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Mercury emissions from artisanal and small-scale gold mining throughout the Global South exceed coal combustion as the largest global source of mercury. We examined mercury deposition and storage in an area of the Peruvian Amazon heavily impacted by artisanal gold mining. Intact forests in the Peruvian Amazon near gold mining receive extremely high inputs of mercury and experience elevated total mercury and methylmercury in the atmosphere, canopy foliage, and soils. Here we show for the first time that an intact forest canopy near artisanal gold mining intercepts large amounts of particulate and gaseous mercury, at a rate proportional with total leaf area. We document substantial mercury accumulation in soils, biomass, and resident songbirds in some of the Amazon’s most protected and biodiverse areas, raising important questions about how mercury pollution may constrain modern and future conservation efforts in these tropical ecosystems. The Peruvian Amazon is facing the highest known input of mercury pollution of any ecosystem globally. Intact forests located near artisanal gold mining are particularly at risk from this toxin.

As biodiversity loss continues to accelerate, there is a critical need for education and biomonitoring across the globe. Portable technologies allow for in situ molecular biodiversity monitoring that has been historically out of reach for many researchers in habitat nations. In the realm of education, portable tools such as DNA sequencers facilitate in situ hands-on training in real-time sequencing and interpretation techniques. Here, we provide step-by-step protocols as a blueprint for a terrestrial conservation genetics field training program that uses low-cost, portable devices to conduct genomics-based training directly in biodiverse habitat countries.

Andean bears ( Tremarctos ornatus ) forage extensively on bromeliads ( Puya spp.) across their range, although their selectivity for bromeliads is less understood. We report on foraging activity by Andean bears on two species of bromeliad, Puya leptostachya and Puya membranacea , in high elevation puna grasslands (3499–3806 m.a.s.l) within and near Manu National Park (MNP) in SE Peru. We established two ridgeline transects (inside and outside MNP) with perpendicular transects running downslope. We recorded whether bromeliad plants were foraged by Andean bears on four separate sampling occasions that included wet and dry seasons from July 2017 to August 2018. We observed foraging by Andean bears at 6.8% of the available individual plants spread across 16.7% of the available patches. We utilized Resource Selection Functions to evaluate the environmental factors influencing the selection of bromeliad patches by Andean bears for foraging. Andean bears showed selection for Puya leptostachya over Puya membranacea , preferring to forage during the dry season at higher density patches of younger vegetative-stage bromeliads, possibly due to the increased bioavailability of nutrients in the basal meristematic plant tissue the bears prefer to eat. Andean bears selected bromeliad patches growing on east-facing, steep, high-altitude slopes, in a band near the cloud forest edge, which likely reflected a combination of optimal growing conditions for the bromeliads and habitat selection by the bears. Observations of foraging on grassland bromeliads occurred almost exclusively within the boundaries of MNP, which may in part reflect bears avoiding cattle impacts outside of the park. Andean bears showed active behavioral selection for bromeliads within the puna grasslands, and we recommend that grassland buffers around the cloud forest should be considered as primary habitat in conservation management plans.

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well‐understood. Here, we describe how the advent of real‐time genomic analyses can benefit One Health and how it can enable timely, in‐depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real‐time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real‐time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself – from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real‐time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations. Graphical Abstract The One Health concept describes the inextricable link between human and environmental health. This review discusses how real‐time genomics can improve our understanding of the interdependencies within ‘One Health’ and enable timely assessments and interventions in many contexts.

Peru ranks among the three countries with the highest bird species diversity globally and a majority of those species are found in the Peruvian Amazon. However, birds in this area are currently facing serious anthropogenic threats. Genetic and genomic methods are becoming important tools for avian biodiversity monitoring and conservation planning. Comprehensive molecular libraries that are publicly available are key to the effective deployment of these tools. We analyze the information gaps for four molecular markers in the most important genetic sequence databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, for bird species of the Peruvian Amazonia. We found that 64% of Peruvian Amazonian bird species have gene sequences for COI, 59.5% have CYTB sequences, 16.4% have 12S sequences, and only 0.6% have 18S sequences. However, these numbers decrease drastically to 4.3% for COI sequences when we only consider specimens sampled in Peru. Our data also showed that 43.8% of Peruvian Amazonian endemic species (n = 32) are missing sequences of any screened marker uploaded to GenBank or BOLD. Our results will encourage and guide efforts of the scientific community to complete reference libraries for Peruvian avian species that will be useful for future DNA-based monitoring projects that include birds.

Peru has 55 primate taxa (including all species and subspecies), a third of which are threatened. The major drivers of habitat loss, degradation and fragmentation are grazing, forestry, agriculture and transport infrastructure. Other activities such as hunting exacerbate these threats. We assessed the threats from degradation and fragmentation facing Peruvian primates to aid in the design and implementation of mitigation strategies. Through GIS-based mapping, statistical modeling and specialist assessments, we evaluated all primate taxa using the IUCN Conservation Measures Partnership Unified Classifications of Direct Threats across five categories (direct threats to primates, threats to habitat, causes of fragmentation, factors exacerbating fragmentation and threats to primates and habitats as a consequence of fragmentation), highlighting which were most common and most severe. Our results showed that all primate taxa were affected by degradation and fragmentation in Peru. The most common and severe direct threat was hunting, whereas housing and urban development, smallholder crop farming, smallholder grazing and large-scale logging were the most common and severe threats across the other categories. The families Cebidae and Atelidae face the highest overall threat. Our analysis showed that the current IUCN listing of Leontocebus leucogenys [LC] underestimates the true threat level this species faces and that Lagothrix lagothricha tschudii [DD] should be listed under one of the threat categories. In Peru, the need for mitigating the threat of habitat fragmentation is clear. To ensure the survival of Peru’s diverse primate taxa, forest connectivity needs to be maintained or recovered through the protection and restoration of key areas considering their biological and social needs.

The microbiome of mammalian scent glands is thought to contribute to the production of odorant compounds involved in sensory communication. Yet, the extent to which glandular microbiomes contain bacteria relevant to odor production and vary by host species, scent marking behavior, or gland morphology remains poorly understood, particularly in wild animals. We sampled microbes collected from skin swabs of suprapubic and sternal scent glands in wild Peruvian saddleback tamarins ( Leontocebus weddelli ; n = 19) and emperor tamarins ( Tamarinus imperator ; n = 20) to better understand glandular microbial communities. We aimed to: (1) profile glandular microbiomes of both species, focusing on odor‐related taxa and metabolic pathways, and (2) determine whether suprapubic glands, more often in contact with the external environment, had higher diversity and distinct composition of odor‐related taxa and pathways compared to sternal glands. We generated metagenomic reads using short‐read DNA shotgun sequencing from glandular swabs. We identified 18 odor‐associated microbial taxa in both tamarin species, mainly Staphylococcus and Corynebacterium , and 26 pathways, including pyruvate fermentation and amino acid metabolism. Suprapubic glands had lower Shannon alpha diversity relative to sternal glands, especially in L. weddelli . The glands of L. weddelli also differed in taxonomic composition, with odor‐related taxa more abundant in suprapubic glands. Our results provide evidence for the involvement of scent gland microbiomes in host communication biology. Glandular specializations differed not only between closely related tamarin species but also between gland types within the same individuals, suggesting a nuanced pattern of host–microbe coevolution that may shape interactions important for olfactory communication.

There is an increased interest in potential zoonotic malarias. To date, Plasmodium malariae that infects humans remains indistinguishable from Plasmodium brasilianum, which is widespread among New World primates. Distributed throughout tropical Central and South America, the Callitrichidae are small arboreal primates in which detection of natural Plasmodium infection has been extremely rare. Most prior screening efforts have been limited to small samples, the use of low-probability detection methods, or both. Rarely have screening efforts implemented a longitudinal sampling design. Through an annual mark-recapture program of two sympatric callitrichids, the emperor (Saguinus imperator) and saddleback (Saguinus fuscicollis) tamarins, whole blood samples were screened for Plasmodium by microscopy and nested PCR of the cytochrome b gene across four consecutive years (2012-2015). Following the first field season, approximately 50% of the samples collected each subsequent year were from recaptured individuals. In particular, out of 245 samples from 129 individuals, 11 samples from 6 individuals were positive for Plasmodium, and all but one of these infections was found in S. imperator. Importantly, the cytochrome b sequences were 100% identical to former isolates of P. malariae from humans and P. brasilianum from Saimiri sp. Chronic infections were detected as evidenced by repeated infections (7) from two individuals across the 4-year study period. Furthermore, 4 of the 5 infected emperor tamarins were part of a single group spanning the entire study period. Overall, the low prevalence reported here is consistent with previous findings. This study identifies two new natural hosts for P. brasilianum and provides evidence in support of chronic infections in wildlife populations. Given that callitrichids are often found in mixed-species associations with other primates and can be resilient to human-disturbed environments, they could contribute to the maintenance of P. malariae populations if future work provides entomological and epidemiological evidence indicating human zoonotic infections.

ABSTRACT Peru holds a high mammalian diversity in its Amazonian region, with 326 species. However, our knowledge about the actual diversity is still considered incomplete, and the molecular information for those species in genetic databases is even less comprehensive. To assess the availability of genetic information for Peruvian Amazonian mammals relative to known diversity, we surveyed the Amazonian mammals with at least one molecular marker in the most widely used repositories for nucleotide sequences, GenBank and BOLD Systems. Our survey focused on widely used molecular markers in evolutionary biology-cytochrome b [cyt-b], cytochrome oxidase I [COI], 12S ribosomal RNA [12S], and the mitogenome [mit]-derived from Peruvian Amazon mammals. Additionally, to gain insights into the current mammalian sampling effort in Peruvian Amazonia, we generated a map of unique sampling localities and a heat map, utilizing 41951 records, which identified six major information gaps. This comprehensive analysis found 1597 genetic sequences corresponding to 180 mammalian species (55.2% of Peruvian Amazonian species): COI (38 species), cyt-b (167 species), 12S (56 species), and mitogenome (16 species). Taxonomically, Rodentia (53 species, four markers), Chiroptera (63 species, three markers), and Didelphimorphia (27 species, four markers) represented most molecular data, with a concentration of molecular markers in the orders Chiroptera (703) and Rodentia (499). Geographically, the Loreto department has the largest genetic information (530 records, 99 species). These results confirm a worrying underrepresentation of Peruvian Amazonian diversity in molecular databases. Consequently, we advocate for the use of scientific collections as an alternative source to systematically generate genetic information for the Amazonian mammal diversity in Peru to compensate for the current underrepresentation.

Environmental DNA (eDNA) includes a set of rapidly emerging technologies that have the potential to support environmental monitoring and biodiversity conservation through novel, non-invasive, cost-effective and democratic methods and tools. Meanwhile, eDNA researchers are developing international standards for eDNA technologies, methods and data outputs. For eDNA technologies to be accessible, useful and appropriate, we must ensure that any standards developed include a broad conception of users from around the world, a diversity of ecological contexts and locations and, most importantly, a realistic outlook on research capacities and infrastructure. In this article, we assemble perspectives on international standardisation of eDNA from a diverse and global group of users and experts from Africa, South America and the Pacific Islands. The authors of this article collaborated by answering and discussing a set of open-ended questions aimed at eliciting hopes, concerns and experiences regarding eDNA standards. The result is a set of emergent themes and a generative consensus to highlight the need for the creation of adaptable standards, the development of regional capacity, increased sensitising to data sovereignty and the viewing of standardisation as a global capacity-building activity.