: (1) to provide the detailed field measurements needed to carry out quantitative studies of wind as an agent of surface geologic change; and (2) to establish a baseline for defining the 'normal' range of climatic conditions that can be expected to occur on a decadal time scale, in areas considered representative of the major American deserts. The Gold Spring locality was selected to represent that part of the Great Basin Desert that extends into northeastern Arizona. The long-term goal for acquiring and analyzing the Desert Winds Project data is to use them to address problems of land resource degradation by wind, whether resulting from climatic variation aridification) or human activities (desertification), or both (see techinfo.doc).

Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws

PubMed Central

Šmajs, David; Norris, Steven J.; Weinstock, George M.

2013-01-01

Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, T. paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections. PMID:22198325

Demonstration of bacterial biofilms in culture-negative silicone stent and jones tube.

PubMed

Parsa, Kami; Schaudinn, Christoph; Gorur, Amita; Sedghizadeh, Parish P; Johnson, Thomas; Tse, David T; Costerton, John W

2010-01-01

To demonstrate the presence of bacterial biofilms on a dacryocystorhinostomy silicone stent and a Jones tube. One dacryocystorhinostomy silicone stent and one Jones tube were removed from 2 patients who presented with an infection of their respective nasolacrimal system. Cultures were obtained, and the implants were processed for scanning electron microscopy and confocal laser scanning microscopy, advanced microscopic methods that are applicable for detection of uncultivable biofilm organisms. Routine bacterial cultures revealed no growth, but bacterial biofilms on outer and inner surfaces of both implants were confirmed by advanced microscopic techniques. To the authors' knowledge, this is the first article that documents the presence of biofilms on a Crawford stent or a Jones tube on patients who presented with infections involving the nasolacrimal system. Although initial cultures revealed absence of any bacterial growth, confocal laser scanning microscopy and scanning electron microscopy documented bacterial colonization. Clinicians should consider the role of biofilms and the limitation of our standard culturing techniques while treating patients with device- or implant-related infections.

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

PubMed

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

2014-02-01

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

Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations

PubMed Central

Hall, Jane; Thompson, Paul; Eden, John-Sebastian; Srivastava, Mukesh; Tiernan, Brendan; Jenkins, Cheryl; Phalen, David

2017-01-01

Multisystemic infections with a morphologically unusual bacterium were first observed in captive critically endangered Lister’s geckos (Lepidodactylus listeri) on Christmas Island in October 2014. Since then the infection was identified in another captive critically endangered lizard species, the blue-tailed skink (Cryptoblepharus egeriae) and two species of invasive geckos; the four clawed gecko (Gehyra mutilata) and Asian house gecko (Hemidactylus frenatus), in a wide geographic range across the east side of the island. The Gram and periodic acid-Schiff positive cocci to diplococci have a propensity to form chains surrounded by a matrix, which ultrastructurally appears to be formed by fibrillar capsular projections. The bacterium was associated with severe and extensive replacement of tissues, but minimal host inflammatory response. Attempts to grow the organism in culture and in embryonated eggs were unsuccessful. Molecular characterisation of the organism placed it as a novel member of the genus Enterococcus. Disease Risk Analyses including this organism should now be factored into conservation management actions and island biosecurity. PMID:28727845

Rumen Bacterial Degradation of Forage Cell Walls Investigated by Electron Microscopy

PubMed Central

Akin, Danny E.; Amos, Henry E.

1975-01-01

The association of rumen bacteria with specific leaf tissues of the forage grass Kentucky-31 tall fescue (Festuca arundinacea Schreb.) during in vitro degradation was investigated by transmission and scanning electron microscopy. Examination of degraded leaf cross-sections revealed differential rates of tissue degradation in that the cell walls of the mesophyll and pholem were degraded prior to those of the outer bundle sheath and epidermis. Rumen bacteria appeared to degrade the mesophyll, in some cases, and phloem without prior attachment to the plant cell walls. The degradation of bundle sheath and epidermal cell walls appeared to be preceded by attachment of bacteria to the plant cell wall. Ultrastructural features apparently involved in the adhesion of large cocci to plant cells were observed by transmission and scanning electron microscopy. The physical association between plant and rumen bacterial cells during degradation apparently varies with tissue types. Bacterial attachment, by extracellular features in some microorganisms, is required prior to degradation of the more resistant tissues. Images PMID:16350017

Diversity of H2/CO2-utilizing acetogenic bacteria from feces of non-methane-producing humans.

PubMed

Bernalier, A; Rochet, V; Leclerc, M; Doré, J; Pochart, P

1996-08-01

The purpose of this work was to study H2/CO2-utilizing acetogenic population in the colons of non-methane-producing individuals harboring low numbers of methanogenic archaea. Among the 50 H2-consuming acetogenic strains isolated from four fecal samples and an in vitro semi-continuous culture enrichment, with H2/CO2 as sole energy source, 20 were chosen for further studies. All isolates were Gram-positive strict anaerobes. Different morphological types were identified, providing evidence of generic diversity. All acetogenic strains characterized used H2/CO2 to form acetate as the sole metabolite, following the stoichiometric equation of reductive acetogenesis. These bacteria were also able to use a variety of organic compounds for growth. The major end product of glucose fermentation was acetate, except for strains of cocci that mainly produced lactate. Yeast extract was not necessary, but was stimulatory for growth and acetogenesis from H2/CO2.

Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

PubMed Central

Marietou, Angeliki

2014-01-01

Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. PMID:25063663

Microbiological profile of maize and rye flours, and sourdough used for the manufacture of traditional Portuguese bread.

PubMed

Rocha, João M; Malcata, F Xavier

2012-08-01

A thorough microbiological study of maize and rye flours, and sourdoughs obtained therefrom for eventual manufacture of broa--a dark sour bread typical in Northern Portugal, following artisanal practices, was carried out. Towards this purpose, samples were supplied by 14 artisanal producers, selected from 4 sub-regions, during two periods of the year. Total viable counts, as well as viable mesophilic and thermophilic microorganisms, yeasts and molds, Gram⁻ rods, endospore-forming and nonsporing Gram⁺ rods, and catalase⁺ and catalase⁻ Gram⁺ cocci were assayed for. The comprehensive experimental dataset unfolded a unique and rather complex wild microflora in flours and sourdoughs throughout the whole region, which did not discriminate among sub-regions or seasons, or flour source for that matter. However, fermentation played a major role upon the numbers of the various microbial groups: the viable counts of yeasts, lactobacilli, streptococci, lactococci, enterococci and leuconostocs increased, whereas those of molds, Enterobacteriaceae, Pseudomonadaceae, staphylococci and micrococci decreased. Copyright © 2012 Elsevier Ltd. All rights reserved.

Isolation, identification, characterization, and evaluation of cadmium removal capacity of Enterobacter species.

PubMed

Abbas, Syed Zaghum; Rafatullah, Mohd; Ismail, Norli; Lalung, Japareng

2014-12-01

This study focused on the isolation and characterization of high cadmium-resistant bacterial strains, possible exploitation of its cadmium-accumulation and cadmium-induced proteins. Cadmium-resistant bacterial strains designated as RZ1 and RZ2 were isolated from industrial wastewater of Penang, Malaysia. These isolates were identified as Enterobacter mori and Enterobacter sp. WS12 on the basis of phenotypic, biochemical and 16S rDNA sequence based molecular phylogenetic characteristics. Both isolates were Gram negative, cocci, and growing well in Lauria-Bertani broth medium at 35 °C temperature and pH 7.0. Results also indicated that Enterobacter mori and Enterobacter sp. WS12are capable to remove 87.75 and 85.11% of the cadmium from 100 µg ml(-1) concentration, respectively. This study indicates that these strains can be useful as an inexpensive and efficient bioremediation technology to remove and recover the cadmium from wastewater. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emerging Bacterial Infection: Identification and Clinical Significance of Kocuria Species

PubMed Central

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

2016-01-01

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

Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria.

PubMed

Lee, E H L; Degener, J E; Welling, G W; Veloo, A C M

2011-05-01

An evaluation of the Vitek 2 ANC card (bioMérieux, Marcy l'Etoile, France) was performed with 301 anaerobic isolates. Each strain was identified by 16S rRNA gene sequencing, which is considered to be the reference method. The Vitek 2 ANC card correctly identified 239 (79.4%) of the 301 clinical isolates to the genus level, including 100 species that were not represented in the database. Correct species identification was obtained for 60.1% (181/301) of the clinical isolates. For the isolates not identified to the species level, a correct genus identification was obtained for 47.0% of them (47/100), and 16 were accurately designated not identified. Although the Vitek 2 ANC card allows the rapid and acceptable identification of the most common clinically important anaerobic bacteria within 6 h, improvement is required for the identification of members of the genera Fusobacterium, Prevotella, and Actinomyces and certain Gram-positive anaerobic cocci (GPAC).

Gram stain microbiological pattern of upper extremities suppuration at Baptist Medical Centre, Ogbomoso Nigeria: a fifteen month review.

PubMed

Oke, A J; Olaolorun, D A; Meier, D E; Tarpley, J L

2011-06-01

Sixty-eight (68) patients with serious upper extremity suppurative infections, presenting within a period of fifteen (15) months, were prospectively studied clinically, Gram stain of aspirates/pus were performed, specimen cultured, planted, and where indicated glucose levels and haemoglobin genotype determined. Half of the patients had hand infections. Staphylococcus aureus was isolated from thirty-nine (39) patients. Gram Negative bacilli, including Salmonella were more isolated from patients with diabetes mellitus or Hgb SS or SC. The Gram stain results correlated with the culture result 90%. When Gram Positive cocci were demonstrated in the primary microscopic examination, cultures were not mandatory. When no organism was demonstrated on primary Gram stain or the patient was diabetic or a sickler, cultures of the specimens were done. The Gram stain, well performed, remains a useful, inexpensive, technologically appropriate laboratory test for abetting decision making in patients with upper extremity suppurative infections. Organisms encountered in this study included: Staphylococcus aureus, Streptococcus pyogenes, Salmonella typhi, Proteus mirabilis, Pseudomonas aeruginosa, and Coliforms.

Non-cultural methods of human microflora evaluation for the benefit of crew medical control in confined habitat

NASA Astrophysics Data System (ADS)

Viacheslav, Ilyin; Lana, Moukhamedieva; Georgy, Osipov; Aleksey, Batov; Zoya, Soloviova; Robert, Mardanov; Yana, Panina; Anna, Gegenava

2011-05-01

Current control of human microflora is a great problem not only for the space medicine but also for practical health care. Due to many reasons its realization by classical bacteriological method is difficult in practical application or cannot be done. To evaluate non-cultural methods of microbial control of crews in a confined habitat we evaluated two different methods. The first method is based on digital treatment of microbial visual images, appearing after gram staining of microbial material from natural sample. This way the rate between gram-positive and gram-negative microbe could be gained as well as differentiation of rods and cocci could be attained, which is necessary for primary evaluation of human microbial cenosis in remote confined habitats. The other non-culture method of human microflora evaluation is gas chromatomass spectrometry (gcms) analysis of swabs gathered from different body sites. Gc-ms testing of swabs allows one to validate quantitative and special microflora based on specific lipid markers analysis.

Monolateral suppurative parotitis in a neonate and review of literature.

PubMed

Decembrino, Lidia; Ruffinazzi, Giulia; Russo, Fabio; Manzoni, Paolo; Stronati, Mauro

2012-07-01

Neonatal suppurative parotitis is a rare condition characterized by swelling, pain, and erythema over the affected gland. Antimicrobials and adequate hydration are an essential part of treatment. Surgical intervention is reserved for organized abscesses and for infections not responding to medical management. A case report and review of the literature. Only few case reports and case series are reported in literature on neonatal parotitis. Transmission of bacteria seems to occur mainly by ascending spread through Stensen's duct, or by hematogenous spread from a distant focus. Dehydration, low birth weight, immune suppression, ductal obstruction, oral trauma and structural abnormalities of the parotid gland are recognised as risk factors. The most common pathogen is Staphylococcus aureus. Other less frequent agents are other Gram-positive cocci, Gram-negative bacilli and rarely anaerobic bacteria. Advances in antimicrobial therapy have improved both outcome and prognosis. Thanks to the prompt antibiotic treatment complications are now drastically reduced. Ultrasound examination may help in the diagnosis and monitoring of clinical course. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Use of PNA FISH for blood cultures growing Gram-positive cocci in chains without a concomitant antibiotic stewardship intervention does not improve time to appropriate antibiotic therapy.

PubMed

Cosgrove, Sara E; Li, David X; Tamma, Pranita D; Avdic, Edina; Hadhazy, Eric; Wakefield, Teresa; Gherna, Michael; Carroll, Karen C

2016-09-01

Peptide nucleic acid fluorescence in situ hybridization (PNA FISH) is a rapid diagnostic assay that can identify certain organisms growing in blood cultures 30-90 min from the time of positive Gram-stain. Existing studies have demonstrated a clinical utility with this assay when antibiotic stewardship programs assist clinicians with interpreting the results. However, the benefit of these rapid assays in the absence of concomitant antibiotic stewardship involvement is unclear. In this randomized study of 220 patients with enterococcal or streptococcal bacteremia, we found that PNA FISH, in the absence of concomitant input from an antibiotic stewardship program, had no impact on time to effective or optimal therapy, length of hospital stay, or in-hospital mortality. Our results suggest that in the absence of guidance from an antibiotic stewardship program, the clinical benefits of rapid diagnostic microbiological tools may be reduced. Copyright © 2016 Elsevier Inc. All rights reserved.

Conservative management of pyothorax in an Amur tiger (Panthera tigris altaica).

PubMed

Schrader, Gabby M; Whiteside, Douglas P; Slater, Owen M; Black, Sandra R

2012-06-01

Therapy for pyothorax, or pleural empyema, has not been described for large felids. This case describes the successful treatment of pyothorax in a captive, large felid. A 15-yr-old multiparous, female Amur tiger (Panthera tigris altaica) presented with nonspecific clinical signs caused by an insidious onset of pyothorax. Management of pyothorax cases in companion animals often involves thoracostomy tube placement with recurrent drainage of the pleural cavity, intensive supportive care, and monitoring. In this case, conservative management was elected because hospitalization was not a viable option. Thoracocentesis was performed to drain as much fluid from the chest cavity as possible, yielding more than 1.3 L. Corynebacterium sp. and unidentified anaerobic gram-positive cocci were cultured. Treatment included cefovecin subcutaneously, oral antibiotic therapy with clindamycin and marbofloxacin, meloxicam, and restricted exercise by minimizing access to the main exhibit. Significant improvement was noted clinically and radiographically 6 wk later, and no relapses were noted in the following weeks. An examination 11.5 mo later confirmed resolution.

A clonal outbreak of acute fatal hemorrhagic pneumonia in intensively housed (shelter) dogs caused by Streptococcus equi subsp. zooepidemicus.

PubMed

Pesavento, P A; Hurley, K F; Bannasch, M J; Artiushin, S; Timoney, J F

2008-01-01

An outbreak of acute, fatal, hemorrhagic pneumonia was observed in more than 1,000 mixed breed dogs in a single animal shelter. The Department of Anatomic Pathology at the University of California at Davis School of Veterinary Medicine performed necropsies on dogs that were found moribund in acute respiratory distress or found dead with evidence of nasal bleeding. All dogs had hemothorax and an acute, fibrinosuppurative pneumonia. Large numbers of gram-positive cocci were observed within the lungs of all dogs and within septic thromboemboli of remote organs in about 50% of cases. Bacterial cultures from the dogs and their environment revealed widespread beta-hemolytic Streptococus equi subspecies zooepidemicus (Lancefield Group C). Extensive diagnostic testing failed to reveal the consistent presence of copathogens in individual cases. The clinical, epidemiologic, molecular biologic, and pathologic data indicate that a single clone of S. zooepidemicus was the cause of an acutely fatal respiratory infection in these dogs.