Arguably, researching the trade and trafficking of natural resources, such as wildlife crime, environmental crime, trafficking of natural commodities, unregulated and unreported fishing, factory ...farming, human–wildlife conflict, to name a few examples, involves all four areas of threat. ...research can be extremely emotionally taxing for both the researcher and research participants. ...it offers the researcher an opportunity to think through potentially “risky”, dangerous, harmful, and ethically compromising fieldwork situations, while reflecting on their own positionality and protection of themselves, research participants, and data. ...they are required to fill out risk assessments and complete specialized training for hostile environments. With increasing use of qualitative research methods within the wildlife trafficking research field, coupled with the growing importance of human–wildlife interactions exacerbated by the COVID-19 pandemic, this disparity in ethical regulations needs imminent addressing. ...with the current emphasis on ‘decoloniality’, an ethical review process could ensure that parachute social science is avoided, and equity and sustainable collaboration between stakeholders are foregrounded in the research.
Abstract
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be ...investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host–microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
We identify research questions in the field of microbial ecology, with emerging themes that recognise vast microbial functions that could benefit humanity, and the need to integrate knowledge across organisms.
Recently, there has been rapidly growing interest in the effects of the microbiota on host physiology and behaviour. Due to the nutritional value of bacteria, gut microflora may be particularly ...important in species that present nuptial gifts during courtship. Here, we explore whether the presence or absence of gut microbiota in males and females of the nuptial gift-giving species Drosophila subobscura (Collin, 1936) alters mating behaviour in terms of female preference, male investment, and female fecundity. We found that females that had been fed antibiotics, compared to females with intact gut bacteria, were more willing to mate with a male that had been fed normally. However female fecundity was higher when both males and females lacked gut bacteria compared to both individuals having a full complement of gut bacteria. This implies that the presence of the microbiota acts to reduce female fecundity in this species, and that male gut bacterial content influences female fecundity. Our results provide further evidence to the growing consensus that the microbiota of an individual may have important effects on both reproductive behaviour and physiology, and suggest that it may also contribute to the nutritional value of the nuptial gift in this system.
The aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed ...additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. There is still a lack of knowledge surrounding the importance and functionality of the teleost gut microbiome in fish nutrition. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host's microbial communities. Several in vitro gut models targeted at monogastric vertebrates are now in operation. Here, we report the development of an Atlantic salmon gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum, and midgut) and associated microbial communities.
The gut model was established in a series of linked bioreactors seeded with biological material derived from farmed adult marine-phase salmon. We first aimed to achieve a stable microbiome composition representative of founding microbial communities derived from Atlantic salmon. Then, in biological triplicate, the response of the in vitro system to two distinct dietary formulations (fishmeal and fishmeal free) was compared to a parallel in vivo trial over 40 days. Metabarcoding based on 16S rDNA sequencing qPCR, ammoniacal nitrogen, and volatile fatty acid measurements were undertaken to survey the microbial community dynamics and function. SalmoSim microbiomes were indistinguishable (p = 0.230) from their founding inocula at 20 days and the most abundant genera (e.g., Psycrobacter, Staphylococcus, Pseudomonas) proliferated within SalmoSim (OTUs accounting for 98% of all reads shared with founding communities). Real salmon and SalmoSim responded similarly to the introduction of novel feed, with majority of the taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa (e.g., a small fraction of Psychrobacter) was differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acid profiles were not significantly different in SalmoSim pre- and post-feed switch.
By establishing stable and representative salmon gut communities, this study represents an important step in the development of an in vitro gut system as a tool for the improvement of fish nutrition and welfare. The steps of the system development described in this paper can be used as guidelines to develop various other systems representing other fish species. These systems, including SalmoSim, aim to be utilised as a prescreening tool for new feed ingredients and additives, as well as being used to study antimicrobial resistance and transfer and fundamental ecological processes that underpin microbiome dynamics and assembly. Video abstract.
Alpha mannose-oligosaccharide (MOS) prebiotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be ...mediated through their impact on host microbial communities and their associated metabolism. Bio-Mos is a commercially available prebiotic currently used in the agri-feed industry, but studies show contrasting results of its effect on fish performance and feed efficiency. Thus, detailed studies are needed to investigate the effect of MOS supplements on the fish microbiome to enhance our understanding of the link between MOS and gut health. To assess Bio-Mos for potential use as a prebiotic growth promoter in salmonid aquaculture, we have modified an established Atlantic salmon
gut model, SalmoSim, to evaluate its impact on the host microbial communities. The microbial communities obtained from ceca compartments from four adult farmed salmon were inoculated in biological triplicate reactors in SalmoSim. Prebiotic treatment was supplemented for 20 days, followed by a 6-day washout period. Inclusion of Bio-Mos in the media resulted in a significant increase in formate (
= 0.001), propionate (
= 0.037) and 3-methyl butanoic acid (
= 0.024) levels, correlated with increased abundances of several, principally, anaerobic microbial genera (
). DNA metabarcoding with the 16S rDNA marker confirmed a significant shift in microbial community composition in response to Bio-Mos supplementation with observed increase in lactic acid producing
. In conjunction with previous
studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of
gut models to complement
trials of microbiome modulators.
In this paper we report the results of the impact of a prebiotic (alpha-MOS supplementation) on microbial communities, using an
simulator of the gut microbial environment of the Atlantic salmon. Our data suggest that Bio-Mos may be of value in salmonid production as it enhances volatile fatty acid production by the microbiota from salmon pyloric ceca and correlates with a significant shift in microbial community composition with observed increase in lactic acid producing
. In conjunction with previous
studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of
gut models to augment
trials of microbiome modulators.
Age is well known to be a basis for female preference of males. However, the mechanisms underlying age-based choices are not well understood, with several competing theories and little consensus. The ...idea that the microbiota can affect host mate choice is gaining traction, and in this study we examine whether the male microbiota influences female preference for older individuals in the fruit fly Drosophila pseudoobscura. We find that an intact microbiota is a key component of attractiveness in older males. However, we found no evidence that this decrease in older male attractiveness was simply due to impaired microbiota generally reducing male quality. Instead, we suggest that the microbiota underlies an honest signal used by females to assess male age, and that impaired microbiota disrupt this signal. This suggests that age-based preferences may break down in environments where the microbiota is impaired, for example when individuals are exposed to naturally occurring antibiotics, extreme temperatures, or in animals reared in laboratories on antibiotic supplemented diet.
Recently, there has been rapidly growing interest in the effects of the microbiota on host physiology and behaviour. Due to the nutritional value of bacteria, gut microflora may be particularly ...important in species that present nuptial gifts during courtship. Here, we explore whether the presence or absence of gut microbiota in males and females of the nuptial gift-giving species Drosophila subobscura (Collin, 1936) alters mating behaviour in terms of female preference, male investment, and female fecundity. We found that females that had been fed antibiotics, compared to females with intact gut bacteria, were more willing to mate with a male that had been fed normally. However female fecundity was higher when both males and females lacked gut bacteria compared to both individuals having a full complement of gut bacteria. This implies that the presence of the microbiota acts to reduce female fecundity in this species, and that male gut bacterial content infl uences female fecundity. Our results provide further evidence to the growing consensus that the microbiota of an individual may have important effects on both reproductive behaviour and physiology, and suggest that it may also contribute to the nutritional value of the nuptial gift in this system.
In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host ...physiology, ecology, behavior, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low‐dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analyzed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low‐dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioral research. Our study raises the important issue that the efficacy of and impacts on the host of these methods require investigation in a case‐by‐case manner, rather than assuming homogeneity across species and laboratories.
In this study, we evaluate some of the methods commonly used to eliminate gut bacteria in studies of the microbiota, in the model organism Drosophila melanogaster. We suggest the most appropriate technique to use, particularly for behavioral studies.
An individual’s gut microbiota is increasingly recognised as having a key role in many host behaviours. In insects, the environment largely determines the host gut microbiota, with the majority ...ingested through the diet. In this thesis, I examine a series of host-gut microbiota relationships within three species of Drosophila with varied ecologies. Initially, I analyse the current methods used to eliminate the gut microbiota in Drosophila melanogaster, key to studying host-microbiota relationships and providing a foundation for this thesis. I then use this information to assess the role of the gut microbiota as an honest signal in age-based mate choice in Drosophila pseduoobscura. Finally, I examine the role the gut microbiota plays in specialisation in Drosophila sechellia, through adaptation to its toxic host plant, Morinda citrifolia.To attribute a specific behaviour to the gut microbiota, it must first be removed. However, removal can have serious physiological side effects on the host organism, and the most effective and least detrimental method of doing this is widely debated. I analyse commonly used methods of removing the gut microbiota in Drosophila melanogaster and find the addition of low-dose streptomycin to the dietary media is more effective and has fewer physiological effects than other methods such as egg dechorionation or rearing on a sterile diet.Female Drosophila pseudoobscura are known to discriminate between males based on age. This may occur through the alteration of the cuticular hydrocarbon (CHC) profile of males, which can alter due to a varied gut microbiota caused by a varied diet. I determine that the gut microbiota influences female preference for older males and is a key component of attractiveness to females.I examine the role of the gut microbiota in Drosophila sechellia, in adaptation to its toxic host plant, Morinda citrifolia, and characterise the gut microbiota of this Drosophilid species for the first time. Rearing flies on M. citrifolia, a standard laboratory diet, and an additional salak (Salacca zalacca) fruit that lacks the toxic compounds present in M. citrifolia, I find that flies reared on a laboratory diet have a significantly reduced weight. However, there is no impact on development time or subsequent mating behaviours when compared to individuals reared on the wild, M. citrifolia diet.Finally, by creating experimental evolution lines of D. melanogaster supplemented with D. sechellia gut microbiota, I disentangle the role of pH in shaping the gut microbiota from the co-evolution of the gut microbiota within D. sechellia. D. melanogaster are highly averse to the scent of octanoic acid, the main toxic constituent within M. citrifolia, whereas D. sechellia are highly attracted. After ten generations D. melanogaster show significantly less aversity to octanoic acid. I determine that Lactobacillus plantarum acts as a detoxifying agent by metabolising octanoic acid, therefore suggesting this bacterium has been fundamental to the ecological transition and specialisation of D. sechellia.Taken together, the chapters of this thesis further uncover the role of hostmicrobiota interactions in important ecological and evolutionary processes within Drosophila, from elucidating a principle method in gut microbiota research, to underlying mate choice mechanisms and finally to dietary specialisation.
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