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1. Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding

   https://doi.org/10.1371/journal.pone.0267761  

   Damian-Serrano, Alejandro ; Hetherington, Elizabeth D. ; Choy, C. Anela ; Haddock, Steven H. ; Lapides, Alexandra ; Dunn, Casey W. ( May 2022 , PLOS ONE)

   Dam, Hans G. (Ed.)

   Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species’ diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the ‘jelly-web’, and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems. 

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2. Intraguild predation is increased in areas of low prey diversity in a generalist predator community

   https://doi.org/10.1111/1365-2656.13901  

   Uiterwaal, Stella F. ; Squires, Amber J. ; Grappone, Bennett A. ; Dillard, Brian ; Castaneda, Ariadne ; Kim, Sora L. ; DeLong, John P. ( February 2023 , Journal of Animal Ecology)

   Niche differentiation and intraguild predation (IGP) can allow ecologically similar species to coexist, although it is unclear which coexistence mechanism predominates in consumer communities. Until now, a limited ability to quantify diets from metabarcoding data has precluded the use of sequencing data to determine the relative importance of these mechanisms.

   Here, we pair a recent metabarcoding quantification approach with stable isotope analysis to examine diet composition in a wolf spider community.

   We compare the prevalence of resource partitioning and IGP in these spiders and test whether factors that influence foraging performance, including individual identity, morphology, prey community and environmental conditions, can explain variation in diet composition and IGP.

   Extensive IGP is likely the primary coexistence mechanism in this community, and other factors to which foraging variation is often attributed do not explain diet composition and IGP here. Rather, IGP increases as prey diversity decreases.

   Foragers are driven to IGP where resource niches are limited. We highlight the need to examine how drivers of predator–prey interaction strengths translate into foraging in natural systems.

    

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3. The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation

   https://doi.org/10.5061/dryad.kwh70rz4s  

   Littleford-Colquhoun, Bethan ; Freeman, Patrick ; Sackett, Violet ; Tulloss, Camille ; McGarvey, Lauren ; Geremia, Chris ; Kartzinel, Tyler ( January 2021 , Dryad)

   Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and lab. One of the earliest and most common strategies for dealing with such sensitivities has been to filter resulting sequence data to remove low-abundance sequences before conducting ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be both necessary and sufficient for cleaning up datasets, evidence to support this perception is lacking and more attention needs to be paid to the related risk of introducing other undesirable errors. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream dietary inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of individual dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and niche partitioning. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address a subset of research questions that focus on a subset of relatively abundant food resources, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data—or similar data such as environmental DNA, microbiomes, or pathobiomes—should be aware of potential drawbacks and consider alternative bioinformatic, experimental, and statistical solutions. We used fecal DNA metabarcoding to characterize the diets of bison and bighorn sheep in winter and summer. Our analyses are based on 35 samples (median per species per season = 10) analyzed using the P6 loop of the chloroplast trnL(UAA) intron together with publicly available plant reference data (Illumina sequence read data are available at NCBI (BioProject: PRJNA780500)). Obicut was used to trim reads with a minimum quality threshold of 30, and primers were removed from forward and reverse reads using cutadapt. All further sequence identifications were performed using obitools; forward and reverse sequences were aligned using the illuminapairedend command using a minimum alignment score of 40, and only joined sequences retained. We used the obiuniq command to group identical sequences and tally them within samples, enabling us to quantify the relative read abundance (RRA) of each sequence. Sequences that occurred ≤2 times overall or that were ≤8 bp were discarded. Sequences were considered to be likely PCR artifacts if they were highly similar to another sequence (1 bp difference) and had a much lower abundance (0.05%) in the majority of samples in which they occurred; we discarded these sequences using the obiclean command. Overall, we characterized 357 plant sequences and a subset of 355 sequences were retained in the dataset after rarefying samples to equal sequencing depth. We then applied relative read abundance thresholds from 0% to 5% to the fecal samples. We compared differences in the inferred dietary richness within and between species based on individual samples, based on average richness across samples, and based on the total richness of each population after accounting for differences in sample size. The readme file contains an explanation of each of the variables in the dataset. Information on the methodology can be found in the associated manuscript referenced above.  

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4. From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package

   https://doi.org/10.1002/ecs2.3842  

   Qin, Clara ; Bartelme, Ryan ; Chung, Y. Anny ; Fairbanks, Dawson ; Lin, Yang ; Liptzin, Daniel ; Muscarella, Chance ; Naithani, Kusum ; Peay, Kabir ; Pellitier, Peter ; et al ( November 2021 , Ecosphere)

   Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON’s newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced byneonMicrobecan be linked to NEON’s other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporatingneonMicrobeinto reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and theneonMicrobeR package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.

    

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5. Zooming in on mechanistic predator–prey ecology: Integrating camera traps with experimental methods to reveal the drivers of ecological interactions

   https://doi.org/10.1111/1365-2656.13264  

   Smith, J. A. ( May 2020 , The journal of animal ecology)

   1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive predator and prey behavior, incorporating environmental realism not possible in the lab while benefiting from the distinct capacity of camera traps to generate large data sets from multiple species with minimal observer interference. However, such pairings of camera traps with experimental methods remain underutilized. 3. We review recent advances in the experimental application of camera traps to investigate fundamental mechanisms underlying predator-prey ecology and present a conceptual guide for designing experimental camera trap studies. 4. Only 9% of camera trap studies on predator-prey ecology in our review mention experimental methods, but the application of experimental approaches is increasing. To illustrate the utility of camera trap-based experiments using a case study, we propose a study design that integrates observational and experimental techniques to test a perennial question in predator-prey ecology: how prey balance foraging and safety, as formalized by the risk allocation hypothesis. We discuss applications of camera trap-based experiments to evaluate the diversity of anthropogenic influences on wildlife communities globally. Finally, we review challenges to conducting experimental camera trap studies. 5. Experimental camera trap studies have already begun to play an important role in understanding the predator-prey ecology of free-living animals, and such methods will become increasingly critical to quantifying drivers of community interactions in a rapidly changing world. We recommend increased application of experimental methods in the study of predator and prey responses to humans, synanthropic and invasive species, and other anthropogenic disturbances. 

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