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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).

International audience; 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.

With the growing global concern on pesticide management, the relationship between its environmental recalcitrance, food security and human health has never been more relevant. Pesticides residues are known to cause significant environmental contamination. Here, we present a case study on long-term no-tillage farming systems in Brazil, where Glyphosate (GLY) has been applied for more than 35 years. GLY and its main breakdown product, aminomethylphosphonic acid (AMPA) were determined in topsoil (0–10 cm) samples from no-tillage fields and nearby subtropical secondary forests by high-performance liquid chromatography coupled with a fluorescence detector. In addition, the presence of carbamates, organochlorines, organophosphates and triazines were also screened for. GLY and AMPA were present in all soil samples, reaching values higher than those described for soils so far in the literature. A significant decrease for AMPA was observed only between the secondary forest and the farm’s middle slope for site B. GLY and AMPA were observed respectively at peak concentrations of 66.38 and 26.03 mg/kg soil. GLY was strongly associated with forest soil properties, while AMPA associated more with no-tillage soil properties. Soil texture was a significant factor contributing to discrimination of the results as clay and sand contents affect GLY and AMPA retention in soils. This was the first study to report DDT and metabolites in consolidated no-tillage soils in Brazil (a pesticide fully banned since 2009). Based on human risk assessment conducted herein and the potential risk of GLY to local soil communities, this study offers a baseline for future studies on potential adverse effects on soil biota, and mechanistic studies. Made available in DSpace on 2021-05-11T15:31:28Z (GMT). No. of bitstreams: 1 Silva-Brown-etal-2021-article-Scientific-Reports.pdf: 1607820 bytes, checksum: cb964e5188232ffe395597376eab01c7 (MD5) Previous issue date: 2021

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 depend 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 characterised. OBJECTIVE This study assesses the associations between internet search volume data relevant to COVID-19, public healthcare statistics and national-scale wastewater monitoring of SARS-CoV-2 across South Wales, UK 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. 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 RT-qPCR SARS-CoV-2 data generated from wastewater in South Wales, UK, using multivariate linear models and correlation analysis. RESULTS Wastewater monitoring data suggests that prevalence of the virus exceeded that reported in self-testing national reports. Google search volumes surrounding the COVID-19 pandemic also decreased across the same period, potentially suggesting a reduction in public interest is reflected in lower volumes of self-testing and reporting with consequential loss of accuracy of those data. CONCLUSIONS Wastewater monitoring presents a valuable means for assessing population-level prevalence of SARS-CoV-2. The importance of such monitoring is increasingly clear as a means of objectively assessing the prevalence of COVID-19 despite 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.

The ability to detect small metallic nanoparticles by optical microscopy inside environmentally relevant species may have a wide impact for ecotoxicology studies. Here, we demonstrate four-wave mixing microscopy on individual small gold nanoparticles inside the hepatopancreas of Oniscus Asellus, a terrestrial isopod, which ingests metals found in the soil. After the exposure to food containing 10 nm radius gold nanoparticles, hepatopancreas tubules were collected, and nanoparticles were imaged by four-wave mixing microscopy with high contrast, locating them with sub-cellular resolution in the volume, despite the significant light scattering from these multi-cellular organs. Notably, the ultrafast dynamics of the four-wave-mixing non-linearity of gold nanoparticles resonantly excited and probed at their localized surface plasmon allows them to be distinguished from other metal deposits in the hepatopancreas, which manifest as a long-lived photothermal contrast. Our findings bring unexpected insight into the location of gold nanoparticles in relation to the cell types forming the hepatopancreas. Considering its simplicity, volumetric imaging capabilities, specificity, and compatibility with living cell studies, four-wave mixing microscopy holds great potential to investigate the fate of metal nanoparticles inside biological systems.

Here, we explore the high-altitude adaptions and acclimatisation of

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.

Context Agricultural land use is expanding and is a major driver of the biodiversity crisis. Land use planning initiatives seeking to optimize wildlife conservation are hindered by a lack of baseline data quantifying species’ tolerance to human-modified landscapes. Objectives We explored the influence of landscape characteristics on the fine-scale space-use patterns of a model generalist carnivore, the Malay civet (Viverra tangalunga), within degraded tropical forests and oil palm plantations. Methods We collected over 20,000 GPS locations from 21 male civets in Sabah, Malaysian Borneo to evaluate the species’ space-use patterns and habitat utilization processes. We used movement-based modeling to determine home ranges, and combined the results with high-resolution remotely sensed habitat characteristics. We developed resource utilization functions to determine individual and population-level functional responses to proximity to plantation edge, distance to water, terrain ruggedness, forest structure, and functional diversity. Results Civets foraged within oil palm plantations, yet all animals utilized forests. Home ranges scaled with proportion of plantation within both total and core ranges. Resource utilization functions reported individualism in the species’ responses to habitat characteristics. At the population-scale, civets consistently and more intensely used habitats closer to plantation edges and taller tree canopies. Conclusions Although plantations did not pose an inhospitable matrix, oil palm agriculture is a less suitable habitat than remnant forests for civets. Proximity measures and forest structure influenced the spatial behaviors of this adaptable generalist, highlighting the importance of protected areas. We recommend land-sparing and -sharing approaches to facilitate carnivore persistence across oil palm degraded landscapes.

The COVID-19 pandemic continues to pose a threat to the general population. The ongoing vaccination programs provide protection to individuals and facilitate the opening of society and a return to normality. However, emergent and existing SARS-CoV-2 variants capable of evading the immune system endanger the efficacy of the vaccination strategy. To preserve the efficacy of SARS-CoV-2 vaccination globally, aggressive and effective surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) is required. 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. In this work, we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to allow rapid and sensitive discrimination of VOCs, that can be used at point of care and/or implemented in the pipelines of small or large testing facilities, and even determine proportion of VOCs in pooled population-level wastewater samples. This technology aims to complement the ongoing sequencing efforts to allow facile and, crucially, rapid identification of individuals infected with VOCs to help break infection chains. Here, 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. In addition, we show the rapid adaptability of the technique for new and emerging VOCs such as Omicron.Short abstractThe COVID-19 pandemic continues to pose a threat as emergent and existing SARS-CoV-2 variants endanger the efficacy of the vaccination strategy. Rapid surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) would be assisted by effective molecular diagnostics procedures. Here we develop the recent SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) for rapid and sensitive discrimination of VOCs to complement sequencing and allow rapid identification of individuals infected with VOC. We show our assays can be implemented with test samples in the pipelines of large testing facilities, as well as determine the proportion of VOCs in pooled population level wastewater samples and has potential applicability at point of care. We demonstrate the optimisation of new VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validate these with samples from the Cardiff University Testing Service, as well as the applicability of VarLOCK to national-level wastewater surveillance of SARS-CoV-2 variants. We also demonstrate the rapid adaptability of the technique for new and emerging VOCs such as Omicron.

Zinc has been known to be essential for cell division for over 40 years but the molecular pathways involved remain elusive. Cellular zinc import across biological membranes necessitates the help of zinc transporters such as the SLC39A family of ZIP transporters. We have discovered a molecular process that explains why zinc is required for cell division, involving two highly regulated zinc transporters, as a heteromer of ZIP6 and ZIP10, providing the means of cellular zinc entry at a specific time of the cell cycle that initiates a pathway resulting in the onset of mitosis. Crucially, when the zinc influx across this heteromer is blocked by ZIP6 or ZIP10 specific antibodies, there is no evidence of mitosis, confirming the requirement for zinc influx as a trigger of mitosis. The zinc that influxes into cells to trigger mitosis additionally changes the phosphorylation state of STAT3 converting it from a transcription factor to a protein that complexes with this heteromer and pS38Stathmin, the form allowing microtubule rearrangement as required in mitosis. This discovery now explains the specific cellular role of ZIP6 and ZIP10 and how they have special importance in the mitosis process compared to other ZIP transporter family members. This finding offers new therapeutic opportunities for inhibition of cell division in the many proliferative diseases that exist, such as cancer. Electronic supplementary material The online version of this article (10.1007/s00018-020-03616-6) contains supplementary material, which is available to authorized users.

A critical question for read across of the hazards of nanomaterials is the degree to which their mechanisms of action differ from those of their bulk chemical constituents. It has been established that metal and metal oxide nanoparticles (NPs) can be accumulated by invertebrate species. Moreover, it has been hypothesised that the observed toxicity resulting on exposure to these nanomaterials is most likely to be associated with the releases of ions from external or internal dissolution leading ultimately to toxicity. However, mechanistic confirmation of the similar modes of action for metal oxide nanomaterials and metal ions in studies invertebrates are largely lacking. Therefore, here we present a toxicogenomic study using exposed individuals of the earthworm Eisenia fetida from a single genetic lineage. We compared gene expression and pathway responses through RNA-seq analysis at equitoxic concentrations (EC50 for reproduction) of ZnO NPs and ionic Zn. We found similar transcriptomic effects for both Zn forms with genetic signatures of tight control of cytosolic Zn concentrations through expression changes of genes encoding several Zn transporters. Activation and regulation of JUN, MAP and JNK kinases indicated a cellular response to the increased Zn concentrations of both forms with compound binding terms also enriched. Our results illustrate the need to consider both toxicokinetic and toxicodynamic mechanisms in the development of adverse outcome pathways for nanomaterials.

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.

Nanopore sequencing facilitates the rapid and cost-effective sequencing of long fragment DNA for a massive range of applications. When looking to holistically analyse low-yield DNA samples using nanopore sequencing, the optimal method is likely to involve the PCR Barcoding Kit. This effectively involves blunt end ligation of priming sites onto all extant DNA for holistic amplification to achieve yields suitable for nanopore sequencing. The currently available kits from nanopore facilitate the multiplexing of 96 samples in one sequencing run using this method, but the reagent costs are inherently multiplicative. This protocol is designed to streamline (in terms of cost, reagents and time) the process of sequencing up to 96 samples of genomic DNA through nanopore sequencing. This protocol is best applied to large numbers of samples (up to 96). For smaller numbers of samples, consider the smaller "PCR Barcoding" kits provided by nanopore which similarly achieve holistic DNA amplification and sequencing, but without the need for additional adapter ligation. The protocol is best suited to samples with low DNA yields (100 ng input is recommended). If you can input 1000 ng of DNA from each of your samples, consider using the 96-well Ligation Kit from Oxford Nanopore which can similarly be streamlined in terms of cost and time, but avoids the amplification step.

Manufactured nanoparticles (MNPs) undergo transformation immediately after they enter wastewater treatment streams and during their partitioning to sewage sludge, which is applied to agricultural soils in form of biosolids. We examined toxicogenomic responses of the model nematode Caenorhabditis elegans to pristine and transformed ZnO-MNPs (phosphatized pZnO- and sulfidized sZnO-MNPs). To account for the toxicity due to dissolved Zn, a ZnSO4 treatment was included. Transformation of ZnO-MNPs reduced their toxicity by nearly ten-fold, while there was almost no difference in the toxicity of pristine ZnO-MNPs and ZnSO4. This combined with the fact that far more dissolved Zn was released from ZnO- compared to pZnO- or sZnO-MNPs, suggests that dissolution of pristine ZnO-MNPs is one of the main drivers of their toxicity. Transcriptomic responses at the EC30 for reproduction resulted in a total of 1161 differentially expressed genes. Fifty percent of the genes differentially expressed in the ZnSO4 treatment, including the three metal responsive genes (mtl-1, mtl-2 and numr-1), were shared among all treatments, suggesting that responses to all forms of Zn could be partially attributed to dissolved Zn. However, the toxicity and transcriptomic responses in all MNP treatments cannot be fully explained by dissolved Zn. Two of the biological pathways identified, one essential for protein biosynthesis (Aminoacyl-tRNA biosynthesis) and another associated with detoxification (ABC transporters), were shared among pristine and one or both transformed ZnO-MNPs, but not ZnSO4. When comparing pristine and transformed ZnO-MNPs, 66% and 40% of genes were shared between ZnO-MNPs and sZnO-MNPs or pZnO-MNPs, respectively. This suggests greater similarity in transcriptomic responses between ZnO-MNPs and sZnO-MNPs, while toxicity mechanisms are more distinct for pZnO-MNPs, where 13 unique biological pathways were identified. Based on these pathways, the toxicity of pZnO-MNPs is likely to be associated with their adverse effect on digestion and metabolism.

Efficient management of drinking water quality is critical for the water supply, so effective monitoring of supply and storage systems is a priority. This project aims to predict the presence of Taste and Odour (T&O) compounds in drinking water reservoirs, using molecular analyses and smart in-situ monitoring systems. The most common T&O compounds, Geosmin and 2-MIB, are secondary metabolites that can be produced in waterbodies by cyanobacteria and actinomycetes and impact drinking water taste and odour. Although there is no evidence of related health risks, they can be perceived by humans at very low concentrations (5-10 ng/L) and the treatment process to remove them from drinking water is costly. Early assessment of T&O risk is crucial, but currently requires time-consuming and costly sampling as well as laboratory analysis which prevents real-time monitoring and a timely management response.Cyanobacterial species responsible for T&O production can be monitored with eDNA techniques and potentially provide an early warning of T&O episodes. Moreover, detection of the genes that are responsible for T&O production within the DNA of the freshwater community can help to speed up analysis. We show that qPCR methods can target the Geosmin synthase gene (geoA) and that this correlates significantly with Geosmin concentrations >15 ng/L. Alternatively, in-situ sensors that can be deployed remotely and transmit data, can provide real-time monitoring for early warning and potentially predictive capacity. Commercially available sensors do not currently exist for T&O compounds, but they do for many other water quality parameters. We consider the analytes that could be effective for T&O warning systems, using a Welsh reservoir as an exemplar case. Assessment of nutrient dynamics suggests N and P ratios are critical, hence we evaluate the sensors that are available for these compounds and associated environmental controls on their behaviour. We present recommendations for the design of an in-situ monitoring programme and introduce the planned tests that will evaluate it.

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.

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.

Agriculture is a major threat to tropical biodiversity. We determined the first hematology and serum biochemistry panels for wild Malay civets persisting within a fragmented landscape. In addition to expected biological drivers of variation, select blood parameters predictably varied with proximity to oil palm agriculture., 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.

With the growing global concern on pesticide management, the relationship between its environmental recalcitrance, food security and human health has never been more relevant. Pesticides residues are known to cause significant environmental contamination. The present study focused on long-term no-tillage farming systems and subtropical forests in Brazil, where Glyphosate (GLY) has been applied for more than 35 years. GLY and the main breakdown product of glyphosate, aminomethylphosphonic acid (AMPA) were determined by high-performance liquid chromatography coupled with a fluorescence detector. In addition, the presence of carbamates, organochlorines, organophosphates and triazines were also detected. GLY and AMPA were omnipresent in soil samples, reaching values higher than those described for soils previously in the literature. GLY and AMPA were observed respectively at peak concentrations of 66.38 and 26.03 mg/kg soil. GLY was strongly associated with forest soil properties, while AMPA associated with no-tillage soil properties. The texture was a significant factor that contributed to the maximum discrimination of the results since clay and sand contents influence GLY and AMPA retention in soils. This was the first study to report DDT and metabolites in consolidated no-tillage soils in Brazil (a pesticide fully banned 2009). Based on human risk assessment and the potential risk of GLY to local soil communities, this study offers a baseline for future studies that will be crucial to understand the toxicity mechanisms on non-target soil biota.

Because it is only possible to test chemicals for effects on a restricted range of species and exposure scenarios, ecotoxicologists are faced with a significant challenge of how to translate the measurements in model species into predictions of impacts for the wider range of species in ecosystems. Because of this challenge, within ecotoxicology there is no more fundamental aspect than to understand the nature of the traits that determine sensitivity. To account for the uncertainties of species extrapolations in risk assessment, “safety factors” or species sensitivity distributions are commonly used. While valuable as pragmatic tools, these approaches have no mechanistic grounding. Here we highlight how mechanistic information that is increasingly available for a range of traits can be used to understand and potentially predict species sensitivity to chemicals. We review current knowledge on how toxicokinetic, toxicodynamic, physiological, and ecological traits contribute to differences in sensitivity. We go on to discuss how this information is being used to make predictions of sensitivity using correlative and trait-based approaches, including comparisons of target receptor orthologs. Finally, we discuss how the emerging knowledge and associated tools can be used to enhance theoretical and applied ecotoxicological research through improvements in mechanistic modeling, predictive ecotoxicology, species sensitivity distribution development, mixture toxicity assessment, chemical design, biotechnology application and mechanistically informed monitoring.

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., All authors were supported by the EU H2020 project PANDORA (GA 671881). The authors gratefully acknowledge the following additional financial support: EU H2020 project ENDONANO (GA 812661; PI, AD, VFP); the Italian Ministry of Research Flagship project InterOmics (DB, PI); the Austrian FWF Doctoral Program W1213: Immunity in Cancer and Allergy (ICA; AD, JHH); Catalan Agència de Gestió d'Ajuts Universitaris i de Recerca (2017‐SGR‐1431; VFP, NGB), Ramon y Cajal program (RYC‐2012‐10991; NGB); Severo Ochoa program from Spanish MINECO (Grant No. SEV‐2017‐0706; VFP, NGB); CERCA Programme/Generalitat de Catalunya (NGB). Supported by the project LO1509 of the Ministry of Education, Youth and Sports (Czech Republic) for providing the electron microscopy images.

Phylogenetically distant parasites often infect the same host. Indeed, co-infections can occur at levels greater than expected by chance and are sometimes hyperparasitic. The amphipod Echinogammarus marinus presents high levels of co-infection by two intracellular and vertically transmitted parasites, a paramyxid (Paramarteilia sp. Em) and a microsporidian strain (Dictyocoela duebenum Em). This co-infection may be hyperparasitic and result from an exploitative ‘hitchhiking’ or a symbiotic relationship between the parasites. However, the best-studied amphipod species are often collected from contaminated environments and may be immune-compromised. Immune-challenged animals frequently present co-infections and contaminant-exposed amphipods present significantly higher levels of microsporidian infection. This suggests the co-infections in E. marinus may result from contaminant-associated compromised immunity. Inconsistent with hyperparasitism, we find that artificial infections transmit Paramarteilia without microsporidian. Our population surveys reveal the co-infection relationship is geographically widespread but find only chance co-infection between the Paramarteilia and another species of microsporidian, Dictyocoela berillonum. Furthermore, we identify a haplotype of the Paramarteilia that presents no co-infection, even in populations with otherwise high co-infection levels. Overall, our results do not support the compromised-immunity hypothesis but rather that the co-infection of E. marinus, although non-hyperparasitic, results from a relationship between specific Paramarteilia and Dictyocoela duebenum strains.

Background Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Furthermore, the occurrence of L. rubellus lineages across the UK allows for inferences of mechanisms associated with drivers of speciation and local adaptation. Results Using RADseq, we were able to define population structure between the two lineages through the use of draft genomes for each, demonstrating an absence of admixture between lineages and that populations over extensive geographic distances form discrete populations. Between the two British lineages, we were able to provide evidence for selection near to genes associated with epigenetic and morphological functions, as well as near a gene encoding a pheromone. Earthworms inhabiting highly contaminated soils bare close genomic resemblance to those from proximal control soils. We were able to define a number of SNPs that largely segregate populations and are indicative of genes that are likely under selection for managing metal toxicity. This includes calcium and phosphate-handling mechanisms linked to lead and arsenic contaminants, respectively, while we also observed evidence for glutathione-related mechanisms, including metallothionein, across multiple populations. Population genomic end points demonstrate no consistent reduction in nucleotide diversity, or increase in inbreeding coefficient, relative to history of exposure. Conclusions Though we can clearly define lineage membership using genomic markers, as well as population structure between geographic localities, it is difficult to resolve markers that segregate entirely between populations in response to soil metal concentrations. This may represent a highly variable series of traits in response to the heterogenous nature of the soil environment, but ultimately demonstrates the maintenance of lineage-specific genetic variation among local populations. L. rubellus appears to provide an exemplary system for exploring drivers for speciation, with a continuum of lineages coexisting across continental Europe, while distinct lineages exist in isolation throughout the UK. Electronic supplementary material The online version of this article (10.1186/s12863-017-0557-8) contains supplementary material, which is available to authorized users.

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.

Amazonian rainforests once thought to hold an innate pristine wilderness, are increasingly known to have been densely inhabited by populations showing a diverse and complex cultural background prior to European arrival. To what extent these societies impacted their landscape is unclear. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies as a result of more sedentary habits. Much is known of the chemistry of these soils, yet their zoology, have been neglected. Hence, we characterised soil macroinvertebrate communities and activity in these soils at nine archaeological sites in three Amazonian regions. We found 667 morphospecies and a tenacious pre-Columbian footprint, with 43% of species found exclusively in ADEs. The soil biological activity is higher in the ADEs when compared to adjacent reference soils, and it is associated with higher biomass and richness of organisms known to engineer the ecosystem. We show that these habits have a unique pool of species, however, the contemporary land-use in ADEs drives nutrient decay and threats biodiversity. These findings support the idea that Humans have built and sustained a contrasting high fertile system that persisted until our days and irreversibly altered the biodiversity patterns in Amazonia.

Zinc has been known to be essential for cell division for over 40 years, but the exact mechanism remains elusive. Cellular zinc import necessitates the help of the SLC39A family of ZIP transporters, two of which are known to be essential for gastrulation, which involves cell rounding and detachment. We have discovered a new molecular process that explains why zinc is required for cell division, involving these two zinc channels ZIP6 (previously LIV-1) and ZIP10 as a heteromer, providing cellular zinc entry to initiate the onset of mitosis. Crucially, blocking this ZIP6/ZIP10 heteromer-mediated zinc influx by specific antibodies completely prevents mitosis, even in the presence of mitosis causing agent nocodazole, confirming the requirement for this zinc influx as a mitosis trigger. This zinc influx additionally changes STAT3 phosphorylation to pS727STAT3, a poorly understood form of STAT3, stopping transcription factor activity and complexing with this heteromer throughout mitosis alongside pS38Stathmin, the form required for mitotic microtubule rearrangement. This discovery clarifies a role for ZIP6, ZIP10 and STAT3 in mitosis in addition to their known role in gastrulation, offering new opportunities for investigating the processes of cell development and cell division.

The scale of variation in species sensitivity to toxicants has been theoretically linked to mode of action. Specifically, it has been proposed there will be greater variations for chemicals with a putative specific biological target than for toxicants with a non-specific narcotic mechanism. Here we test the hypothesis that mode of action is related to variation in sensitivity in a specifically designed experiment for species from a single ecologically important terrestrial taxa, namely earthworms. Earthworm toxicity tests were conducted with five species for four chemicals, providing a series of increasingly complex modes of action: a putative narcotic polycyclic aromatic hydrocarbon (fluoranthene), and three insecticides (chlorpyrifos, cypermethrin, imidacloprid) with known neuronal receptor targets. Across all the chemicals, the standard epigeic test species Eisenia fetida and Lumbricus rubellus, were generally among the two least sensitive, while the endogenic Aporrectodea caliginosa and Megascolecidae Amynthas gracilis were generally more sensitive (never being among the two least sensitive species). This indicates a potential for bias in the earthworm ecotoxicology literature, which is dominated by studies in epigeic Lumbricidae, but contains few endogeic or Megascolecidae data. Results confirmed the lowest range of variation in sensitivities for effects on reproduction was for fluoranthene (2.5 fold). All insecticides showed greater variation for species sensitivity (cypermethrin: 7.5 fold, chlorpyrifos: 10.3 fold, imidacloprid: 31.5 fold) consistent with the specific mechanisms of the pesticides. Difference in toxicodynamics, based on mode of action specificity and receptor complexity was reflected in the magnitude of sensitivity variation. However, measurements of tissue concentrations also indicated the potential importance of toxicokinetics in explaining species sensitivity variations for chlorpyrifos and cypermethrin.