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At least 289 records · Page 16Linked to original sources
USGS2005

Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt) sequences of the VHSV glycoprotein ( G ) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G -gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-length G -gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes. Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G -gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis was shown to approximate the level of genetic discrimination obtained by other, more labour-intensive, molecular techniques such as the ribonuclease protection assay or sequence analysis. In addition, 37 previously uncharacterised isolates from diverse sources were assigned to specific genotypes. While the assay was able to distinguish between marine and continental isolates of VHSV, the differences did not correlate with the pathogenicity of the isolates.

Veterinary Microbiology↗
USGS2007

Sequence analysis of the msp4 gene of Anaplasma ovis strains

Anaplasma ovis (Rickettsiales: Anaplasmataceae) is a tick-borne pathogen of sheep, goats and wild ruminants. The genetic diversity of A. ovis strains has not been well characterized due to the lack of sequence information. In this study, we evaluated bighorn sheep ( Ovis canadensis ) and mule deer (Odocoileus hemionus ) from Montana for infection with A. ovis by serology and sequence analysis of the msp4 gene. Antibodies to Anaplasma spp. were detected in 37% and 39% of bighorn sheep and mule deer analyzed, respectively. Four new msp4 genotypes were identified. The A. ovis msp4 sequences identified herein were analyzed together with sequences reported previously for the characterization of the genetic diversity of A. ovis strains in comparison with other Anaplasma spp. The results of these studies demonstrated that although A. ovis msp4 genotypes may vary among geographic regions and between sheep and deer hosts, the variation observed was less than the variation observed between A. marginale and A. phagocytophilum strains. The results reported herein further confirm that A. ovis infection occurs in natural wild ruminant populations in Western United States and that bighorn sheep and mule deer may serve as wildlife reservoirs of A. ovis . ?? 2006.

Veterinary Microbiology↗
USGS2011

Isolation of Bartonella capreoli from elk

The aim of the present study was to investigate the presence of Bartonella infections in elk populations. We report the isolation of four Bartonella strains from 55 elk blood samples. Sequencing analysis demonstrated that all four strains belong to Bartonella capreoli, a bacterium that was originally described in the wild roe deer of Europe. Our finding first time demonstrated that B. capreoli has a wide geographic range, and that elk may be another host for this bacterium. Further investigations are needed to determine the impact of this bacterium on wildlife.

Veterinary Microbiology↗
USGS2012

Viral tropism and pathology associated with viral hemorrhagic septicemia in larval and juvenile Pacific herring

Viral hemorrhagic septicemia virus (VHSV) genotype IVa causes mass mortality in wild Pacific herring, a species of economic value, in the Northeast Pacific Ocean. Young of the year herring are particularly susceptible and can be carriers of the virus. To understand its pathogenesis, tissue and cellular tropisms of VHSV in larval and juvenile Pacific herring were investigated with immunohistochemistry, transmission electron microscopy, and viral tissue titer. In larval herring, early viral tropism for epithelial tissues (6d post-exposure) was indicated by foci of epidermal thickening that contained heavy concentrations of virus. This was followed by a cellular tropism for fibroblasts within the fin bases and the dermis, but expanded to cells of the kidney, liver, pancreas, gastrointestinal tract and meninges in the brain. Among wild juvenile herring that underwent a VHS epizootic in the laboratory, the disease was characterized by acute and chronic phases of death. Fish that died during the acute phase had systemic infections in tissues including the submucosa of the gastrointestinal tract, spleen, kidney, liver, and meninges. The disease then transitioned into a chronic phase that was characterized by the appearance of neurological signs including erratic and corkscrew swimming and darkening of the dorsal skin. During the chronic phase viral persistence occurred in nervous tissues including meninges and brain parenchymal cells and in one case in peripheral nerves, while virus was mostly cleared from the other tissues. The results demonstrate the varying VHSV tropisms dependent on the timing of infection and the importance of neural tissues for the persistence and perpetuation of chronic infections in Pacific herring.

Veterinary Microbiology↗
USGS2013

Comparative analysis of Edwardsiella isolates from fish in the eastern United States identifies two distinct genetic taxa amongst organisms phenotypically classified as E. tarda

Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, has been implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of E. tarda isolates from 4 different fish species in the eastern United States. Repetitive sequence mediated PCR (rep-PCR) using 4 different primer sets (ERIC I & II, ERIC II, BOX, and GTG 5 ) and multi-locus sequence analysis of 16S SSU rDNA, groEl, gyrA, gyrB, pho, pgi, pgm, and rpoA gene fragments identified two distinct genotypes of E. tarda (DNA group I; DNA group II). Isolates that fell into DNA group II demonstrated more similarity to E. ictaluri than DNA group I, which contained the reference E. tarda strain (ATCC #15947). Conventional PCR analysis using published E. tarda-specific primer sets yielded variable results, with several primer sets producing no observable amplification of target DNA from some isolates. Fluorometric determination of G + C content demonstrated 56.4% G + C content for DNA group I, 60.2% for DNA group II, and 58.4% for E. ictaluri. Surprisingly, these isolates were indistinguishable using conventional biochemical techniques, with all isolates demonstrating phenotypic characteristics consistent with E. tarda. Analysis using two commercial test kits identified multiple phenotypes, although no single metabolic characteristic could reliably discriminate between genetic groups. Additionally, anti-microbial susceptibility and fatty acid profiles did not demonstrate remarkable differences between groups. The significant genetic variation (<90% similarity at gyrA, gyrB, pho, phi and pgm; <40% similarity by rep-PCR) between these groups suggests organisms from DNA group II may represent an unrecognized, genetically distinct taxa of Edwardsiella that is phenotypically indistinguishable from E. tarda.

Veterinary Microbiology↗
USGS2013

Experimental infection studies demonstrating Atlantic salmon as a host and reservoir of viral hemorrhagic septicemia virus type IVa with insights into pathology and host immunity

In British Columbia, Canada (BC), aquaculture of finfish in ocean netpens has the potential for pathogen transmission between wild and farmed species due to the sharing of an aquatic environment. Viral hemorrhagic septicemia virus (VHSV) is enzootic in BC and causes serious disease in wild Pacific herring, Clupea pallasii, which often enter and remain in Atlantic salmon, Salmo salar, netpens. Isolation of VHSV from farmed Atlantic salmon has been previously documented, but the effects on the health of farmed salmon and the wild fish sharing the environment are unknown. To determine their susceptibility, Atlantic salmon were exposed to a pool of 9 isolates of VHSV obtained from farmed Atlantic salmon in BC by IP-injection or by waterborne exposure and cohabitation with diseased Pacific herring. Disease intensity was quantified by recording mortality, clinical signs, histopathological changes, cellular sites of viral replication, expression of interferon-related genes, and viral tissue titers. Disease ensued in Atlantic salmon after both VHSV exposure methods. Fish demonstrated gross disease signs including darkening of the dorsal skin, bilateral exophthalmia, light cutaneous hemorrhage, and lethargy. The virus replicated within endothelial cells causing endothelial cell necrosis and extensive hemorrhage in anterior kidney. Infected fish demonstrated a type I interferon response as seen by up-regulation of genes for IFNα, Mx, and ISG15. In a separate trial infected salmon transmitted the virus to sympatric Pacific herring. The results demonstrate that farmed Atlantic salmon can develop clinical VHS and virus can persist in the tissues for at least 10 weeks. Avoiding VHS epizootics in Atlantic salmon farms would limit the potential of VHS in farmed Atlantic salmon, the possibility for further host adaptation in this species, and virus spillback to sympatric wild fishes.

Veterinary Microbiology↗
USGS2014

Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring ( Clupea pallasii )

Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring ( Clupea pallasii ) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.

Veterinary Microbiology↗
USGS2015

Biofilm formation of Francisella noatunensis subsp. orientalis

Francisella noatunensis subsp. orientalis ( Fno ) is an emergent fish pathogen in both marine and fresh water environments. The bacterium is suspected to persist in the environment even without the presence of a suitable fish host. In the present study, the influence of different abiotic factors such as salinity and temperature were used to study the biofilm formation of different isolates of Fno including intracellular growth loci C (iglC) and pathogenicity determinant protein A (pdpA) knockout strains. Finally, we compared the susceptibility of planktonic and biofilm to three disinfectants used in the aquaculture and ornamental fish industry, namely Virkon &reg; , bleach and hydrogen peroxide. The data indicates that Fno is capable of producing biofilms within 24 h where both salinity as well as temperature plays a role in the growth and biofilm formation of Fno . Mutations in the iglC or pdpA , both known virulence factors, do not appear to affect the capacity of Fno to produce biofilms, and the minimum inhibitory concentration, and minimum biocidal concentration for the three disinfectants were lower than the minimum biofilm eradication concentration values. This information needs to be taken into account if trying to eradicate the pathogen from aquaculture facilities or aquariums.

Veterinary Microbiology↗
USGS2005

Microbial biogeochemistry of uranium mill tailings

Uranium mill tailings (UMT) are the crushed ore residues from the extraction of uranium (U) from ores. Among the radioactive wastes associated with the nuclear fuel cycle, UMT are unique in terms of their volume and their limited isolation from the surficial environment. For this latter reason, their management and long-term fate has many interfaces with environmental microbial communities and processes. The interactions of microorganisms with UMT have been shown to be diverse and with significant consequences for radionuclide mobility and bioremediation. These radionuclides are associated with the U-decay series. The addition of organic carbon and phosphate is required to initiate the reduction of the U present in the groundwater down gradient of the mills. Investigations on sediment and water from the U-contaminated aquifer, indicates that the addition of a carbon source stimulates the rate of U removal by microbial reduction. Moreover, most attention with respect to passive or engineered removal of U from groundwaters focuses on iron-reducing and sulfate-reducing bacteria.

Advances in Applied Microbiology↗
USGS2003

Applicability of tetrazolium salts for the measurement of respiratory activity and viability of groundwater bacteria

A study was undertaken to measure aerobic respiration by indigenous bacteria in a sand and gravel aquifer on western Cape Cod, MA using tetrazolium salts and by direct oxygen consumption using gas chromatography (GC). In groundwater and aquifer slurries, the rate of aerobic respiration calculated from the direct GC assay was more than 600 times greater than that using the tetrazolium salt 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride (INT). To explain this discrepancy, the toxicity of INT and two additional tetrazolium salts, sodium 3′-[1-(phenylamino)-carbonyl]-3,4-tetrazolium]-bis(4-methoxy-6-nitro) benzenesulfonic acid hydrate (XTT) and 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), to bacterial isolates from the aquifer was investigated. Each of the three tetrazolium salts was observed to be toxic to some of the groundwater isolates at concentrations normally used in electron transport system (ETS) and viability assays. For example, incubation of cells with XTT (3 mM) caused the density of four of the five groundwater strains tested to decline by more than four orders of magnitude. A reasonable percentage (>57%) of cells killed by CTC and INT contained visible formazan crystals (the insoluble, reduced form of the salts) after 4 h of incubation. Thus, many of the cells reduced enough CTC or INT prior to dying to be considered viable by microscopic evaluation. However, one bacterium ( Pseudomonas fluorescens ) that remained viable and culturable in the presence of INT and CTC, did not incorporate formazan crystals into more than a few percent of cells, even after 24 h of incubation. This strain would be considered nonviable based on traditional tetrazolium salt reduction assays. The data show that tetrazolium salt assays are likely to dramatically underestimate total ETS activity in groundwater and, although they may provide a reasonable overall estimate of viable cell numbers in a community of groundwater bacteria, some specific strains may be falsely considered nonviable by this assay due to poor uptake or reduction of the salts.

Massachusetts↗
USGS2003

A procedure for quantitation of total oxidized uranium for bioremediation studies

A procedure was developed for the quantitation of complexed U(VI) during studies on U(VI) bioremediation. These studies typically involve conversion of soluble or complexed U(VI) (oxidized) to U(IV) (the reduced form which is much less soluble). Since U(VI) freely exchanges between material adsorbed to the solid phase and the dissolved phase, uranium bioremediation experiments require a mass balance of U in both its soluble and adsorbed forms as well as in the reduced sediment bound phase. We set out to optimize a procedure for extraction and quantitation of sediment bound U(VI). Various extractant volumes to sediment ratios were tested and it was found that between 1:1 to 8:1 ratios (v/w) there was a steady increase in U(VI) recovered, but no change with further increases in v/w ratio. Various strengths of NaHCO 3 , Na-EDTA, and Na-citrate were used to evaluate complexed U(VI) recovery, while the efficiency of a single versus repeated extraction steps was compared with synthesized uranyl-phosphate and uranyl-hydroxide. Total recovery with 1 M NaHCO 3 was 95.7% and 97.9% from uranyl-phosphate and uranyl-hydroxide, respectively, compared to 80.7% and 89.9% using 450 mM NaHCO 3 . Performing the procedure once yielded an efficiency of 81.1% and 92.3% for uranyl-phosphate and uranyl-hydroxide, respectively, as compared to three times. All other extractants yielded 7.9–82.0% in both experiments.

Journal of Microbiological Methods↗
USGS1997

Effect of flagellates on free-living bacterial abundance in an organically contaminated aquifer

Little is known about the role of protists in the saturated subsurface. Porous media microcosms containing bacteria and protists, were used to determine whether flagellates from an organically contaminated aquifer could substantively affect the number of free- living bacteria (FLB). When flagellates were present, the 3-40% maximum breakthrough of fluorescent y labelled FLB injected into the microcosms was much lower than the 60-130% observed for killed controls Grazing and clearance rates (3-27 FLB flag-1 h-1 and 12-23 nI flag-1 h-1, respectively) calculated from the data were in the range reported for flagellates in other aqueous environments. The data provide evidence that flagellate bacterivory is an important control on groundwater FLB populations.

FEMS Microbiology Reviews↗
USGS1997

Protistan communities in aquifers: A review

Eukaryotic microorganisms (protists) are a very important component of microbial communities inhabiting groundwater aquifers This is not unexpected when one considers that many protists feed heterotrophically, by means of either phagotrophy (bacterivory) or osmotrophy. Protistan numbers are usually low (<102 per g dw of aquifer material) in pristine, uncontaminated aquifers but may increase by several orders of magnitude in aquifers subject to organic pout on Stoa flagellates (typically 2-3(5) ??m in size in situ) are by far the dominant protists in aquifers although amoebae and occasionally ciliates may also be present much lower numbers. A though a wealth of new taxonomic information is waiting to be brought to light, interest in the identity of aquifer protists is not exclusively academic If verified, the following hypotheses may prove to be important towards our understanding of the functioning of microbial communities in aquifers: (1) Differences in swimming behavior between species of flagellates lead to feeding heterogeneity and niche differentiation, implying that bacterivorous flagellates graze on different subsets of the bacterial community, and therefore play different roles in controlling bacterial densities. (2) Bacterivorous flagellates grazing on bacteria capable of degrading Organic compounds have an indirect effect on the overall rates of biodegradation.

FEMS Microbiology Reviews↗
USGS2002

Dissimilatory arsenate reductase activity and arsenate-respiring bacteria in bovine rumen fluid, hamster feces, and the termite hindgut

Bovine rumen fluid and slurried hamster feces completely reduced millimolar levels of arsenate to arsenite upon incubation under anoxic conditions. This activity was strongly inhibited by autoclaving or aerobic conditions, and partially inhibited by tungstate or chloramphenicol. The rate of arsenate reduction was faster in feces from a population of arsenate-watered (100 ppm) hamsters compared to a control group watered without arsenate. Using radioisotope methods, arsenate reductase activity in hamster feces was also detected at very low concentrations of added arsenate (∼10 μM). Bacterial cultures were isolated from these materials, as well as from the termite hindgut, that grew using H 2 as their electron donor, acetate as their carbon source, and arsenate as their respiratory electron acceptor. The three cultures aligned phylogenetically either with well-established enteric bacteria, or with an organism associated with feedlot fecal wastes. Because arsenite is transported across the gut epithelium more readily than arsenate, microbial dissimilatory reduction of arsenate in the gut may promote the body's absorption of arsenic and hence potentiate its toxicity.

FEMS Microbiology Ecology↗
USGS2003

Growth and survival of Escherichia coli and enterococci populations in the macro-alga Cladophora (Chlorophyta)

The macro-alga Cladophora glomerata is found in streams and lakes worldwide. High concentrations of Escherichia coli and enterococci have been reported in Cladophora along the Lake Michigan shore. The objective of this study was to determine if Cladophora supported growth of these indicator bacteria. Algal leachate readily supported in vitro multiplication of E. coli and enterococci, suggesting that leachates contain necessary growth-promoting substances. Growth was directly related to the concentration of algal leachate. E. coli survived for over 6 months in dried Cladophora stored at 4&deg;C; residual E. coli grew after mat rehydration, reaching a carrying capacity of 8 log CFU g -1 in 48 h. Results of this study also show that the E. coli strains associated with Cladophora are highly related; in most instances they are genetically different from each other, suggesting that the relationship between E. coli and Cladophora may be casual. These findings indicate that Cladophora provides a suitable environment for indicator bacteria to persist for extended periods and to grow under natural conditions.

FEMS Microbiology Ecology↗
USGS2012

Microbial colonization and controls in dryland systems

Drylands constitute the most extensive terrestrial biome, covering more than one-third of the Earth's continental surface. In these environments, stress limits animal and plant life, so life forms that can survive desiccation and then resume growth following subsequent wetting assume the foremost role in ecosystem processes. In this Review, we describe how these organisms assemble in unique soil- and rock-surface communities to form a thin veneer of mostly microbial biomass across hot and cold deserts. These communities mediate inputs and outputs of gases, nutrients and water from desert surfaces, as well as regulating weathering, soil stability, and hydrological and nutrient cycles. The magnitude of regional and global desert-related environmental impacts is affected by these surface communities; here, we also discuss the challenges for incorporating the consideration of these communities and their effects into the management of dryland resources.

Nature Reviews Microbiology↗
USGS2018

Understanding how microbiomes influence the systems they inhabit

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Nature Microbiology↗