WHAM-FTOXβ – An aquatic toxicity model based on intrinsic metal toxic potency and intrinsic species sensitivity

We developed a model that quantifies aquatic cationic toxicity by a combination of the intrinsic toxicities of metals and protons and the intrinsic sensitivities of the test species. It is based on the WHAM-FTOX model, which combines the calculated binding of cations by the organism with toxicity coefficients (αH, αM) to estimate the variable FTOX, a measure of toxic effect; the key parameter αM,max (applying at infinite time) depends upon both the metal and the test species. In our new model, WHAM-FTOXβ, values of αM,max are given by the product αM* × β, where αM* has a single value for each metal, and β a single value for each species. To parameterise WHAM-FTOXβ, we assembled a set of 2182 estimates of αM,max obtained by applying the basic model to laboratory toxicity data for 76 different test species, covering 15 different metals, and including results for metal mixtures. Then we fitted the log10 αM,max values with αM* and β values (a total of 91 parameters). The resulting model accounted for 72% of the variance in log10 αM,max. The values of αM* increased markedly as the chemical character of the metal changed from hard (average αM* = 4.4) to intermediate (average αM* = 25) to soft (average αM* = 560). The values of log10 β were normally distributed, with a 5–95 percentile range of -0.73 to +0.56, corresponding to β values of 0.18 to 3.62. The WHAM-FTOXβ model entails the assumption that test species exhibit common relative sensitivity, i.e. the ratio αM,max / αM* is constant across all metals. This was tested with data from studies in which the toxic responses of a single organism towards two or more metals had been measured (179 examples for the most-tested metals Ni, Cu, Zn, Ag, Cd, Pb), and statistically-significant (p < 0.003) results were obtained

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

peer-reviewedCrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks

Isolation of a Novel Phage with Activity against Streptococcus mutans Biofilms

peer-reviewedStreptococcus mutans is one of the principal agents of caries formation mainly, because of its ability to form biofilms at the tooth surface. Bacteriophages (phages) are promising antimicrobial agents that could be used to prevent or treat caries formation by S. mutans. The aim of this study was to isolate new S. mutans phages and to characterize their antimicrobial properties. A new phage, ɸAPCM01, was isolated from a human saliva sample. Its genome was closely related to the only two other available S. mutans phage genomes, M102 and M102AD. ɸAPCM01 inhibited the growth of S. mutans strain DPC6143 within hours in broth and in artificial saliva at multiplicity of infections as low as 2.5x10-5. In the presence of phage ɸAPCM01 the metabolic activity of a S. mutans biofilm was reduced after 24 h of contact and did not increased again after 48 h, and the live cells in the biofilm decreased by at least 5 log cfu/ml. Despite its narrow host range, this newly isolated S. mutans phage exhibits promising antimicrobial properties

Using WHAM-FTOX to understand proton and metal mixture toxicity in the laboratory and field

It is a well-attested fact that the uptake and toxicity of cationic metals to organisms are dependent on the chemistry of the exposure medium. Considerable research effort has been devoted to development of modelling tools to understand, explain and predict these medium effects. Predominant among the developed models is the Biotic Ligand Model (BLM), which considers exposure to be directly related to metal bound to specific uptake sites (biotic ligands) on the target organism, with chemical speciation in the medium and competition for binding to the biotic ligand(s) accounted for. Similarly to the BLM, WHAM-FTOX is based around the concept of computing amounts of metal bound to the organism. However, rather than computing amounts of metals bound to assumed specific biotic ligands, WHAM-FTOX assumes that exposure to metals is proportional to the amount of metal bound by all weak-acid coordination sites on or in the organism, in equilibrium with the surrounding medium. An overall toxic response for mixtures of cations (metals and protons) is quantified as a toxicity function FTOX, given by FTOX = ∑ αi ϴi where the exposure to each cation is given by ϴi (the fractional occupancy of binding sites) and αi is a toxicity coefficient specific to each cation. Amounts of bound cations are computed using the WHAM chemical speciation model, taking the amounts bound to humic acid (HA) as proxies for amounts bound to organisms. This approach has the advantage that constants for cation binding are already available, rather than needing to be derived as with the BLM, and that mixture effects are readily computed. Furthermore, the toxic effects of proton binding can be included in the mixture exposure modelling. Initial applications of WHAM-FTOX focused on describing field community effects in freshwaters impacted by acidification and metal contamination in a number of locations including the UK and North America. Subsequent work has focused on modelling accumulation and mixture effects in laboratory toxicity tests. Most recently, the model has been used in a meta-analysis of single metal–single species laboratory toxicity data with the aim of providing a unifying picture of toxic effects through time and across metals and organisms. Collectively, this body of work demonstrates the utility of WHAM-FTOX as a unifying tool for understanding and predicting the toxicity of cation mixtures from the laboratory to the field, from single species to whole communities. Prospects for the future include the use of the model to predict mixture field effects based on calibration to laboratory data

RNA phage biology in a metagenomic era

The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies

Human cytomegalovirus epidemiology and relationship to tuberculosis and cardiovascular disease risk factors in a rural Ugandan cohort.

Human cytomegalovirus (HCMV) infection has been associated with increased mortality, specifically cardiovascular disease (CVD), in high-income countries (HICs). There is a paucity of data in low- and middle-income countries (LMICs) where HCMV seropositivity is higher. Serum samples from 2,174 Ugandan individuals were investigated for HCMV antibodies and data linked to demographic information, co-infections and a variety of CVD measurements. HCMV seropositivity was 83% by one year of age, increasing to 95% by five years. Female sex, HIV positivity and active pulmonary tuberculosis (TB) were associated with an increase in HCMV IgG levels in adjusted analyses. There was no evidence of any associations with risk factors for CVD after adjusting for age and sex. HCMV infection is ubiquitous in this rural Ugandan cohort from a young age. The association between TB disease and high HCMV IgG levels merits further research. Known CVD risk factors do not appear to be associated with higher HCMV antibody levels in this Ugandan cohort

Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1

The tail tape measure protein (TMP) of tailed bacteriophages (also called phages) dictates the tail length and facilitates DNA transit to the cell cytoplasm during infection. Here, a thorough mutational analysis of the TMP from lactococcal phage TP901-1 (TMPTP901-1) was undertaken. We generated 56 mutants aimed at defining TMPTP901-1 domains that are essential for tail assembly and successful infection. Through analysis of the derived mutants, we determined that TP901-1 infectivity requires the N-terminal 154 aa residues, the C-terminal 60 residues and the first predicted hydrophobic region of TMPTP901-1 as a minimum. Furthermore, the role of TMPTP901-1 in tail length determination was visualized by electron microscopic imaging of TMP-deletion mutants. The inverse linear correlation between the extent of TMPTP901-1-encoding gene deletions and tail length of the corresponding virion provides an estimate of TMPTP901-1 regions interacting with the connector or involved in initiator complex formation. This study represents the most thorough characterisation of a TMP from a Gram-positive host-infecting phage and provides essential advances to understanding its role in virion assembly, morphology and infection

Complete genome sequence of Escherichia coli phage APC_JM3.2 isolated from a chicken cecum

Avian pathogenic Escherichia coli (APEC) bacteria are a significant challenge to the poultry industry. Bacteriophages (phages) have the potential to control APEC strains, increasing animal welfare and economic productivity. Here, we report the isolation of an E. coli-infecting phage, APC_JM3.2, isolated from the cecum of a broiler chicken in Ireland

Structure and Assembly of TP901-1 Virion Unveiled by Mutagenesis

International audienceBacteriophages of the Siphoviridae family represent the most abundant viral morphology in the biosphere, yet many molecular aspects of their virion structure, assembly and associated functions remain to be unveiled. In this study, we present a comprehensive mutational and molecular analysis of the temperate Lactococcus lactis-infecting phage TP901-1. Fourteen mutations located within the structural module of TP901-1 were created; twelve mutations were designed to prevent full length translation of putative proteins by nonsense mutations, while two additional mutations caused aberrant protein production. Electron microscopy and Western blot analysis of mutant virion preparations, as well as in vitro assembly of phage mutant combinations, revealed the essential nature of many of the corresponding gene products and provided information on their biological function(s). Based on the information obtained, we propose a functional and assembly model of the TP901-1 Siphoviridae virion

An empirical parameterization of subsurface entrainment temperature for improved SST anomaly simulations in an intermediate ocean model

An empirical model for the temperature of subsurface water entrained into the ocean mixed layer (Te) is presented and evaluated to improve sea surface temperature anomaly (SSTA) simulations in an intermediate ocean model (IOM) of the tropical Pacific. An inverse modeling approach is adopted to estimate Te from an SSTA equation using observed SST and simulated upper-ocean currents. A relationship between Te and sea surface height (SSH) anomalies is then obtained by utilizing a singular value decomposition (SVD) of their covariance. This empirical scheme is able to better parameterize Te anomalies than other local schemes and quite realistically depicts interannual variability of Te, including a nonlocal phase lag relation of Te variations relative to SSH anomalies over the central equatorial Pacific. An improved Te parameterization naturally leads to better depiction of the subsurface effect on SST variability by the mean upwelling of subsurface temperature anomalies. As a result, SSTA simulations are significantly improved in the equatorial Pacific; a comparison with other schemes indicates that systematic errors of the simulated SSTAs are significantly small—apparently due to the optimized empirical Teparameterization. Cross validation and comparisons with other model simulations are made to illustrate the robustness and effectiveness of the scheme. In particular it is demonstrated that the empirical Te model constructed from one historical period can be successfully used to improve SSTA simulations in another