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.
The Blue Tit
Cyanistes caeruleus
prefer to use nest boxes to raise their young rather than nests in natural tree cavities. However, nest boxes provide a warm, humid microclimate that is favourable to ...the growth of rich bacterial communities. In this study we investigated how the bacterial community developed throughout the breeding season and whether it had any effect on egg or nestling mortality. Samples were collected across six sites and three breeding seasons at the completion of nest building, clutch completion and immediately post fledging. Bacterial counts were obtained for each sample, including a total bacterial count using non-selective media and bacterial counts on selective media for
Staphylococcus
spp. and
Enterobacter
spp, which may indicate pathogenicity to the birds. There were significantly more bacteria (total counts and counts for
Staphylococcus
spp. and
Enterobacter
spp. specifically) present within the nest box at the post fledging stage compared to the two earlier stages, likely due to increased activity by the adult birds (feeding of the nestlings and defecating) and less time by the adult birds for self-preening and nest sanitation. No positive relationship was found between bacterial counts and either egg mortality, nestling mortality or brood size; however, a negative relationship between egg mortality and total bacterial count was identified. Although somewhat unexpected, this negative relationship may indicate the presence of a greater number of symbiotic bacteria, which could offer a greater level of protection.
Birds face many challenges during a breeding attempt including predation, food availability, pathogens and parasite load. Cyanistes caeruleus (blue tit) prefer human placed nest boxes, however the ...stable microclimate presented within the nest box exacerbates the challenges posed by ectoparasites and potentially pathogenic bacteria, with reductions in breeding success reported. The addition of green plant material to help control these deleterious effects has been reported within Mediterranean climes but comparable studies have not been undertaken in temperate regions. This study introduces novel molecular approaches including next generation sequencing methods to assess the nest microbiome. This approach avoids the culturing bias of previous work in this area. Terminal-Restriction Fragment length Polymorphism (T-RFLP) analysis was used to assess bacterial richness progression through the breeding attempt with more traditional methods used to assess bacterial load. DNA barcoding was performed to identify bacteria, ectoparasites and vascular plant fragments present within the nest with vegetation surveys conducted around a subset of nests to assess if any active selection of plant material was occurring. Bacterial species richness and load were relatively stable between nest build and clutch completion with a significant increase in both post fledging, following the introduction of nestling faeces in the nest and reduced time for nest sanitation. DNA barcoding provided marked increases in the taxonomic knowledge of nest dwelling biota with 169 bacterial taxa, thirteen species of ectoparasite and 154 vascular plant taxa identified. Although ectoparasites and pathogenic bacteria were detected within the nest no effect was seen upon hatching or fledging success. It is more likely that a reduction in fitness would be observed post fledging. A high proportion of plant material containing volatile compounds was recorded within the nest, however active selection could not be confirmed.
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