Finnegan, L. | bioRxiv Science

bioRxiv2024

Vulnerable caribou and moose populations display contrasting responses to mountain pine beetle outbreaks and management.

O_LIRising global temperatures and changing landscape conditions have led to widespread mountain pine beetle (MPB) outbreaks in western North America. Extensive management has been implemented in response, via forest harvesting and prescribed burning. However, the impacts of MPB and MPB-management on ungulate populations, particularly caribou and moose, remain poorly studied. Given the differing specialisations of these species (caribou are habitat specialists, moose are generalists), their responses to these disturbances may vary. This could, in turn, lead to unintended, indirect effects (e.g., disturbance-mediated apparent competition, whereby increased moose presence results in increased predator presence, with resultant caribou declines). Unravelling these responses is crucial for informing MPB management and ensuring that applied actions do not exacerbate adverse effects. C_LIO_LIWe assessed the effects of early-stage MPB-infestation, harvest, and fire, on habitat selection by caribou (boreal and central mountain designatable units) and moose in west-central Alberta. We built resource selection functions and functional response models using GPS collar data collected 3-5 years after MPB infestation and found that responses varied between species. C_LIO_LICaribou had complex seasonal responses to MPB, generally avoiding areas with more MPB disturbance in winter but using them in summer. Caribou typically avoided harvested and burned areas, though this was dependent on the overall degree of disturbance within their ranges. In contrast, moose had positive responses to both MPB and burned areas year-round. C_LIO_LIThese findings suggest that MPB may negatively impact long-term winter habitat availability for threatened caribou populations, but may have positive impacts on moose habitat. However, moose use of MPB-impacted areas could further affect caribou by contributing to disturbance-mediated apparent competition. C_LIO_LISynthesis and applications: The negative impacts of forest harvest and burning on caribou suggests that less intensive actions are required for MPB management within caribou ranges.. While moose selectively used harvested and burned areas, it is possible that they may have adverse responses to cumulative disturbance over time. As caribou and moose responded to MPB soon after infestation, ongoing monitoring is required to detect MPB early and facilitate proactive management, though further study is needed to determine the most effective actions. C_LI

ecology↗

bioRxiv2020

Fermented food metagenomics reveals substrate-associated differences in taxonomy, health-associated- and antibiotic resistance-determinants

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that the consumption of these foods that help to address the negative consequences of industrialization of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented food microbiota to better harness desirable traits. Here we considerably expand the understanding of fermented food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity and functional potential (including antimicrobial resistance, carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from around the Globe. Food type, i.e., dairy-, sugar- or brine-type fermented foods, was to be the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Lactobacillus, Leuconostoc and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than non-fermented equivalents, with waterkefirs, sauerkrauts and kvasses containing the greatest numbers of potentially health-associated gene clusters (PHAGCs). Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date, and yields novel information regarding their relative health-promoting potential. ImportanceFermented foods are regaining popularity in Western society due in part to an appreciation of the potential for fermented food microbiota to positively impact on health. Many previous studies have studied fermented microbiota using classical culture-based microbiological methods, older molecular techniques or, where deeper analyses have been performed, have involved a relatively small number of one specific food type. Here, we have used a state-of-the-art shotgun metagenomic approach to investigate 58 different fermented foods of different type and origin. Through this analysis, we were able to identify the differences in the microbiota across these foods, the factors that drove their microbial composition, and the relative potential functional benefits of these microbes. The information provided here will provide significant opportunities for the further optimisation of fermented food production and the harnessing of their health promoting potential.

microbiology↗