Compound‐specific isotope analysis of amino acids as a new tool to uncover trophic chains in soil food webs

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.

The main strategies for soil pollution apportionment: A review of the numerical methods

Nowadays, a large number of compounds with different physical and chemical properties have been determined in soil. Environmental behaviors and source identification of pollutants in soil are the foundation of soil pollution control. Identification and quantitative analysis of potential pollution sources are the prerequisites for its prevention and control. Many efforts have made to develop methods for identifying the sources of soil pollutants. These efforts have involved the measurement of source and receptor parameters and the analysis of their relationships via numerical statistics methods. We have comprehensively reviewed the progress made in the development of source apportionment methodologies to date and present our synthesis. The numerical methods, such as spatial geostatistics analysis, receptor models, and machine learning methods are addressed in depth. In most cases, however, the effectiveness of any single approach for source apportionment remains limited. Combining multiple methods to address soil quality problems can reduce uncertainty about the sources of soil pollution. This review also constructively highlights the key strategies of combining mathematical models with the assessment of chemical profiles to provide more accurate source attribution. This review intends to provide a comprehensive summary of source apportionment methodologies to help promote further development.

Trophic resources of the edaphic microarthropods: A worldwide review of the empirical evidence

Ecosystem sustainable use requires reliable information about its biotic and abiotic structure and functioning. Accurate knowledge of trophic relations is central for the understanding of ecosystem dynamics, which in turn, is essential for food web stability analyzes and the development of sustainable practices. There is a rapid growth in the knowledge on how belowground biodiversity regulates the structure and functioning of terrestrial ecosystems. Although, the available information about trophic relationships is hard to find and fragmented. Most of the information available worldwide about the food resources of soil microarthropods suggested that out of 3105 hits of initial research on this aspect only a total of 196 published works related particular species, genera, and families to particular trophic resources, the majority of them dealing with soils of the Palearctic region. From the 196 publications we extracted 3009 records relating specific taxonomic groups to their trophic resources, 20 percent mention saprophytic fungi as a food resource, 16 percent cite microfauna, 11 percent mention bacteria, 10 percent litter and 8 percent cite Springtails. The available information was highly skewed, the 73.71 percent comes from Acari, and within these, 50.62 percent correspond just to Sarcoptiformes. The literature on Collembola is very scarce and most of the information is on arthropleona. The review also highlights that available research on the use of trophic resources comes from European sites and the information on this aspect from other parts of the soils of the world is still at large but unknown.

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.

Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica

Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.

Stable isotopes in monitoring terrestrial arthropods

Monitoring of arthropods focuses typically on changes in population and range size over time. Yet, there are a myriad of other aspects that could and should be monitored under the ongoing global and local environmental change. Stable isotope analysis, widely employed in short-term ecological studies, has potential in long-term monitoring of arthropods. Here we discuss the use of stable isotopes in monitoring terrestrial arthropods, provide some empirical examples of the use of bulk tissue samples in stable isotope analysis, and outline future directions in using compound-specific stable isotope analysis in monitoring. We performed a literature search for 2012–2021 to see if stable isotopes have been specifically used in monitoring of terrestrial arthropods. The literature shows that stable isotopes have been successfully used to reveal ecological phenomena (dispersal, trophic interactions, resource use) that would have been difficult or impossible to detect by other means. Yet, stable isotopes have been underused in arthropod monitoring programs, but the growing number of basic studies on stable isotope ecology and methodology provides crucial basis needed for developing monitoring programs. Stable isotopes provide technically, economically and ecologically feasible addition to the traditional monitoring methods of terrestrial arthropods.

Integrating DNA-based Prey Occurrence Probability Into Stable Isotope Mixing Models

The introduction of laboratory methods to animal dietary studies has allowed researchers to obtain results with accuracy and precision not possible with observational techniques. For example, DNA barcoding, or the identification of prey with taxon-specific DNA sequences, allows researchers to classify digested prey tissues to the species-level, while stable isotope analysis paired with Bayesian mixing models can quantify dietary contributions by comparing a consumer's isotopic values to those derived from their prey. However, DNA-based methods are currently only able to classify, but not quantify, the taxa present in a diet sample, while stable isotope analysis can only quantify dietary taxa that are identified a priori as prey isotopic values are a result of life history traits, not phylogenetic relatedness. Recently, researchers have begun to couple these techniques in dietary studies to capitalize on the reciprocal benefits and drawbacks offered by each approach, with some even integrating DNA-based results directly into Bayesian mixing models as informative priors. As the informative priors used in these models must represent known dietary compositions (e.g., percentages of prey biomasses), researchers have scaled the DNA-based frequency of occurrence of major prey groups so that their normalized frequency of occurrence sums to 100%. Unfortunately, such an approach is problematic as priors stemming from binomial, DNA-based data do not truly reflect quantitative information about the consumer's diet and may skew the posterior distribution of prey quantities as a result. Therefore, we present a novel approach to incorporate DNA-based dietary information into Bayesian stable isotope mixing models that preserves the binomial nature of DNA-based results. This approach uses community-wide frequency of occurrence or logistic regression-based estimates of prey occurrence to dictate the probability that each prey group is included in each mixing model iteration, and, in turn, the probability that each iteration's results are included in the posterior distribution of prey composition possibilities. Here, we demonstrate the utility of this method by using it to quantify the prey composition of nestling Louisiana waterthrush (Parkesia motacilla).

Amino acid nitrogen and carbon isotope data: Potential and implications for ecological studies

Explaining food web dynamics, stability, and functioning depend substantially on understanding of feeding relations within a community. Bulk stable isotope ratios (SIRs) in natural abundance are well‐established tools to express direct and indirect feeding relations as continuous variables across time and space. Along with bulk SIRs, the SIRs of individual amino acids (AAs) are now emerging as a promising and complementary method to characterize the flow and transformation of resources across a diversity of organisms, from microbial domains to macroscopic consumers. This significant AA‐SIR capacity is based on empirical evidence that a consumer's SIR, specific to an individual AA, reflects its diet SIR coupled with a certain degree of isotopic differences between the consumer and its diet. However, many empirical ecologists are still unfamiliar with the scope of applicability and the interpretative power of AA‐SIR. To fill these knowledge gaps, we here describe a comprehensive approach to both carbon and nitrogen AA‐SIR assessment focusing on two key topics: pattern in AA‐isotope composition across spatial and temporal scales, and a certain variability of AA‐specific isotope differences between the diet and the consumer. On this basis we review the versatile applicability of AA‐SIR to improve our understanding of physiological processes as well as food web functioning, allowing us to reconstruct dominant basal dietary sources and trace their trophic transfers at the specimen and community levels. Given the insightful and opportunities of AA‐SIR, we suggest future applications for the dual use of carbon and nitrogen AA‐SIR to study more realistic food web structures and robust consumer niches, which are often very difficult to explain in nature.

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.

Fatty acid metabolism in an oribatid mite: de novo biosynthesis and the effect of starvation

The fatty acid (FA) composition of lipids in animals is influenced by factors such as species, life stage, availability and type of food, as well as the ability to synthesize certain FAs de novo. We investigated the effect of starvation on the neutral lipid (NLFA) and phospholipid (PLFA) fatty acid patterns of the oribatid mite Archegozetes longisetosus Aoki. Furthermore, we performed stable-isotope labeled precursors feeding experiments under axenic conditions to delineate de novo FA synthesis by profiling ¹³C and deuterium incorporation via single-ion monitoring. Starvation of mites resulted in a decline in the total amount of NLFAs and significantly changed the fatty acid patterns, indicating that NLFAs were metabolized selectively. Biochemical tracer experiments confirmed that oribatid mites, like other animals, can produce stearic (18:0) and oleic acid (18:1ω9) de novo. Mass spectrometric data also revealed that they appear to synthesize linoleic acid [18:2ω6,9 = (9Z,12Z)-octadeca-9,12-dienoic acid]-an ability restricted only to a few arthropod taxa, including astigmatid mites. The physiological and biosynthesis processes revealed here are crucial to understand the potential biomarker function of fatty acids-especially 18:2ω6,9-in oribatid mites and their applicability in soil animal food web studies.

Characterizing niche differentiation among marine consumers with amino acid δ13C fingerprinting

Marine food webs are highly compartmentalized, and characterizing the trophic niches among consumers is important for predicting how impact from human activities affects the structuring and functioning of marine food webs. Biomarkers such as bulk stable isotopes have proven to be powerful tools to elucidate trophic niches, but they may lack in resolution, particularly when spatiotemporal variability in a system is high. To close this gap, we investigated whether carbon isotope (δ13C) patterns of essential amino acids (EAAs), also termed δ13CAA fingerprints, can characterize niche differentiation in a highly dynamic marine system. Specifically, we tested the ability of δ13CAA fingerprints to differentiate trophic niches among six functional groups and ten individual species in the Baltic Sea. We also tested whether fingerprints of the common zooplanktivorous fishes, herring and sprat, differ among four Baltic Sea regions with different biochemical conditions and phytoplankton assemblages. Additionally, we investigated how these results compared to bulk C and N isotope data for the same sample set. We found significantly different δ13CAA fingerprints among all six functional groups. Species differentiation was in comparison less distinct, due to partial convergence of the species' fingerprints within functional groups. Herring and sprat displayed region-specific δ13CAA fingerprints indicating that this approach could be used as a migratory marker. Niche metrics analyses showed that bulk isotope data had a lower power to differentiate between trophic niches than δ13CAA fingerprinting. We conclude that δ13CAA fingerprinting has a strong potential to advance our understanding of ecological niches, and trophic linkages from producers to higher trophic levels in dynamic marine systems. Given how management practices of marine resources and habitats are reshaping the structure and function of marine food webs, implementing new and powerful tracer methods are urgently needed to improve the knowledge base for policy makers.

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.