Dietary Exposure to Environmentally Relevant Levels of Chemical Contaminants Reduces Growth and Survival in Juvenile Chinook Salmon.

Chemical pollution can degrade aquatic ecosystems. Chinook salmon in contaminated habitats are vulnerable to health impacts from toxic exposures. Few studies have been conducted on adverse health outcomes associated with current levels and mixtures of contaminants. Fewer still address effects specific to the juvenile life-stage of salmonids. The present study evaluated contaminant-related effects from dietary exposure to environmentally relevant concentrations and mixture profiles in juvenile Chinook salmon from industrialized waterways in the U.S. Pacific Northwest using two end points: growth assessment and disease susceptibility. The dose and chemical proportions were reconstituted based on environmental sampling and analysis using the stomach contents of juvenile Chinook salmon recently collected from contaminated, industrialized waterways. Groups of fish were fed a mixture with fixed proportions of 10 polychlorinated biphenyls (PCBs), 3 dichlorodiphenyltrichloroethanes (DDTs), and 13 polycyclic aromatic hydrocarbons (PAHs) at five concentrations for 35 days. These contaminant compounds were selected because of elevated concentrations and the widespread presence in sediments throughout industrialized waterways. Fork length and otolith microstructural growth indicators were significantly reduced in fish fed environmentally relevant concentrations of these contaminants. In addition, contaminant-exposed Chinook salmon were more susceptible to disease during controlled challenges with the pathogen Aeromonas salmonicida. Our results indicate that dietary exposure to contaminants impairs growth and immune function in juvenile Chinook salmon, thereby highlighting that current environmental exposure to chemicals of potential management concern threatens the viability of exposed salmon.

Biological Responses of Pacific Herring Embryos to Crude Oil Are Quantifiable at Exposure Levels Below Conventional Limits of Quantitation for PAHs in Water and Tissues.

Pacific herring (Clupea pallasii), a cornerstone of marine food webs, generally spawn on marine macroalgae in shallow nearshore areas that are disproportionately at risk from oil spills. Herring embryos are also highly susceptible to toxicity from chemicals leaching from oil stranded in intertidal and subtidal zones. The water-soluble components of crude oil trigger an adverse outcome pathway that involves disruption of the physiological functions of cardiomyocytes in the embryonic herring heart. In previous studies, impaired ionoregulation (calcium and potassium cycling) in response to specific polycyclic aromatic hydrocarbons (PAHs) corresponds to lethal embryolarval heart failure or subtle chamber malformations at the high and low ends of the PAH exposure range, respectively. Sublethal cardiotoxicity, which involves an abnormal outgrowth (ballooning) of the cardiac ventricular chamber soon after hatching, subsequently compromises juvenile heart structure and function, leading to pathological hypertrophy of the ventricle and reduced individual fitness, measured as cardiorespiratory performance. Previous studies have not established a threshold for these sublethal and delayed-in-time effects, even with total (∑)PAH exposures as low as 29 ng/g of wet weight (tissue dose). Here, we extend these earlier findings showing that (1) cyp1a gene expression provides an oil exposure metric that is more sensitive than typical quantitation of PAHs via GC-MS and (2) heart morphometrics in herring embryos provide a similarly sensitive measure of toxic response. Early life stage injury to herring (impaired heart development) thus occurs below the quantitation limits for PAHs in both water and embryonic tissues as a conventional basis for assessing oil-induced losses to coastal marine ecosystems.

Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS: We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.

Achromobacter xylosoxidans is the predominant Achromobacter species isolated from diverse non-respiratory samples.

Achromobacter spp. are emerging opportunistic Gram-negative rods responsible for diverse nosocomial or community-acquired infections. We describe, for the first time, the distribution of Achromobacter spp., defined by nrdA gene sequencing, and their antimicrobial susceptibility in a variety of non-respiratory samples recovered from hospitalized patients from 2010 to 2015. Of the 63 isolates studied, A. xylosoxidans was the most prevalent (41 isolates), and with the exception of A. insuavis (four isolates), the remaining 10 species identified were represented by one or two isolates only. All isolates were uniformly susceptible to piperacillin and piperacillin-tazobactam and 97% to meropenem, but 76% showed resistance to ciprofloxacin. This study confirms the diversity of Achromobacter spp. in non-cystic fibrosis (CF) isolates and the predominance of A. xylosoxidans, as previously reported for CF sputum isolates. There was no apparent link between the clinical site of infection and the species of Achromobacter.

Lost ecosystem services as a measure of oil spill damages: a conceptual analysis of the importance of baselines.

The assessment and quantification of damages resulting from marine oil spills is typically coordinated by NOAA, and has historically utilized Habitat Equivalency Analysis (HEA) to estimate damages. Resource economists and others have called for the damage assessment process to instead estimate injuries through the valuation of lost ecosystem services. Our conceptual analysis explores ecosystem service valuation from the perspective of "baselines," which are a fundamental component of both primary and compensatory restoration activities. In practice, baselines have been defined in ecological terms, with minimal consideration of the socioeconomic side of ecosystem service provision. We argue that, for the purposes of scaling compensatory restoration, it is more appropriate to characterize baselines in value terms, thereby integrating non-market valuation approaches from the onset of the damage assessment process. Benefits and challenges of this approach are discussed, along with guidelines for practitioners to identify circumstances in which socioeconomic variables are likely to be important for baseline characterization.

Using US Natural Resource Damage Assessment to understand the environmental consequences of the war in Ukraine.

Military conflict has led to large-scale environmental changes throughout recorded human history. Pollution from war contaminates surface water and soil, releases large volumes of greenhouse gases into the air, and directly harms wildlife and biodiversity. Although much is understood about the human toll of war, numerous examples of postwar reconstruction suggest that underestimating the severity of wartime damages to ecosystems and natural resources results in prolonged or incomplete recovery of the environment. A data-driven scientific approach closely aligned with the evidentiary rules standard in western legal systems is needed to quantify the injury, destruction, or loss of natural resources and inform the estimation of the reparations necessary to restore the environment fully. The US Natural Resource Damage Assessment (NRDA) process and the European Union environmental liability directive are well-suited for a systematic and science-based analysis of the ecological injuries incurred during armed conflicts. Both approaches include a preliminary damage assessment process, which could be initiated during wartime to document and predict the likely severity of the injuries and prioritize, in advance, rehabilitation activities after the cessation of hostilities. In this article, we refer to news reporting of Russia's February 2022 invasion of Ukraine as an example of how a preliminary damage assessment could be conducted remotely and later modified by in-country inspections and analysis to verify and refine the scale of injuries and to develop reparation proposals. Integr Environ Assess Manag 2023;19:366-375. © 2022 SETAC.

Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS).

OBJECTIVES: Achromobacter spp. are emerging pathogens in respiratory samples from cystic fibrosis patients. The current reference methods (nrdA-sequencing or multilocus sequence typing) can identify 18 species which are often misidentified by conventional techniques as A. xylosoxidans. A few studies have suggested that matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) provides accurate identification of the genus but not of species. The aims of this study were (a) to generate a database for MALDI-TOF/MS Bruker including the 18 species, (b) to evaluate the suitability of the database for routine laboratory identification, and (c) to compare its performance with that of the currently available Bruker default database. METHODS: A total of 205 isolates belonging to the 18 species identified by nrdA sequencing were used to build a local database. Main spectra profiles (MSPs) were created according to Bruker's recommendations for each isolate with the Biotyper software. Performance of the default Bruker database and ours for routine use were compared by testing 167 strains (including 38 isolates used from MSP creation) belonging to the 18 species identified by nrdA sequencing directly from colonies cultivated on various media. RESULTS: Our new database accurately identified 99.4% (166/167) of the isolates from the 18 species (score ≥2.0) versus only 50.9% (85/167) with the Bruker database. In the Bruker database 17.3% of the isolates (29/167) were incorrectly identified as another species despite a score of ≥2.0. CONCLUSIONS: The use of MALDI-TOF/MS in combination with a database developed with samples from 18 Achromobacter species provides rapid and accurate identification. This tool could be used to help future clinical studies.

Integrating marine oil snow and MOSSFA into oil spill response and damage assessment.

Marine snow formation and vertical transport are naturally occurring processes that carry organic matter from the surface to deeper waters, providing food and sequestering carbon. During the Deepwater Horizon well blowout, oil was incorporated with marine snow aggregates, triggering a Marine Oil Snow (MOS) Sedimentation and Flocculent Accumulation (MOSSFA) event, that transferred a significant percentage of the total released oil to the seafloor. An improved understanding of processes controlling MOS formation and MOSSFA events is necessary for evaluating their impacts on the fate of spilled oil. Numerical models and predictive tools capable of providing scientific support for oil spill planning, response, and Natural Resource Damage Assessment are being developed to provide information for weighing the ecological trade-offs of response options. Here we offer considerations for oil spill response and recovery when assessing the potential for a MOSSFA event and provide tools to enhance decision-making.

Study of 109 Achromobacter spp. isolates from 9 French CF centres reveals the circulation of a multiresistant clone of A. xylosoxidans belonging to ST 137.

We previously reported the distribution of Achromobacter spp. (species and Sequence Types (ST)) in our French Cystic Fibrosis (CF) centre. In the present study we collected 109 Achromobacter isolates (1/patient) from 9 other French CF Centres for species identification, antimicrobial susceptibility testings and Multilocus-Sequence-Typing (MLST) analysis. Ten species were detected, A. xylosoxidans being the most predominant one (73.4% of the isolates). Piperacillin-tazobactam, ceftazidime, imipenem, meropenem and ciprofloxacin were respectively active against 88, 70, 79, 72 and 23% of the isolates. Among the 79 A. xylosoxidans isolates, 46 STs were detected. Interestingly, ST 137, recovered in 4 centres (5 patients), was previously detected in our centre (2 patients). The strains from the 7 patients belonged to the same pulsotype (pulsed-field-gel-electrophoresis analysis) and harboured acquired resistance to meropenem, ceftazidime, ciprofloxacin, and except for 2 isolates, to imipenem and piperacillin-tazobactam. This is the first description in France of a circulating multiresistant A. xylosoxidans strain.

Recovery of Bordetella bronchiseptica sequence type 82 and B. pseudohinzii from urban rats in Terengganu, Malaysia.

Rodents have historically been associated with zoonotic pandemics that claimed the lives of large human populations. Appropriate pathogen surveillance initiatives could contribute to early detection of zoonotic infections to prevent future outbreaks. Bordetella species are bacteria known to cause mild to severe respiratory disease in mammals and, some have been described to infect, colonize and spread in rodents. There is a lack of information on the population diversity of bordetellae among Malaysian wild rodents. Here, bordetellae recovered from lung tissues of wild rats were genotypically characterized using 16S rDNA sequencing, MLST and nrdA typing. A novel B. bronchiseptica ST82, closely related to other human-derived isolates, was discovered in three wild rats (n=3) from Terengganu (5.3333° N, 103.1500° E). B. pseudohinzii, a recently identified laboratory mice inhabitant, was also recovered from one rat (n=1). Both bordetellae displayed identical antimicrobial resistance profiles, indicating the close phylogenetic association between them. Genotyping using the 765-bp nrdA locus was shown to be compatible with the MLST-based phylogeny, with the added advantage of being able to genotype non-classical bordetellae. The recovery of B. pseudohinzii from wild rat implied that this bordetellae has a wider host range than previously thought. The findings from this study suggest that bordetellae surveillance among wild rats in Malaysia has to be continued and expanded to other states to ensure early identification of species capable of causing public health disorder.

Histopathology of brown bullhead (Ameiurus nebulosus), smallmouth bass (Micropterus dolomieu), and yellow perch (Perca flavescens) in relation to polychlorinated biphenyl (PCB) contamination in the Hudson River.

From the 1940s through 1977, at least 590,000kg of polychlorinated biphenyls (PCBs) were released into the Hudson River from General Electric manufacturing plants located in Hudson Falls and Fort Edward, New York. In 1984, the U.S. Environmental Protection Agency designated a nearly 322km reach as the Hudson River PCBs Superfund Site. Here we describe a Fish Health Assessment study, part of a Natural Resource Damage Assessment, that evaluated the prevalence of toxicopathic lesions in adult brown bullhead (Ameiurus nebulosus), smallmouth bass (Micropterus dolomieu), and yellow perch (Perca flavescens). In fall 2001, 29-51 fish of each species were collected in fall 2001 from highly contaminated areas below the plants (Thompson Island Pool (TIP) and Stillwater Dam Pool (STW)), an upriver reference area (Feeder Dam Pool (FDP)), and a reference lake, Oneida Lake (ODA). The focus was on histopathologic lesions and observations associated with contaminant exposure: liver-neoplasms, foci of cellular alteration, bile duct hyperplasia; testes-ovotestis (testicular oocytes), germ cell degeneration, altered developmental stage; ovaries-atresia and altered developmental stage. Lesions associated with PCB exposure were defined as those with significantly greater prevalence and/or severity in TIP and STW compared with ODA and FDP. For brown bullhead and smallmouth bass, no lesions or changes in gonadal development met those criteria. In yellow perch, ovarian atresia was the only lesion associated with PCB exposure. Prevalence was 53% in FDP, 75% in ODA, and 100% in both STW and TIP; severity increased from mostly minimal to mild-moderate. Because of the high prevalence of atresia in reference collections, it is likely that factors other than PCBs are also involved. As part of a post-dredging monitoring plan, we recommend assessing gonad structure and function in yellow perch collected at the time of spawning in locations with a range of PCB contamination.

Uncovering Differences in Virulence Markers Associated with Achromobacter Species of CF and Non-CF Origin.

Achromobacter spp. are recognized as emerging pathogens in hospitalized as well as in cystic fibrosis (CF) patients. From 2012 to 2015, we collected 69 clinical isolates (41 patient) of Achromobacter spp. from 13 patients with CF (CF isolates, n = 32) and 28 patients receiving care for other health conditions (non-CF isolates, n = 37). Molecular epidemiology and virulence potential of isolates were examined. Antimicrobial susceptibility, motility, ability to form biofilms and binding affinity to mucin, collagen, and fibronectin were tested to assess their virulence traits. The nrdA gene sequencing showed that A. xylosoxidans was the most prevalent species in both CF and non-CF patients. CF patients were also colonized with A. dolens/A. ruhlandii, A. insuavis, and A. spiritinus strains while non-CF group was somewhat less heterogenous, although A. insuavis, A. insolitus, and A. piechaudii strains were detected beside A. xylosoxidans. Three strains displayed clonal distribution, one among patients from the CF group and two among non-CF patients. No significant differences in susceptibility to antimicrobials were observed between CF and non-CF patients. About one third of the isolates were classified as strong biofilm producers, and the proportion of CF and non-CF isolates with the ability to form biofilm was almost identical. CF isolates were less motile compared to the non-CF group and no correlation was found between swimming phenotype and biofilm formation. On the other hand, CF isolates exhibited higher affinity to bind mucin, collagen, and fibronectin. In generall, CF isolates from our study exhibited in vitro properties that could be of importance for the colonization of CF patients.

Natural resource damage assessment for the Hebei Spirit oil spill: An application of Habitat Equivalency Analysis.

Sixteen oil spills occurred in Korea between 1995 and 2010, including the Hebei Spirit oil spill (HSOS) in 2007, the largest (77,857 barrels) in Korean history. Yet compensation for environmental damages has never been claimed under the International Oil Pollution Compensation Fund for any of these accidents, because there is no adequate natural resource damage assessment (NRDA) procedure and there are no internationally-admissible economic quantification methods established in Korea. The objective of this study is to propose a methodology to overcome these shortcomings. We propose the use of Habitat Equivalency Analysis, which has dominated the US NRDA process for oil spills, and apply it to the HSOS as a case study. A Base Case analysis estimates the compensatory costs of fishery habitat damages (34,703.5ha) with a 10-year recovery rate at $119.4 million. We also conduct sensitivity analyses under several alternative assumptions.

Impacts of the Deepwater Horizon oil spill on the salt marsh vegetation of Louisiana.

The coastal wetland vegetation component of the Deepwater Horizon oil spill Natural Resource Damage Assessment documented significant injury to the plant production and health of Louisiana salt marshes exposed to oiling. Specifically, marsh sites experiencing trace or greater vertical oiling of plant tissues displayed reductions in cover and peak standing crop relative to reference (no oiling), particularly in the marsh edge zone, for the majority of this four year study. Similarly, elevated chlorosis of plant tissue, as estimated by a vegetation health index, was detected for marsh sites with trace or greater vertical oiling in the first two years of the study. Key environmental factors, such as hydrologic regime, elevation, and soil characteristics, were generally similar across plant oiling classes (including reference), indicating that the observed injury to plant production and health was the result of plant oiling and not potential differences in environmental setting. Although fewer significant impacts to plant production and health were detected in the latter years of the study, this is due in part to decreased sample size occurring as a result of erosion (shoreline retreat) and resultant loss of plots, and should not be misconstrued as indicating full recovery of the ecosystem.

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK.

BACKGROUND: We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients. METHODS: nrdA sequence clustering was used to identify 147 Achromobacter isolates from 96 patients from 27 hospitals to species level. Potential cross-infection was investigated by MLST, pulsed-field gel electrophoresis and whole genome sequencing (WGS). RESULTS: Achromobacter xylosoxidans was the most prevalent species affecting 59 of 96 (61%) patients, followed by Achromobacter insuavis and Achromobacter dolens (12.4% and 8%, respectively). Three novel nrdA clusters were identified. One was further characterised by sequencing the intrinsic blaOXA gene, revealing novel variants. WGS of A. insuavis 2a isolates from four patients attending the same paediatric unit revealed that three were ST144, but differed from one another by a minimum of 385 SNPs, suggesting cross-infection was unlikely. CONCLUSIONS: nrdA sequence clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.

Distribution of innate efflux-mediated aminoglycoside resistance among different Achromobacter species.

Achromobacter spp. are emerging respiratory pathogens in cystic fibrosis patients. Since 2013 the genus Achromobacter includes 15 species for which innate antibiotic resistance is unknown. Previously the AxyXY-OprZ efflux system has been described to confer aminoglycoside (AG) resistance in A. xylosoxidans. Nevertheless, some Achromobacter spp. strains are susceptible to AG. This study including 49 Achromobacter isolates reveals that AG resistance is correlated with different Achromobacter spp. It is noteworthy that the axyXY-oprZ operon is detected only in AG-resistant species, including the most frequently encountered in cystic fibrosis patients: A. xylosoxidans, A. ruhlandii, A. dolens and A. insuavis.