Using Parasitic Load to Measure the Effect of Anthropogenic Disturbance on Vervet Monkeys

Vervet monkeys, Chlorocebus pygerythrus, thrive in urban areas of KwaZulu-Natal, South Africa, and present a suitable model to assess parasitic load as a measure of anthropogenic disturbance, such as urbanization. We collected vervet monkey faecal samples from four study sites representing a gradient of land use and urbanization. We assessed faecal parasites using the faecal flotation method calculating eggs per gram and parasite richness. Overall, the more urban vervet monkey populations had a significantly higher parasite richness and abundance. Our study shows the applicability of using parasite load to measure the effect of urbanization on wildlife.     

Cross‐scale controls on carbon emissions from boreal forest megafires

Climate warming and drying is associated with increased wildfire disturbance and the emergence of megafires in North American boreal forests. Changes to the fire regime are expected to strongly increase combustion emissions of carbon (C) which could alter regional C balance and positively feedback to climate warming. In order to accurately estimate C emissions and thereby better predict future climate feedbacks, there is a need to understand the major sources of heterogeneity that impact C emissions at different scales. Here, we examined 211 field plots in boreal forests dominated by black spruce (Picea mariana) or jack pine (Pinus banksiana) of the Northwest Territories (NWT), Canada after an unprecedentedly large area burned in 2014. We assessed both aboveground and soil organic layer (SOL) combustion, with the goal of determining the major drivers in total C emissions, as well as to develop a high spatial resolution model to scale emissions in a relatively understudied region of the boreal forest. On average, 3.35 kg C m^?2 was combusted and almost 90% of this was from SOL combustion. Our results indicate that black spruce stands located at landscape positions with intermediate drainage contribute the most to C emissions. Indices associated with fire weather and date of burn did not impact emissions, which we attribute to the extreme fire weather over a short period of time. Using these results, we estimated a total of 94.3 Tg C emitted from 2.85 Mha of burned area across the entire 2014 NWT fire complex, which offsets almost 50% of mean annual net ecosystem production in terrestrial ecosystems of Canada. Our study also highlights the need for fine‐scale estimates of burned area that represent small water bodies and regionally specific calibrations of combustion that account for spatial heterogeneity in order to accurately model emissions at the continental scale.     

Emerging new crown symptoms on Castanea sativa (Mill.): Attempting to model interactions among pests and fungal pathogens

In the 2015–2016 growing seasons, two novel symptoms were assessed on the crown of trees in orchards and coppices of chestnut groves in Central Italy. The first symptom was flagging of annual shoots with green leaves undergoing sudden wilt and turning brown later in the season. The second symptom consisted of leaves on annual shoots turning yellow before wilting in absence of flagging represented the second symptom. Samples were collected along transects in early summer, late summer and winter, and processed in the laboratory. The flagging symptom was associated in early summer with the presence of C. parasitica in cryptic dried buds on stems from the previous year's growth. The pathogen was also found in dormant buds in winter, suggesting that the infection could take place in summer during the Chinese gall wasp oviposition period. Cryphonectria parasitica was also isolated from abandoned galls in winter supporting the hypothesis that galls are a potential source of inoculum for crown infections. Aetiology of yellowing was not clarified and no fungal taxa were specifically associated with this symptom. Gnomoniopsis castanea, C. parasitica and, in early summer, Colletotrichum acutatum were the most abundant fungal taxa isolated from chestnut shoots and buds.     

Profiling microbial strains in urban environments using metagenomic sequencing data

Background

The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.

Results

We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.

Conclusion

We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.

Reviewers

This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.

     

Enhancing theoretical understanding of a practical biology course using active and self-directed learning strategies

Laboratories are recognised as central in science education, allowing students to consolidate knowledge and master practical skills, however, their effectiveness has been questioned. Whilst laboratory practicals are useful for students’ learning of basic procedures, they have been shown to be less effective for developing conceptual understanding of the subject. Interactive lectures and bespoke digital resources were utilised in order to enhance theoretical understanding of laboratory practical molecular sessions, thus enabling students to take responsibility for and direct their own learning, encouraging inquiry-based learning. Providing easy to access additional learning resources offered students an opportunity to better prepare themselves for the laboratory, and consolidate their knowledge through subsequent review and self-testing in their own time. Grades before and after implementation of these active learning strategies were analysed to look at the impact on student learning and this study demonstrates that integrating these into a challenging practical biology course improved grades significantly with a concomitant increase in the number of ‘A’ grades attained. Feedback to evaluate use and perceptions of both interactive lectures and digital resources were also analysed. It has been shown here that these activities enhanced student experience and understanding of the course.     

Functional Amyloid and Other Protein Fibers in the Biofilm Matrix

Biofilms are ubiquitous in the natural and man-made environment. They are defined as microbes that are encapsulated in an extracellular, self-produced, biofilm matrix. Growing evidence from the genetic and biochemical analysis of single species biofilms has linked the presence of fibrous proteins to a functional biofilm matrix. Some of these fibers have been described as functional amyloid or amyloid-like fibers. Here we provide an overview of the biophysical and biological data for a wide range of protein fibers found in the biofilm matrix of Gram-positive and Gram-negative bacteria.     

Protoporphyrin‐based eggshell pigmentation predicts hatching success and offspring sex ratio in the barn swallow

Inter‐ and intraspecific variation in eggshell colouration has long fascinated evolutionary biologists. Among species, such variation may accomplish different functions, the most obvious of which is camouflage and background matching. Within species, it has been proposed that inter‐female variation in eggshell pigmentation patterns can reflect egg, maternal or paternal traits and hence may provide cues to conspecifics about egg, maternal or paternal phenotypic quality. However, the relationship between protoporphyrin‐based eggshell pigmentation and egg or maternal/paternal traits appears to be highly variable among species. We investigated patterns of intraspecific variation in Eurasian barn swallow Hirundo r. rustica protoporphyrin‐based eggshell pigmentation, and analysed its association with egg and clutch characteristics, maternal/paternal phenotypic traits and parental feeding effort. Eggshell pigmentation pattern significantly varied between breeding colonies, was significantly repeatable in first clutches laid by the same females in different years (intraclass correlation coefficient ranging between 0.56 and 0.63), but it was not significantly associated with egg traits, such as position in the laying sequence, egg mass, yolk testosterone concentration and antioxidant capacity. It was weakly or non‐significantly associated with female and male traits (sexual ornaments), but females laying darker (higher pigment intensity) first clutches had higher hatching success, suggesting that eggshell pigment intensity may predict fitness. Male nestling feeding effort was not predicted by eggshell pigmentation. In addition, females with darker breast plumage colouration (a melanin‐based trait related to fitness) laid highly protoporphyrin‐covered eggs, suggesting the presence of a previously unappreciated link between protoporphyrin biosynthesis and plumage melanisation. Moreover, the proportion of male offspring increased in clutches originating from highly protoporphyrin‐covered eggs, suggesting that parents could acquire visual cues about their future brood sex composition before egg hatching. Our results support the idea that intraspecific signalling via eggshell pigmentation is a species‐specific rather than a general feature of avian taxa.     

The role played by invasive species in interactions with endangered and threatened species in the United States: a systematic review

Invasive species are considered to be a leading cause of the decline of threatened species. However, this view has been disputed because much of the evidence base is anecdotal. This systematic review, through an extensive, repeatable search using agreed selection criteria, examined the available scientific evidence on invasive species’ interactions with the 1363 endangered and threatened species protected under the United States Endangered Species Act (ESA). The review found scientific evidence available for 116 endangered or threatened species (8.5% of the ESA list). Of these, 85 species (6.2%) were reported as being negatively impacted by invasive species: 39 located on the continental US and 39 on islands, with seven marine species. The relative percentages of species impacted differed according to location: 4.3% (n?=?906) on the continental US, 9.3% (n?=?420) on islands. It was found that predation by invasive vertebrates on birds on islands and competition between invasive plants and endangered or threatened plants on the mainland were the main mechanisms of impact. The results of this study contrast markedly with a previous study which found that 49% of imperilled species in the United States were threatened by invasive species. Further research is essential in order to evaluate the impact of invasive species on imperilled species on the ESA list; this would help to reduce the high degree of uncertainty regarding the threat of invasive species due to the lack of empirical information.     

Survival strategies of a frugivore,the sun bear,in a forest-oil palm landscape

As large areas of forest are lost throughout the tropics, prime habitat of many species decline and become fragmented. The island of Borneo is a prime example, with accelerated clearing of forests primarily for oil palm expansion. Borneo is recognized as an important stronghold for the conservation of the sun bear (Helarctos malayanus), but it is unclear how habitat reduction and fragmentation is affecting this frugivore. We used camera traps and sign surveys to understand patterns of sun bear habitat use in a matrix of fragmented forests and extensive oil palm development, which has existed as such for?>?15 years: the Lower Kinabatangan floodplain in Sabah, Malaysian Borneo. Within these small forest fragments, squeezed between a major river and oil palm plantations, bears exhibited selection for areas farther from human activity (plantations, river boat traffic, and buildings), and were rarely active during the day, demonstrating both spatial and temporal avoidance of potential human-related threats. They selected large trees to feed and rest, and also exploited adjacent plantations to feed on oil palm fruits. We conclude that even relatively small forest fragments (~?2000 ha) within large agricultural landscapes can be important for sun bears. Our research highlights the remarkable adaptations this species has employed to persist in a drastically modified landscape.