Combining bulk and amino acid stable isotope analyses to quantify trophic level and basal resources of detritivores: a case study on earthworms

Enhanced gut microbiome supplementation of essential amino acids in Diploptera punctata fed low-protein plant-based diet

Introduction

Building on our previous work, we investigate how dietary shifts affect gut microbial essential amino acid (EAA) provisioning in the lactating cockroach Diploptera punctata.

Method

To that end, we fed cockroaches three distinct diets: a plant-only Gari diet composed of starchy and granulated root tuber Yucca (Manihot esculenta), a dog food diet (DF), and a cellulose-amended dog food (CADF) diet. We anticipated that the high carbohydrate, low protein Gari would highlight increased microbial EAA supplementation to the host.

Results

By day 28, we observed distinct profiles of 14 bacterial families in the insect gut microbiomes of the three dietary groups. CADF-fed insects predominantly harbored cellulolytic and nitrogen-fixing bacteria families Streptococcaceae and Xanthomonadaceae. In contrast, Gari-fed insects were enriched in anaerobic lignocellulolytic bacteria families Paludibacteraceae and Dysgonomonadaceae, while DF-fed insects had a prevalence of proteolytic anaerobes Williamwhitmaniaceae and sulfate-reducing bacteria Desulfovibrionaceae. Furthermore, we confirmed significantly higher EAA supplementation in Gari-fed insects than in non-Gari-fed insects based on δ13C-EAA offsets between insect and their diets. The δ13C-EAA offsets between DF and CADF were nearly indistinguishable, highlighting the relevance of using the plant-based Gari in this experiment to unequivocally demonstrate this function in this insect. These results were underscored by lower standard metabolic rate (SMR) relative to the DF insect in Gari-fed (intermediate SMR and dietary quality) and CADF (least SMR and dietary quality) insects.

Discussion

The influence of diet on EAA provisioning and SMR responses in insects underscores the need for further exploration into the role of gut microbial functions in modulating metabolic responses.

New insights from an eight-year study on per- and polyfluoroalkyl substances in an urban terrestrial ecosystem

Per- and polyfluoroalkyl substances (PFAS) were analysed in a high number of terrestrial samples of soil, earthworm, bird eggs and liver from red fox and brown rat in an urban area in Norway from 2013 to 2020. PFOS and the long chain PFCAs were the most dominating compounds in all samples, proving their ubiquitous distribution. Other less studied compounds such as 6:2 FTS were first and foremost detected in earthworm. 8:2 FTS was found in many samples of fieldfare egg, sparrowhawk egg and earthworm, where the eggs had highest concentrations. Highest concentrations for both 6:2 FTS and 8:2 FTS were detected at present and former industry areas. FOSA was detected in many samples of the species with highest concentrations in red fox liver and brown rat liver of 3.3 and 5.5 ng/g ww. PFAS concentrations from the urban area were significantly higher than from background areas indicating that some of the species can be suitable as markers for PFAS emissions in an urban environment. Fieldfare eggs had surprisingly high concentrations of PFOS and PFCA concentrations from areas known to be or have been influenced by industry. Biota-soil-accumulation factor and magnification calculations indicate accumulation and magnification potential for several PFAS. Earthworm and fieldfare egg had average concentrations above the Canadian and European thresholds in diet for avian wildlife and predators. For earthworms, 18 % of the samples exceeded the European threshold (33 ng/g ww) of PFOS in prey for predators, and for fieldfare eggs, 35 % of the samples were above the same threshold. None of the soil samples exceeded a proposed PNEC of PFOS for soil living organisms of 373 ng/g dw.

Structure and diversity of earthworm communities in long-term irrigated soils with raw effluent and treated wastewater

This study was conducted in two natural meadows: first, soils were irrigated with raw wastewater (SIRWW) and in the second, soils were irrigated with treated wastewater (SITWW). Earthworms were sampled in eight soil blocks spaced 10 m apart at each site. Earthworm community was characterized and compared using density, biomass, composition, structure, species richness, and diversity parameters. At both meadows, 459 earthworm individuals from two families and seven species were collected. The highest earthworm density and species richness were recorded at SIRWW. Nicodrilus caligenus was the most abundant species. Most of earthworm community parameters decreased significantly at SITWW. Only two species (N. caligenus and Octodrilus complanatus) were common between the two grasslands. Among the seven species identified at both meadows, four (Allolobophora longa, Eisenia foetida, Allolobophora rosea, Allolobophora chlorotica) were exclusively present in SIRWW, whereas a single species (Amynthas sp.) was characterized in SITWW. Three ecological earthworm groups (epigeic, endogeic, and anectic) were represented in SIRWW, with the dominance of endogeics. Further studies are needed to quantify pollution in this soils and the accumulation of pollutant load in earthworms. It is also important to highlight the relationship between the abundance and diversity of earthworms in these two ecosystems with soil biological activity.

First Short-Term Study of the Relationship between Native and Invasive Earthworms in the Zone of Soil Freezing in Western Siberia—Experiments in Mesocosms

Earthworm invasions often reduce biodiversity and affect the ability of ecosystems to perform ecosystem functions. Over the past few decades, European lumbricid species have spread widely in natural habitats in Western Siberia, without completely displacing the native species. The aim of the present experiment is to study the survival, reproductive potential, vertical distribution, abundance, and biomass of Aporrectodea caliginosa and Lumbricus rubellus invasive species for the region and the native species Eisenia nordenskioldi and their influence on each other. For this purpose, winter and vegetation experiments were conducted in mesocosms simulating the real situation of invasions in the same communities on the same types of soils with the same amount and composition of litter. The authors found that the native species was significantly inferior to A. caliginosa in reproduction rate, number of offspring, and final biomass, but had an advantage over L. rubellus. The native species was positively influenced by the presence of A. caliginosa. In the experiment, there was a significant rejuvenation of the populations of the studied species, as well as an increase in abundance and relative mass under interaction conditions compared to mono variants. The native species had advantages over the invasive species in terms of winter survival. The natural volume of litter used in the experiment was insufficient for L. rubellus. According to the results of the experiment, it can be assumed that the spread of L. rubellus will continue to be limited to non-freezing biotopes rich in organic matter. A. caliginosa will spread in natural communities and agrocenoses of Western Siberia.

The coupling of green and brown food webs regulates trophic position in a montane mammal guild

Food web ecology has revolutionized our understanding of ecological processes, but the drivers of food web properties like trophic position (TP) and food chain length are notoriously enigmatic. In terrestrial ecosystems, above- and belowground systems were historically compartmentalized into "green" and "brown" food webs, but the coupling of these systems by animal consumers is increasingly recognized, with potential consequences for trophic structure. We used stable isotope analysis (δ¹³ C, δ¹⁵ N) of individual amino acids to trace the flow of essential biomolecules and jointly measure multichannel feeding, food web coupling, and TP in a guild of small mammals. We then tested the hypothesis that brown energy fluxes to aboveground consumers increase terrestrial food chain length via cryptic trophic transfers during microbial decomposition. We found that the average small mammal consumer acquired nearly 70% of their essential amino acids (69.0% ± 7.6%) from brown food webs, leading to significant increases in TP across species and functional groups. Fungi were the primary conduit of brown energy to aboveground consumers, providing nearly half the amino acid budget for small mammals on average (44.3% ± 12.0%). These findings illustrate the tightly coupled nature of green and brown food webs and show that microbially mediated energy flow ultimately regulates food web structure in aboveground consumers. Consequently, we propose that the integration of green and brown energy channels is a cryptic driver of food chain length in terrestrial ecosystems.

Multifunctionality of belowground food webs: resource, size and spatial energy channels

The belowground compartment of terrestrial ecosystems drives nutrient cycling, the decomposition and stabilisation of organic matter, and supports aboveground life. Belowground consumers create complex food webs that regulate functioning, ensure stability and support biodiversity both below and above ground. However, existing soil food-web reconstructions do not match recently accumulated empirical evidence and there is no comprehensive reproducible approach that accounts for the complex resource, size and spatial structure of food webs in soil. Here I build on generic food-web organisation principles and use multifunctional classification of soil protists, invertebrates and vertebrates, to reconstruct a 'multichannel' food web across size classes of soil-associated consumers. I infer weighted trophic interactions among trophic guilds using feeding preferences and prey protection traits (evolutionarily inherited traits), size and spatial distributions (niche overlaps), and biomass-dependent feeding. I then use food-web reconstruction, together with assimilation efficiencies, to calculate energy fluxes assuming a steady-state energetic system. Based on energy fluxes, I propose a number of indicators, related to stability, biodiversity and multiple ecosystem-level functions such as herbivory, top-down control, translocation and transformation of organic matter. I illustrate this approach with an empirical example, comparing it with traditional resource-focused soil food-web reconstruction. The multichannel reconstruction can be used to assess 'trophic multifunctionality' (analogous to ecosystem multifunctionality), i.e. simultaneous support of multiple trophic functions by the food web, and compare it across communities and ecosystems spanning beyond the soil. With further empirical validation of the proposed functional indicators, this multichannel reconstruction approach could provide an effective tool for understanding animal diversity-ecosystem functioning relationships in soil. This tool hopefully will inspire more researchers to describe soil communities and belowground-aboveground interactions comprehensively. Such studies will provide informative indicators for including consumers as active agents in biogeochemical models, not only locally but also on regional and global scales.

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.

Multidimensional trophic niche revealed by complementary approaches: Gut content, digestive enzymes, fatty acids and stable isotopes in Collembola

Trophic niche differentiation may explain coexistence and shape functional roles of species. In complex natural food webs, however, trophic niche parameters depicted by single and isolated methods may simplify the multidimensional nature of consumer trophic niches, which includes feeding processes such as food choice, ingestion, digestion, assimilation and retention. Here we explore the correlation and complementarity of trophic niche parameters tackled by four complementary methodological approaches, that is, visual gut content, digestive enzyme, fatty acid and stable isotope analyses-each assessing one or few feeding processes, and demonstrate the power of method combination. Focusing on soil ecosystems, where many omnivore species with cryptic feeding habits coexist, we chose Collembola as an example. We compiled 15 key trophic niche parameters for 125 species from 40 studies. We assessed correlations among trophic niche parameters and described variation of these parameters in different Collembola species, families and across life-forms, which represent microhabitat specialisation. Correlation between trophic niche parameters was weak in 45 out of 64 pairwise comparisons, pointing at complementarity of the four methods. Jointly, the results indicated that fungal- and plant-feeding Collembola assimilate storage, rather than structural polysaccharides, and suggested bacterial feeding as a potential alternative feeding strategy. Gut content and fatty acid analyses suggested alignment between ingestion and assimilation/retention processes in fungal- and plant-feeding Collembola. From the 15 trophic niche parameters, six were related to Collembola family identity, suggesting that not all trophic niche dimensions are phylogenetically structured. Only three parameters were related to the life-forms, suggesting that species use various feeding strategies when living in the same microenvironments. Consumers can meet their nutritional needs by varying their food choices, ingestion and digestion strategies, with the connection among different feeding processes being dependent on the consumed resource and consumer adaptations. Multiple methods reveal different dimensions, together drawing a comprehensive picture of the trophic niche. Future studies applying the multidimensional trophic niche approach will allow us to trace trophic complexity and reveal niche partitioning of omnivorous species and their functional roles, especially in cryptic environments such as soils, caves, deep ocean or benthic ecosystems.

Improving the application of quantitative fatty acid signature analysis in soil food webs: The effects of diet fat content

Quantitative fatty acid signature analysis (QFASA) as a biochemical tool to study the diet composition of predators is frequently used in marine ecology to infer trophic links in vertebrate consumers. However, the potential and challenges of this method in other ecosystems have only recently been studied. The application in soil ecosystems leads to hurdles not encountered in the marine, such as the low similarity of fatty acid signatures between resource and consumer. So far, diet estimation attempts have been semisuccessful, necessitating to adapt QFASA for use in soil food webs. Dietary fat content may play an important role, as it influences consumer metabolism, and thus calibration coefficients for fatty acid trophic transfer. A series of feeding trials with baker's yeast spiked with five different pure fatty acids at various concentrations was conducted with Collembola, and the changes in calibration coefficients were observed. From there, equations were gained through regression analysis and new sets of calibration coefficients were calculated. QFASA was applied on a range of basal resources and the results compared with previously defined calibration coefficients. Calibration coefficients changed with the proportion of fatty acids in the diet and differed between the three Collembolan species. The re-estimation of diets showed an improvement of model performance by the new calibration coefficients and indicated several modes of fatty acid assimilation. These greatly influence the outcome of diet estimation, for example, algal and bacterial diets are likely underestimated due to high metabolic turnover rates. The application of QFASA in soil ecosystems remains challenging. The variation in calibration coefficients and the resulting decrease in estimation deviation indicate the merit of calculating calibration coefficients from consumer signatures through linear or exponential equations. Ideally, the method should, when extended to the entire fatty acid signature, allow correct determination of consumer diets in soil food webs.

Size compartmentalization of energy channeling in terrestrial belowground food webs

Size-structured food webs form integrated trophic systems where energy is channeled from small to large consumers. Empirical evidence suggests that size structure prevails in aquatic ecosystems, whereas in terrestrial food webs trophic position is largely independent of body size. Compartmentalization of energy channeling according to size classes of consumers was suggested as a mechanism that underpins functioning and stability of terrestrial food webs including those belowground, but their structure has not been empirically assessed across the whole size spectrum. Here we used stable isotope analysis and metabolic regressions to describe size structure and energy use in eight belowground communities with consumers spanning 12 orders of magnitude in living body mass, from protists to earthworms. We showed a negative correlation between trophic position and body mass in invertebrate communities and a remarkable nonlinearity in community metabolism and trophic positions across all size classes. Specifically, we found that the correlation between body mass and trophic level is positive in the small-sized (protists, nematodes, arthropods below 1 μg in body mass), neutral in the medium-sized (arthropods of 1 μg to 1 mg), and negative in the large-sized consumers (large arthropods, earthworms), suggesting that these groups form compartments with different trophic organization. Based on this pattern, we propose a concept of belowground food webs being composed of (1) size-structured micro-food web driving fast energy channeling and nutrient release, for example in microbial loop; (2) arthropod macro-food web with no clear correlation between body size and trophic level, hosting soil arthropod diversity and subsidizing aboveground predators; and (3) "trophic whales," sequestering energy in their large bodies and restricting its propagation to higher trophic levels in belowground food webs. The three size compartments are based on a similar set of basal resources, but contribute to different ecosystem-level functions and respond differently to variations in climate, soil characteristics and land use. We suggest that the widely used vision of resource-based energy channeling in belowground food webs can be complemented with size-based energy channeling, where ecosystem multifunctionality, biodiversity, and stability are supported by a balance across individual size compartments.

Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles

Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13C, δ15N, and Δ14C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.

Isotopic discrimination between carrion and elytra clippings of lab-reared American burying beetles (Nicrophorus americanus): Implications for conservation and evaluation of feeding relationships in the wild

RATIONALE

Differences in stable isotope composition between an animal and its diet are quantified by experimentally derived diet-tissue discrimination factors. Appropriate discrimination factors between consumers and prey are essential for interpreting stable isotope patterns in ecological studies. While available for many taxa, these values are rarely estimated for organisms within the carrion food web.

METHODS

We used a controlled-diet stable isotope feeding trial to quantify isotopic diet-tissue discrimination factors of carbon (δ¹³ C values) and nitrogen (δ¹⁵ N values) from laboratory-reared Nicrophorus americanus raised on carrion. We used exoskeleton samples of beetle elytra (wing covers) to determine diet-tissue discrimination factors using a continuous flow isotope ratio mass spectrometer equipped with an elemental analyzer. We also measured the isotopic compositions of five species of co-occurring, wild-caught burying beetles and evaluated feeding relationships.

RESULTS

We found differences in stable carbon discrimination between carrion sources (mammalian and avian) and lab-reared beetles, but no difference in stable nitrogen discrimination. Values for δ¹³ C did not differ among wild-caught burying beetle species, but values for δ¹⁵ N were significantly different for the three species with overlapping breeding seasons. Furthermore, wild-caught burying beetles within our study area do not appear to use avian carrion resources to rear their young.

CONCLUSIONS

This study informs future interpretation of stable isotope data for insects within the carrion food web. In addition, these results provide insight into carrion resources used by co-occurring burying beetle species in situ. We also demonstrated that independent of adult food type, the larval food source has a significant impact on the isotopic signatures of adult beetles, which can be estimated using a minimally invasive elytra clipping.

Shifting systems: prerequisites for the application of quantitative fatty acid signature analysis in soil food webs

Quantitative fatty acid signature analysis (QFASA) is widely used to investigate trophic interactions in marine ecosystems, as nutritionally important ω3 long-chain polyunsaturated fatty acids at the food web base allow tracing of their trophic transfer in the food chain. By contrast, the basal resources in soil food webs comprise a wider array of trophic markers, including branched-chain, cyclopropane as well as several mono- and polyunsaturated fatty acids. These diverse markers allow distinguishing between the three dominant soil carbon and energy channels, the root, bacterial and fungal pathway. QFASA has not been applied yet to soil ecosystems owing to the lack of a priori data to fit the model. The present work investigates the transfer of absolute and relative trophic marker fatty acids into Collembola as dominant representatives of the soil mesofauna. Three different species were fed on a variety of single diets characteristic for the green and brown food chain. Calibration coefficients were calculated and diet estimation trials for mixed diet set-ups were performed, using a library comprising 50 different resources. However, estimation of Collembola diet was only partially successful, identifying the main components, but not the correct relative proportions. Adjustments by fat content or diet group exclusion did not improve the results. Nonetheless, this work provides, to our knowledge, a first comprehensive dataset to translate the application of QFASA from marine to soil ecosystems. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

Role of the gut microbiome in mediating standard metabolic rate after dietary shifts in the viviparous cockroach, Diploptera punctata

Diet may be a significant determinant of insect gut microbiome composition. However, the extent to which dietary shifts shape both the composition and relevant functions of insect gut microbiomes, and ultimately impact host energy balance (i.e. metabolic phenotype), is not well understood. We investigated the impacts of diet switching on Diploptera punctata females maintained on a dog food (DF) diet relative to those fed a comparatively sub-optimal cellulose-amended dog food (CADF) diet for 4 weeks. After this period, dietary shift resulted in a significantly higher average mass-specific standard metabolic rate (SMR) in CADF-fed females compared with DF-fed females. We also uncovered significant 13C-enrichment in DF-fed insect samples relative to CADF-fed insect samples and lowered bacterial essential amino acid (EAA) provisioning in CADF-fed samples. Differences in SMR and EAA provisioning were not accompanied by significant differences in overall microbiome composition between the two groups. However, cellulolytic and nitrogen-fixing bacterial families dominant in wild omnivorous cockroaches and wood-feeding termites were significantly enriched in CADF-fed females than in DF-fed females, at the end of the study. We propose that these changes in microbiome composition after dietary shifts are associated with changes in EAA provisioning and possibly SMR. Further studies are needed to comprehensively understand the relative importance of gut microbial functions among the complexity of factors known to underscore SMR responses in insects under varying dietary conditions.

Elucidating stygofaunal trophic web interactions via isotopic ecology

Subterranean ecosystems host highly adapted aquatic invertebrate biota which play a key role in sustaining groundwater ecological functioning and hydrological dynamics. However, functional biodiversity studies in groundwater environments, the main source of unfrozen freshwater on Earth, are scarce, probably due to the cryptic nature of the systems. To address this, we investigate groundwater trophic ecology via stable isotope analysis, employing δ¹³C and δ¹⁵N in bulk tissues, and amino acids. Specimens were collected from a shallow calcrete aquifer in the arid Yilgarn region of Western Australia: a well-known hot-spot for stygofaunal biodiversity. Sampling campaigns were carried out during dry (low rainfall: LR) and the wet (high rainfall: HR) periods. δ¹³C values indicate that most of the stygofauna shifted towards more ¹³C-depleted carbon sources under HR, suggesting a preference for fresher organic matter. Conversion of δ¹⁵N values in glutamic acid and phenylalanine to a trophic index showed broadly stable trophic levels with organisms clustering as low-level secondary consumers. However, mixing models indicate that HR conditions trigger changes in dietary preferences, with increasing predation of amphipods by beetle larvae. Overall, stygofauna showed a tendency towards opportunistic and omnivorous habits—typical of an ecologically tolerant community—shaped by bottom-up controls linked with changes in carbon flows. This study provides baseline biochemical and ecological data for stygofaunal trophic interactions in calcretes. Further studies on the carbon inputs and taxa-specific physiology will help refine the interpretation of the energy flows shaping biodiversity in groundwaters. This will aid understanding of groundwater ecosystem functioning and allow modelling of the impact of future climate change factors such as aridification.