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The application of advanced technologies to the study of little-known species is a necessary step in generating effective conservation strategies. Despite the biological importance of the small carnivore guild, a paucity of data exists in terms of the spatial ecology of these species, largely due to logistical constraints of large and bulky collar units. This study reports the first known satellite collaring of a viverrid, the Malay civet ( Viverra tangalunga), in Sabah, Malaysian Borneo. Stationary tests of two generations of 65-70 g e-obs GmbH 'Collar 1A' units recorded high fix success rates and good accuracy and precision under semi-open canopy. From October 2013-August 2015, nine adult V. tangalunga were fit with e-obs collars recording hourly nocturnal GPS locations. Collars were successfully deployed for 27-187 days. Field GPS fix success varied from 22 to 88.3 %, with the study documenting a total GPS success of 58.1 % across all individuals. Despite this large in-field performance range, the quality and quantity of data collected by these units surpass that of previous VHF studies on Asian viverrids, collecting on average a 16-fold increase in locations per collaring day. The successful application of satellite technology to these little-known carnivores carries significant biological and conservation implications, and it is recommended that satellite collars are a viable technology to conduct detailed and well-designed ecological studies of Viverridae species. [ABSTRACT FROM AUTHOR]

• Anthropogenic dark earth (ADE) has high concentrations of TOC and TN in the soil. • The TOC in ADE was 45% higher than in references soils of Brazil's humid tropic. • The clay fraction was responsible for 27–46% of the incremental TOC in the ADE. • The C:N ratio in the clay size fraction of ADE indicates microbial origin. The anthropogenic dark earths (ADEs) are being assumed in recent years as a model representing the result of sustainable soil management practices carried out by Pre-Columbian peoples. However, little is known about the role of mineral-organic associations in organic matter storage in those soils compared to the emphasis generally given to the role of pyrogenic structures. We quantified the changes of carbon and nitrogen and their distribution in physical fractions of ADEs in relation to the reference (adjacent) soil. Four ADEs sites having the different soil textural classes of sandy clay loam, sandy clay, clayey, and very clayey were selected in the Amazon region of Brazil. Soil samples were collected from the 0–10 cm layer and a subset of the sample was separated into large aggregates (>500 μm) and small aggregates (<500 μm). The ADEs stored on average 45% more total organic carbon (TOC) and 44% more total nitrogen (TN) than the reference soils. Of the incremental TOC and TN in ADE relative to the reference soil, the silt size fraction stored on average 92% of this TOC and 37% of this TN and had C:N ratios as high as 25, which may indicate the presence of pyrogenic material. The clay fraction stored a substantial share of 27–46% of the incremental TOC and 27–66% of the incremental TN. The C:N ratio in the clay size fraction of ADEs, on average 10.5, was lower or not different than in the clay fraction of reference soil (average of 11.1), indicating that the organic matter in the clay fraction even of ADEs was predominantly of microbial origin, and not pyrogenic. We therefore conclude that the clay fraction proved to be an important location to the accumulation and stabilization of TOC and TN in these Anthrosols, possibly by mineral-organic association mechanisms. [ABSTRACT FROM AUTHOR]

C16H15NO5, monoclinic, P21/ n (no. 14), a = 6.7689(5) Å, b = 45.219(3) Å, c = 10.1102(6) Å, β = 101.360(7)°, V = 3033.9(4) Å3, T = 298(2) K. [ABSTRACT FROM AUTHOR]

Patterns and practices of agricultural expansion threaten the persistence of global biodiversity. Wildlife species surviving large-scale land use changes can be exposed to a suite of contaminants that may deleteriously impact their health. There is a paucity of data concerning the ecotoxicological impacts associated with the global palm oil (Elaeis guineensis) industry. We sampled wild Malay civets (Viverra tangalunga) across a patchwork landscape degraded by oil palm agriculture in Sabah, Malaysian Borneo. Using a non-lethal methodology, we quantified the levels of 13 essential and non-essential metals within the hair of this adaptable small carnivore. We robustly assessed the biological and environmental drivers of intrapopulation variation in measured levels. Metal concentrations were associated with civet age, weight, proximity to a tributary, and access to oxbow lakes. In a targeted case study, the hair metal profiles of 16 GPS-collared male civets with differing space use patterns were contrasted. Civets that entered oil palm plantations expressed elevated aluminium, cadmium, and lead, and lower mercury hair concentrations compared to civets that remained exclusively within the forest. Finally, we paired hair metal concentrations with 34 blood-based health markers to evaluate the possible sub-lethal physiological effects associated with varied hair metal levels. Our multi-facetted approach establishes these adaptable carnivores as indicator species within an extensively altered ecosystem, and provides critical and timely evidence for future studies. [Display omitted] • Agricultural production may impact species surviving within fragmented landscapes. • Metal levels in Malay civet hair varied with biological and spatial parameters. • Elevated hair Ba, Cd, Cr, and Fe detected in civets sampled closer to tributaries. • Collared civets using plantations had higher Al, Cd, and Pb than forest-only males. • Blood markers correlated with hair metals suggesting possible sub-lethal effects. [ABSTRACT FROM AUTHOR]

Abstract: The current consensus is that Microsporidia belong to a select group of parasites capable of causing both intersexuality and complete sex reversal in their hosts. Indeed, species such as Nosema granulosis and Dictyocoela duebenum, which infect amphipod crustaceans, are regularly referred to as ‘feminising microsporidians’. This categorisation is based on a combination of findings: that these species are vertically transmitted and occur at a high prevalence of infection in intersex and female amphipods, that infected amphipod populations are female-biased, and that infected females have significantly female-biased broods with no concurrent increase in mortality. In this study, we report on a population of the amphipod Echinogammarus marinus presenting both female bias and high levels of intersexuality, which are infected with D. deubenum. In keeping with its feminising classification, infection is prevalent in animals presenting female and intersex phenotypes. However, a further screen revealed the presence of a previously unknown paramyxean parasite related to organisms of the genus Marteilia, a group known to cause catastrophic sexual dysfunction in bivalves. We found that the paramyxean parasite was also vertically transmitted, with infections being more prevalent in females and intersex animals. Critically, every animal infected with D. deubenum was also co-infected with the paramyxean, with few animals presenting an independent paramyxean infection. In contrast, co-infection of E. marinus with a paramyxean and the non-feminising microsporidian Dictyocoela berillonum rarely occurred. These observations raise a new hypothesis, namely, that D. duebenum and other feminising microsporidians are not actually capable of host feminisation but instead ‘hitch-hike’ together with a feminising paramyxean parasite. [Copyright &y& Elsevier]

[Display omitted] • A meta-analysis of extractable micronutrients in Amazonian Dark Earths was performed. • Micronutrient contents were compared at 20 sites with ADEs and adjacent soils. • Ni, Cu, Zn, Mn and Fe were studied at depth in 9 sites with forest and agriculture. • Zn, Mn and Cu contents were higher in ADEs and Fe was higher in adjacent soils. • Modern agriculture at some sites had lower contents of extractable Fe or Mn. Amazonian Dark Earths (ADEs) are highly fertile soils in areas with predominance of unfertile soils. However, the variation in nutrient availability between regions and the resilience of ADEs to modern agricultural use is still little known, particularly regarding micronutrient contents. Hence, the present study synthesized current information of ADE impacts on extractable micronutrient (Cu, Ni, Fe, Mn, Zn, B) contents at different soil depths and assessed in detail the role of both soil depth and land-use type on extractable Cu, Ni, Fe, Mn and Zn in nine ADEs and adjacent (ADJ) soils from different Amazonian regions. The land-use systems chosen were secondary old (OF) or young (YF) forests, and agricultural systems (AS) in Iranduba, Belterra and Porto Velho. Only eight studies compared extractable (Mehlich-1) micronutrient contents at 21 sites with ADEs and ADJ soils, but only four studies included depths greater than 30 cm, and B and Ni were evaluated in only one study. Higher Mn and Zn, but lower Fe contents were found in ADEs both from literature data and in the present study, especially in the first 30 cm depth. Increases in extractable Ni and Cu in ADEs varied according to the site and the land use considered. Micronutrient contents tended to decrease with depth, but varied depending on the element, site, soil type and land use. Sites with modern agriculture showed few differences in extractable micronutrient contents, except for a decrease in Fe in Belterra and Mn in Porto Velho. Considering the high amounts of some micro- and macronutrients in ADEs further work is warranted concerning soil management and nutrient balance in plants grown on these soils. [ABSTRACT FROM AUTHOR]

Polychaetes are vital for evaluating the effects of toxic metals in marine systems, and sensitive molecular biomarkers should be integral to monitoring efforts. However, the few polychaete markers that exist are inconsistent, even within the same species, failing to identify gene expression changes in metal-exposed animals incurring clear metabolic costs. Comparing previously characterised polychaete metal-responsive genes with those of another carefully selected species could identify biomarkers applicable across polychaetes. The ragworm Alitta virens (Sars, 1835) is particularly suited for such comparisons due to its dominance of fully saline coastal areas, widespread distribution, large biomass, and its phylogenetic position relative to other polychaete 'omic' resources. A transcriptome atlas for A. virens was generated and an RNASeq-qPCR screening approach was used to characterise the response to chronic exposures of environmentally relevant concentrations of copper and zinc in controlled mesocosms. Genes presenting dramatic expression changes in A. virens were compared with known metal-responsive genes in other polychaetes to identify new possible biomarkers and assess those currently used. This revealed some current markers should probably be abandoned (e.g. Atox1), while others, such as GST-Omega , should be used with caution, as different polychaete species appear to upregulate distinct GST-Omega orthologues. In addition, the comparisons give some indication of genes that are induced by metal exposure across phylogenetically divergent polychaetes, including a suite of haemoglobin subunits and linker chains that could play conserved roles in metal-stress response. Although such newly identified markers need further characterisation, they offer alternatives to current markers that are plainly insufficient. Unlabelled Image • We provide a comprehensive transcriptome for the polychaete Alitta virens. • Metal-induced genes across divergent polychaetes are identified. • Current markers should be abandoned (Atox1) or used conservatively (GST-Omega). • Haemoglobins induced in divergent metal-exposed polychaetes may be better markers. [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology (WBE) is a crucial tool for health and environmental monitoring, providing real-time data on public health indicators by analysis of sewage samples. Ensuring the integrity of these samples from collection to analysis is paramount. This study investigates the effects of different cold-storage conditions on the integrity of wastewater samples, focusing on both microbiological markers (such as extractable nucleic acids, SARS-CoV-2, and crAssphage) and physicochemical parameters (including ammonium, orthophosphate, pH, conductivity, and turbidity). Composite samples from the raw wastewater influent from five wastewater treatment works in South Wales, UK, were stored at 4°C, -20°C, and -80°C, and subjected to up to six freeze-thaw cycles over one year. The study found significant effects of storage temperature on the preservation of certain WBE markers, with the best yield most frequently seen in samples stored at -80°C. However, the majority of WBE markers showed no significant difference between storage at -80°C or at 4°C, demonstrating that it may not always be necessary to archive wastewater samples at ultra-low temperatures, thus reducing CO 2 emissions and laboratory energy costs. These findings underscore the importance of optimized storage conditions to maintain sample integrity, while ensuring accurate and reliable WBE data for public health and environmental monitoring., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Objective: The worldwide spread of SARS-CoV-2 and the resulting COVID-19 pandemic has been driven by international travel. This has led to the desire to develop surveillance approaches which can estimate the rate of import of pathogenic organisms across international borders. The aim of this study was to investigate the use of wastewater-based approaches for the surveillance of viral pathogens on commercial short-haul (3.5 h transit time) roll-on/roll-off passenger/freight ferries operating between the UK and the Republic of Ireland., Methods: Samples of toilet-derived wastewater (blackwater) were collected from two commercial ships over a 4-week period and analysed for SARS-CoV-2, influenza, enterovirus, norovirus, the faecal-marker virus crAssphage and a range of physical and chemical indicators of wastewater quality., Results: A small proportion of the wastewater samples were positive for SARS-CoV-2 (8% of the total), consistent with theoretical predictions of detection frequency (4%-15% of the total) based on the national COVID-19 Infection Survey and defecation behaviour. In addition, norovirus was detected in wastewater at low frequency. No influenza A/B viruses, enterovirus or enterovirus D68 were detected throughout the study period., Conclusion: We conclude that testing of wastewater from ships that cross international maritime boundaries may provide a cost-effective and relatively unbiased method to estimate the flow of infected individuals between countries. The approach is also readily applicable for the surveillance of other disease-causing agents., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Jones, Bridgman, Pellett, Weightman, Kille, García Delgado, Cross, Cobley, Howard-Jones, Chadwick and Farkas.)

The COVID-19 pandemic demonstrated the need for rapid molecular diagnostics. Vaccination programs can provide protection and facilitate the opening of society, but newly emergent and existing viral variants capable of evading the immune system endanger their efficacy. Effective surveillance for Variants of Concern (VOC) is therefore important. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. Here we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to provide rapid and sensitive discrimination of SARS-CoV-2 VOCs that can be used at point of care, implemented in the pipelines of small or large testing facilities, and even determine the proportion of VOCs in pooled population-level wastewater samples. This technology complements sequencing efforts to allow facile and rapid identification of individuals infected with VOCs to help break infection chains. We show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants and the rapid adaptability of the technique for new and emerging VOCs., (© 2023. The Author(s).)

Background: The COVID-19 pandemic necessitated rapid real-time surveillance of epidemiological data to advise governments and the public, but the accuracy of these data depends on myriad auxiliary assumptions, not least accurate reporting of cases by the public. Wastewater monitoring has emerged internationally as an accurate and objective means for assessing disease prevalence with reduced latency and less dependence on public vigilance, reliability, and engagement. How public interest aligns with COVID-19 personal testing data and wastewater monitoring is, however, very poorly characterized., Objective: This study aims to assess the associations between internet search volume data relevant to COVID-19, public health care statistics, and national-scale wastewater monitoring of SARS-CoV-2 across South Wales, United Kingdom, over time to investigate how interest in the pandemic may reflect the prevalence of SARS-CoV-2, as detected by national testing and wastewater monitoring, and how these data could be used to predict case numbers., Methods: Relative search volume data from Google Trends for search terms linked to the COVID-19 pandemic were extracted and compared against government-reported COVID-19 statistics and quantitative reverse transcription polymerase chain reaction (RT-qPCR) SARS-CoV-2 data generated from wastewater in South Wales, United Kingdom, using multivariate linear models, correlation analysis, and predictions from linear models., Results: Wastewater monitoring, most infoveillance terms, and nationally reported cases significantly correlated, but these relationships changed over time. Wastewater surveillance data and some infoveillance search terms generated predictions of case numbers that correlated with reported case numbers, but the accuracy of these predictions was inconsistent and many of the relationships changed over time., Conclusions: Wastewater monitoring presents a valuable means for assessing population-level prevalence of SARS-CoV-2 and could be integrated with other data types such as infoveillance for increasingly accurate inference of virus prevalence. The importance of such monitoring is increasingly clear as a means of objectively assessing the prevalence of SARS-CoV-2 to circumvent the dynamic interest and participation of the public. Increased accessibility of wastewater monitoring data to the public, as is the case for other national data, may enhance public engagement with these forms of monitoring., (©Jordan P Cuff, Shrinivas Nivrutti Dighe, Sophie E Watson, Rafael A Badell-Grau, Andrew J Weightman, Davey L Jones, Peter Kille. Originally published in JMIR Infodemiology (https://infodemiology.jmir.org), 23.11.2023.)

Tributyltin (TBT) is a biocide introduced in the 1960s in antifouling paints. Despite legislation banning its use, its persistence in the environment still causes significant harm to organisms. Tributyltin is a ligand of retinoid X receptors (RXR) and ecdysteroid receptors (EcRs), which in arthropods act as homologs of RXR. Focusing on Metazoan species, this study used genomic and proteomic information from different sources to compare their three-dimensional structure, phylogenetic distribution, and amino acid sequence alterations. The objective was to identify possible patterns that relate organisms' sensitivity to TBT using the species Triops longicaudatus as the basis for the comparisons. The results showed great conservation of this protein across several species when comparing the interaction amino acids described to RXR (an EcR analog) in Homo sapiens . The three-dimensional comparison of RXR showed little conformational variation between different sequences by maintaining the interaction pocket. As for the Species Sensitivity Distribution (SSD) curve, an HC 05 = 0.2649 [0.0789-0.7082] µg/L was obtained with no specific distribution between the different taxa. Protein-ligand docking analysis was then used to confirm the SSD curve ranking of species. Still, the results showed an opposite trend that may be related, for example, to differences in the LC 50 values used in the calculations. This study serves as the first step for applying bioinformatics techniques to produce information that can be used as an alternative to animal or cellular experimentation. These techniques could be adapted to various chemicals and proteins, allowing for observations in a shorter timeframe and providing information on a broader spectrum.

We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length., Competing Interests: No competing interests were disclosed., (Copyright: © 2023 Blaxter ML et al.)

Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes., Competing Interests: No competing interests were disclosed., (Copyright: © 2023 Short S et al.)

The area destined for agricultural production in Paraná state in Brazil is ~6 million hectares, of which 79% are under no-tillage systems (NTS) that can positively affect earthworm populations. Furthermore, earthworm abundance and richness can be valuable soil quality. This study assessed earthworm communities in long-term no-tillage sites (NTS) and nearby secondary Atlantic Forest (SF) fragments. Sampling was performed in June 2018 and May 2019 using the quantitative Tropical Soil Biology and Fertility handsorting method (ISO-TSBF), complemented by qualitative sampling in three municipalities: Faxinal, Mauá da Serra and Palmeira, in NTS and SF. Eleven earthworm species, belonging to five families (Benhamiidae, Glossoscolecidae, Megascolecidae, Ocnerodrilidae, and Rhinodrilidae) were found along with seven native species (Glossoscolex sp.22, Glossoscolex sp.23, Fimoscolex sp.21, Fimoscolex sp.24, Fimoscolex sp.42, Andiorrhinus duseni and Urobenus brasiliensis) and four exotic or cosmopolitan species (Dichogaster gracilis, Amynthas gracilis, Metaphire californica and Pontoscolex corethrurus). The cosmopolitan P. corethrurus dominated Faxinal and Mauá da Serra, while in Palmeira Fimoscolex and Glossoscolex were the most abundant. Six species belonging to Glossoscolex and Fimoscolex were new to science and must be described. Overall, 239 individuals were found. In 2018 126 individuals were found (76 in NTS and 50 in SF) and in 2019, only 112 individuals were found (45 in NTS and 67 in SF). The highest earthworm abundance was in Faxinal (123 individuals), with 76 individuals in NTS and 47 in SF. In Mauá da Serra the same pattern was observed (SF>NTS), while in Palmeira in overall, fewer individuals (38) were collected (24 in NTS and 14 in SF). The NTS at Faxinal and SF Mauá da Serra in 2019 had only/more exotic/cosmopolitan species, while at the other dates and sites >50% of the specimens sampled were native species. Overall, forests had more native species than exotics: in 2018, natives represented > 75% of all specimens, but in 2019 both Faxinal and Mauá da Serra had more exotic species (> 65%), while at Palmeira, they represented 50% of the individuals. Earthworm total biomass for forest sites was higher in Faxinal (3.2 g) and NTS in Mauá da Serra (1.7 g) in 2019. Overall, the total biomass was higher in SF sites than NTS. Using a classification available for earthworm populations in no-tillage systems, all three sites were considered to have poor quality in terms of abundance (ind m-2), while for species richness, they were considered to have moderate (Faxinal and Mauá da Serra) and good quality (Palmeira).

Lepidopteran species can be both pests and also beneficial pollinators for agricultural crops. However, despite these important roles, the effects of pesticides on this diverse taxa are relatively understudied. To facilitate the assessment of pesticides and other chemical hazards on this taxa, we present a novel bioassay capable of testing chemical sensitivity to lepidopteran larvae through dietary exposure. We used Mamestra brassicae caterpillars as a model lepidopteran and tested their sensitivity for the organophosphate insecticide chlorpyrifos. We exposed larvae to an artificial diet spiked with chlorpyrifos and monitored survival over time, as well as weight change over a 96-hour exposure period. To test the repeatability and reliability of the developed bioassay, the experiment was repeated three times. The survival in time data collected enabled analysis with the General Unified Threshold of Survival (GUTS) model, recently recognized by EFSA as a ready-to-use tool for regulatory purposes. The GUTS modelling was used to derive a set of relevant toxicokinetic and toxicodynamic parameters relating to the larval response to exposure over time. We found that across the three repeats studies there was no more than a threefold difference in LC₅₀ values (13.1, 18.7 and 8.1 mg/Kg) at 48 h and fourfold difference at 96 h, highlighting the repeatability of the bioassay. We also highlighted the potential of the method to observe sub-lethal effects such as changes in weight. Finally, we discuss the applications of this new bioassay method to chemical risk assessments and its potential for use in other scenarios, such as mixture or pulsed exposure testing., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:David Spurgeon reports financial support was provided by UK Research and Innovation. Claire Badder reports financial support was provided by UKRI., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Early and accurate diagnosis is key to mitigating the impact of infectious diseases, along with efficient surveillance. This however is particularly challenging in aquatic environments due to hidden biodiversity and physical constraints. Traditional diagnostics, such as visual diagnosis and histopathology, are still widely used, but increasingly technological advances such as portable next generation sequencing (NGS) and artificial intelligence (AI) are being tested for early diagnosis. The most straightforward methodologies, based on visual diagnosis, rely on specialist knowledge and experience but provide a foundation for surveillance. Future computational remote sensing methods, such as AI image diagnosis and drone surveillance, will ultimately reduce labour costs whilst not compromising on sensitivity, but they require capital and infrastructural investment. Molecular techniques have advanced rapidly in the last 30 years, from standard PCR through loop-mediated isothermal amplification (LAMP) to NGS approaches, providing a range of technologies that support the currently popular eDNA diagnosis. There is now vast potential for transformative change driven by developments in human diagnostics. Here we compare current surveillance and diagnostic technologies with those that could be used or developed for use in the aquatic environment, against three gold standard ideals of high sensitivity, specificity, rapid diagnosis, and cost-effectiveness., (© 2022 The Authors. Reviews in Aquaculture published by John Wiley & Sons Australia, Ltd.)

Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through F st and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments., (© 2022 Perry et al.)

This study reports on the effects of long-term exposure to the metals arsenic (As), cadmium (Cd) and the polycyclic aromatic hydrocarbon fluoranthene on the survival, growth, development and DNA methylation status of the earthworm Lumbricus rubellus . Exposures to the three chemicals were conducted over their whole juvenile developmental period from egg to adult. Significant effects on one or more measured endpoints were found for all three chemicals. Arsenic had no effect on survival, but had a significant effect on growth rates at concentrations of 36 mg/kg or higher and also slowed the rate of maturation. Cadmium significantly reduced juvenile survival at 500 mg/kg, juvenile growth at 148 mg/kg and maturation rates at all tested concentrations. Fluoranthene had no effect on survival or the developmental period, but did significantly reduce growth rates at 800 mg/kg. Effects at these concentrations are consistent with the known effects of these three chemicals on earthworms from previous studies conducted mainly with Eisenia fetida . Both As and Cd had no effect on DNA methylation patterning in earthworms measured at the end of the exposure. Fluoranthene was shown, for the first time. to have an effect on a species' DNA methylation levels. These results suggest that apical phenotypic changes for As and Cd are not necessarily associated with changes in DNA methylation profiles. However, exposure to the organic chemical fluoranthene influenced DNA methylation patterns, suggesting wider remodelling of the epigenome for this chemical.

Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia., (© 2021 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Neonicotinoids are currently licensed for use in 120 countries, making accurate nontarget species sensitivity predictions critical. Unfortunately, such predictions are fraught with uncertainty, as sensitivity is extrapolated from only a few test species and neonicotinoid sensitivities can differ greatly between closely related taxa. Combining classical toxicology with de novo toxicogenomics could greatly improve sensitivity predictions and identify unexpectedly susceptible species. We show that there is a >30-fold differential species sensitivity (DSS) for the neonicotinoid imidacloprid between five earthworm species, a critical nontarget taxon. This variation could not be explained by differential toxicokinetics. Furthermore, comparing key motif expression in subunit genes of the classical nicotinic acetylcholine receptor (nAChR) target predicts only minor differences in the ligand binding domains (LBDs). In contrast, predicted dissimilarities in LBDs do occur in the highly expressed but nonclassical targets, acetylcholine binding proteins (AChBPs). Critically, the predicted AChBP divergence is capable of explaining DSS. We propose that high expression levels of putative nonsynaptic AChBPs with high imidacloprid affinities reduce imidacloprid binding to critical nAChRs involved in vital synaptic neurotransmission. This study provides a clear example of how pragmatic interrogation of key motif expression in complex multisubunit receptors can predict observed DSS, thereby informing sensitivity predictions for essential nontarget species.

Agricultural development is a major threat to global biodiversity, and effective conservation actions are crucial. Physiological repercussions of life alongside human-modified landscapes can undermine adaptable species' health and population viability; however, baseline data are lacking for many wildlife species. We assessed the physiological status of a generalist carnivore, the Malay civet ( Viverra tangalunga ), persisting within an extensively human-modified system in Sabah, Malaysian Borneo. We characterized hematology and serum biochemistry panels from civets sampled across a mosaic landscape comprising tropical forest fragments and oil palm plantations. Intra-population variation in certain blood parameters were explained by expected biological drivers such as sex, age category and sampling season. Furthermore, we determined several erythrocyte measures, immune cell counts and dietary biochemistry markers significantly varied with proximity to oil palm plantation boundaries. These findings were supported by a case study, whereby blood profiles of GPS collared male civets were contrasted based on their exclusive use of forests or use of oil palm plantations. These data provide robust and valuable first insights into this species' physiological status and suggest agricultural landscapes are impacting the persisting population., (© The Author(s) 2020. Published by Oxford University Press and the Society for Experimental Biology.)

The interaction of a living organism with external foreign agents is a central issue for its survival and adaptation to the environment. Nanosafety should be considered within this perspective, and it should be examined that how different organisms interact with engineered nanomaterials (NM) by either mounting a defensive response or by physiologically adapting to them. Herein, the interaction of NM with one of the major biological systems deputed to recognition of and response to foreign challenges, i.e., the immune system, is specifically addressed. The main focus is innate immunity, the only type of immunity in plants, invertebrates, and lower vertebrates, and that coexists with adaptive immunity in higher vertebrates. Because of their presence in the majority of eukaryotic living organisms, innate immune responses can be viewed in a comparative context. In the majority of cases, the interaction of NM with living organisms results in innate immune reactions that eliminate the possible danger with mechanisms that do not lead to damage. While in some cases such interaction may lead to pathological consequences, in some other cases beneficial effects can be identified., (© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Silver nanoparticles (Ag NPs) have been used in numerous consumer products and may enter the soil through the land application of biosolids. However, little is known about the relationship between Ag NP exposure and their bioavailability for soil organisms. This study aims at comparing the uptake and elimination kinetics of Ag upon exposures to different Ag forms (NPs and ionic Ag (as AgNO3)) in the isopod Porcellionides pruinosus. Isopods were exposed to contaminated Lufa 2.2 soil or alder leaves as food. Uptake and elimination rate constants for soil exposure did not significantly differ between Ag NPs and ionic Ag at 30 and 60 mg Ag/kg. For dietary exposure, the uptake rate constant was up to 5 times higher for Ag NPs than for AgNO3, but this was related to feeding activity and exposure concentrations, while no difference in the elimination rate constants was found. When comparing both routes, dietary exposure resulted in lower Ag uptake rate constants but elimination rate constants did not differ. A fast Ag uptake was observed from both routes and most of the Ag taken up seemed not to be eliminated. Synchrotron X-ray fluorescence showed Ag in the S-cells of the hepatopancreas, thus supporting the observations from the kinetic experiment (i.e. low elimination). In addition, our results show that isopods have an extremely high Ag accumulation capacity, suggesting the presence of an efficient Ag storage compartment.

Copper, though toxic in excess, is an essential trace element that serves as a cofactor in many critical biological processes such as respiration, iron transport, and oxidative stress protection. To maintain this balance between requirement and toxicity, biological systems have developed intricate systems allowing the preservation of homeostasis while ensuring delivery of copper to the appropriate cellular component. The nematode Caenorhabditis elegans was exploited to assess the effects of copper toxicity at the population level to identify key changes in life cycle traits including, lethality, brood size, generation time, growth, and life span. To enhance our understanding of the complexities of copper homeostasis at the genetic level, the expression profile and functional significance of a putative copper cytoplasmic metallochaperone cutc-1 were analyzed. Using quantitative PCR technology, cutc-1 was found to be downregulated with increasing CuSO(4) concentrations. However, although total (whole body) copper levels increased in nematodes exposed to elevated levels of copper, wild-type and knock down of cutc-1 by RNA-mediated interference (RNAi) were statistically indistinguishable. Nevertheless, RNAi of cutc-1 affected brood size, growth and induced a marked increase in protruding vulva and bagging phenotypes at higher copper exposures. This indicates that cutc-1 plays a crucial role in the protection from excess copper.

The ubiquitous protein metallothionein (MT) has proven to be a major player not only in the homeostasis of Cu(I) and Zn(II), but also binds all the Group 11 and 12 metals. Metallothioneins are characterised by the presence of numerous cys-x-cys and cys-cys motifs in the sequence and are found naturally with either one domain or two, linked, metal-binding domains. The use of chains of these metal-thiolate domains offers the possibility of creating chemically tuneable and, therefore, chemically dependent electrochemical or photochemical surface modifiers or as nanomachinery with nanomechanical properties. In this work, the metal-binding properties of the Cd(4)-containing domain of alpha-rhMT1a assembled into chains of two and three concatenated domains, that is, "necklaces", have been studied by spectrometric techniques, and the interactions within the structures modelled and interpreted by using molecular dynamics. These chains are metallated with 4, 8 or 12 Cd(II) ions to the 11, 22, and 33 cysteinyl sulfur atoms in the alpha-rhMT1a, alphaalpha-rhMT1a, and alphaalphaalpha-rhMT1a proteins, respectively. The effect of pH on the folding of each protein was studied by ESI-MS and optical spectroscopy. MM3/MD simulations were carried out over a period of up to 500 ps by using force-field parameters based on the reported structural data. These calculations provide novel information about the motion of the clustered metallated, partially demetallated, and metal-free peptide chains, with special interest in the region of the metal-binding site. The MD energy/time trajectory conformations show for the first time the flexibility of the metal-sulfur clusters and the bound amino acid chains. We report unexpected and very different sizes for the metallated and demetallated proteins from the combination of experimental data, with molecular dynamics simulations.

Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.

This study sets out to examine the potential of a suite of novel molecular biomarkers as early warning indicators of environmental state and damage. Transcriptional responses of four genes, metallothionein 1 and 2, amine oxidase, and the lysosomal associated glycoprotein, were measured in the earthworm Lumbricus rubellus exposed to increasing concentrations of cadmium and copper in OECD soil. These responses were compared to metal body concentrations and lifecycle parameters: survival, cocoon production, and growth. Adverse physiological effects were observed at concentrations 1/3rd to 1/10th those of the artificial soil LC50. Multivariate statistics, principal component analysis (PCA), was used to investigate the correlations between the different variables. Three key components were derived explaining 77.6% of the variance, with component 1 contributing 32.4%, component 2 contributing 26.7%, and component 3 contributing 18.5%. These components were interpreted in terms of population health, pollutant exposure, and detoxification pathways, respectively. It is proposed that the use of such a suite of biomarkers could serve as indicators of the "health" of the soil environment and provide early warning signals of potential danger to the biota or as a means of monitoring soil remediation.

A beta-ketoacyl-acyl carrier protein (ACP) synthase III (KAS III; short-chain condensing enzyme) has been partly purified from pea leaves. The enzyme, which had acetyl-CoA:ACP acyltransferase (ACAT) activity, was resolved from a second, specific, ACAT protein. The KAS III enzyme had a derived molecular mass of 42 kDa (from its cDNA sequence) and operated as a dimer. Its enzymological characteristics were similar to those of two other plant KAS III enzymes except for its inhibition by thiolactomycin. A derivative of thiolactomycin containing a longer (C8 saturated) hydrophobic side-chain (compound 332) was a more effective inhibitor of pea KAS III and showed competitive inhibition towards malonyl-ACP whereas thiolactomycin showed uncompetitive characteristics at high concentrations. This difference may be due to the better fit of compound 332 into a hydrophobic pocket at the active site. A full-length cDNA for the pea KAS III was isolated. This was expressed in Escherichia coli as a fusion protein with glutathione S-transferase in order to facilitate subsequent purification. Demonstrated activity in preparations from E. coli confirmed that the cDNA encoded a KAS III enzyme. Furthermore, the expressed KAS III had ACAT activity, showing that the latter was inherent. The derived amino acid sequence of the pea cDNA showed 81-87% similarity to that for other plant dicotyledon KAS IIIs, somewhat less for Allium porrum (leek, 71%) and for Porphyra spp. (62%), Synechocystis spp. (65%) and various bacteria (42-65%). The pea KAS III exhibited four areas of homology, three of which were around the active-site Cys(123), His(323) and Asn(353). In addition, a stretch of 23 amino acids (residues 207-229 in the pea KAS III) was almost completely conserved in the plant KAS IIIs. Modelling this stretch showed they belonged to a peptide fragment that fitted over the active site and contained segments suggested to be involved in substrate binding and in conformational changes during catalysis, as well as an arginine suggested to participate in the acid-base catalytic mechanism.