The blowfly Chrysomya latifrons inhabits fragmented rainforests, but lacks genetic diversity and population structure

Climate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. It is not currently feasible to assess the population structure of every invertebrate species, so there is a compelling need to identify indicator species that are broadly indicative of habitat-level patterns and processes. Blowflies are an ideal candidate, because they are widespread, abundant, and can be easily collected within rainforests. Here, we present the first study of the blowfly Chrysomya latifrons , which is endemic to the rainforests of New South Wales, Australia. We genotyped 188 flies from 15 isolated rainforests and found low overall genetic diversity and a complete lack of genetic structure between populations, suggesting the presence of a single large panmictic population along 1,000 km of the Australian east coast. This highlights that: (1) Ch. latifrons inhabits every rainforest in NSW and undoubtedly plays an important role in these ecosystems, but low genetic diversity may cause it to struggle to adapt to a changing climate; (2) strongly dispersing insects have the capacity to migrate between isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens with them to form crucial trophic networks; and (3) there is an urgent need for similar studies on poorly dispersing rainforest insects, as these may be the most fragmented and at highest risk of local extinction.

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P.stercorea or F.prausnitzii and were found to develop steadily with age, whereas P.copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.

Analysis of complex trophic networks reveals the signature of land-use intensification on soil communities in agroecosystems

Increasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and food web structure for temperate agroecosystems along a gradient of land-use intensity. We tested for response patterns in key properties of the soil food webs in sixteen fields ranging from arable crops to grazed permanent grasslands as part of a long-term management experiment. We found that agricultural intensification drives reductions in trophic group diversity, although taxa richness remained unchanged. Intensification generally reduced the complexity and connectance of soil interaction networks and induced consistent changes in energy pathways, but the magnitude of management-induced changes depended on the variable considered. Average path length (an indicator of food web redundancy and resilience) did not respond to our management intensity gradient. Moreover, turnover of network structure showed little response to increasing management intensity. Our data demonstrates the importance of considering different facets of trophic networks for a clearer understanding of agriculture-biodiversity relationships, with implications for nature-based solutions and sustainable agriculture.

Towards omics-based predictions of planktonic functional composition from environmental data

Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters’ distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters’ abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.

Food Webs

Ciliates are important elements of the trophic networks of aquatic and terrestrial environments, they can be primary producers (myxotrophs), consumers of bacteria, algae, flagellates, even other ciliates and can serve as food for metazoans, for all the above they are the link between different levels of food webs. The structure of the ciliates varies according to the seasons of the year and depending on the trophic conditions of the aquatic systems. Ciliated communities have modifications and adaptations in response to environmental perturbations. The objective of this chapter is to describe the importance of different trophic groups of ciliates in different ecosystems, including anthropogenic perturbations and their impact on trophic webs.

Do Roads Alter the Trophic Behavior of the Mesocarnivore Community Living Close to Them?

Roads have impacts on the fauna arising from habitat fragmentation, roadkill and the barrier effect. Furthermore, roads lead species to change their activity with repercussions on predator–prey interactions and trigger indirect effects that are currently unknown. This study analyzes the effect of a motorway on the trophic behavior of the terrestrial carnivore community of its surroundings. Monthly scat sampling was conducted over a year at three distances from a motorway (0–50 m, 500–550 m and 1000–1050 m). We collected 498 scats, these originating from red fox (39.16%), cat (24.50%), stone marten (24.09%) and badger (12.25%). The relative abundance of the trophic resources in them was estimated together with the trophic diversity and niche overlap of the carnivore species. The results showed a distinct effect of distance from the road on trophic behavior of carnivores, as well as differences between species and seasons. The scats nearest the road had 10–20% more biomass of small mammals, equivalent in relative terms to a 21–48% increase in small mammals’ biomass when compared with scats collected further from the road. This finding indicates changes in predator–prey interactions near the road and shows that the human-generated structural and functional changes to ecosystems spread throughout trophic networks.

The Importance of Low-Intensive Agricultural Landscape for Birds of Prey

Low-intensive agricultural areas of Romania sustain high species diversity. Together with natural habitats, these areas are very important for European biodiversity. The ecosystem´s health is reflected in the predator status because of their position at the top of the trophic networks. The Common Buzzard (Buteo buteo) is the most common bird of prey species in Europe. During the first survey census conducted in Eastern Romania (2011–2012 breeding seasons), 8.55–10.35 breeding pairs/100 square km have been counted. The Common Buzzard density varies between breeding seasons and with differences in habitat structure. Their density is positively influenced by the density of forest edge and Simpson diversity index of habitats but is negatively influenced by the total habitat fragmentation and mean daily temperature. According to this analysis, the selection of breeding territories by common buzzards is positively influenced by a heterogeneous landscape in an area with low-intensive agriculture and with large areas of open habitats made up of natural or semi-natural vegetation.

For flux’s sake: General considerations for energy-flux calculations in ecological communities

Global change alters ecological communities with consequences for ecosystem processes. Such processes and functions are a central aspect of ecological research and vital to understanding and mitigating the consequences of global change, but also those of other drivers of change in organism communities. In this context, the concept of energy flux through trophic networks integrates food-web theory and biodiversity-ecosystem functioning theory and connects biodiversity to multitrophic ecosystem functioning. As such, the energy flux approach is a strikingly effective tool to answer central questions in ecology and global-change research. This might seem straight forward, given that the theoretical background and software to efficiently calculate energy flux are readily available. However, the implementation of such calculations is not always straight forward, especially for those who are new to the topic and not familiar with concepts central to this line of research, such as food-web theory or metabolic theory. To facilitate wider use of energy flux in ecological research, we thus provide a guide to adopting energy-flux calculations for people new to the method, struggling with its implementation, or simply looking for background reading, important resources, and standard solutions to the problems everyone faces when starting to quantify energy fluxes for their community data. First, we introduce energy flux and its use in community and ecosystem ecology. Then, we provide a comprehensive explanation of the single steps towards calculating energy flux for community data. Finally, we discuss remaining challenges and exciting research frontiers for future energy-flux research.

Bacterial microbiota similarity between predators and prey in a blue tit trophic network

Trophic networks are composed of many organisms hosting microbiota that interact with their hosts and with each other. Yet, our knowledge of the factors driving variation in microbiota and their interactions in wild communities is limited. To investigate the relation among host microbiota across a trophic network, we studied the bacterial microbiota of two species of primary producers (downy and holm oaks), a primary consumer (caterpillars), and a secondary consumer (blue tits) at nine sites in Corsica. To quantify bacterial microbiota, we amplified 16S rRNA gene sequences in blue tit feces, caterpillars, and leaf samples. Our results showed that hosts from adjacent trophic levels had a more similar bacterial microbiota than hosts separated by two trophic levels. Our results also revealed a difference between bacterial microbiota present on the two oak species, and among leaves from different sites. The main drivers of bacterial microbiota variation within each trophic level differed across spatial scales, and sharing the same tree or nest box increased similarity in bacterial microbiota for caterpillars and blue tits. This study quantifies host microbiota interactions across a three-level trophic network and illustrates how the factors shaping bacterial microbiota composition vary among different hosts.