More Like this

1. Current practice in plankton metabarcoding: optimization and error management

   https://doi.org/10.1093/plankt/fbz041  

   Santoferrara, Luciana F. ( October 2019 , Journal of Plankton Research)

   High-throughput sequencing of a targeted genetic marker is being widely used to analyze biodiversity across taxa and environments. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations. Improved study designs and alternative sampling, lab and bioinformatic procedures have progressively enhanced data quality, but some problems persist. This article provides a framework to recognize and bypass the main types of errors that can affect metabarcoding data: false negatives, false positives, artifactual variants, disproportions and incomplete or incorrect taxonomic identifications. It is crucial to discern potential error impacts on different ecological parameters (e.g. taxon distribution, community structure, alpha and beta-diversity), as error management implies compromises and is thus directed by the research question. Synthesis of multiple plankton metabarcoding evaluations (mock sample sequencing or microscope comparisons) shows that high-quality data for qualitative and some semiquantitative goals can be achieved by implementing three checkpoints: first, rigorous protocol optimization; second, error minimization; and third, downstream analysis that considers potentially remaining biases. Conclusions inform us about the reliability of metabarcoding for plankton studies and, because plankton provides unique chances to compare genotypes and phenotypes, the robustness of this method in general.

    

   more » « less
2. 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. 

   more » « less
3. The community ecology perspective of omics data

   https://doi.org/10.1186/s40168-022-01423-8  

   Jurburg, Stephanie D. ; Buscot, François ; Chatzinotas, Antonis ; Chaudhari, Narendrakumar M. ; Clark, Adam T. ; Garbowski, Magda ; Grenié, Matthias ; Hom, Erik F. ; Karakoç, Canan ; Marr, Susanne ; et al ( December 2022 , Microbiome)

   Abstract The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples ( ɑ -diversity) and to assess how these profiles change in response to experimental treatments or across gradients ( β -diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ - and β -diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. 

   more » « less
4. Which moths might be pollinators? Approaches in the search for the flower‐visiting needles in the Lepidopteran haystack

   https://doi.org/10.1111/een.12782  

   Van Zandt, Peter A. ; Johnson, Daytona D. ; Hartley, Chad ; LeCroy, Kathryn A. ; Shew, H. Wayne ; Davis, Brandon T. ; Lehnert, Matthew S. ( July 2019 , Ecological Entomology)

   1. The natural history of pollination has been studied for centuries and is well documented for diurnal insect species, such as bees and butterflies, but less so for moths. There are notable cases of pollination systems among moths, but given their enormous diversity and primarily nocturnal habits, the role of moths as flower visitors is poorly understood. One potential issue with studying moth‐pollination systems is determining which approach to use in order to acquire data and reveal pollination patterns and dynamics. Based on reports from the literature and the authors' own research, this paper outlines eight approaches that can be employed to search for patterns of flower visitation by moths.

   2. The outlined approaches include searching the internet and online databases, sampling ecosystems, monitoring specific flowers, using artificial baits and floral scent lures, using moth phylogeny, proboscis morphology, and DNA and environmental DNA metabarcoding, which are supplemented with a brief description of the techniques and examples for each approach.

   3. Each approach has the potential to increase researchers' knowledge of associations between moths and the flowers that they visit, but their relative strengths and limitations are dependent on scope, efficacy of application, technical expertise, and level of effort.

   4. Each of these approaches, alone or in combination, are likely to be useful in the search for novel information on the natural history of flower visitation by moths and other potential pollinators.

    

   more » « less
5. Phytoplankton prey of an abundant estuarine copepod identified in situ using DNA metabarcoding

   https://doi.org/10.1093/plankt/fbac002  

   Holmes, Ann E. ; Kimmerer, Wim J. ; Koski, ed., Marja ( February 2022 , Journal of Plankton Research)

   Plankton trophic interactions play a crucial role in ecosystem processes. Diet analysis using high-throughput sequencing methods such as metabarcoding can provide new insight where traditional methods have been limited. We used 16S ribosomal RNA gene metabarcoding to identify phytoplankton from the guts of the copepod Pseudodiaptomus forbesi and in seston from the Cache Slough Complex, a tidal freshwater reach of the San Francisco Estuary, California, USA. Cyanobacteria, assumed to have low nutritional value for copepods, were detected in all copepod samples and comprised the highest relative read abundance in metabarcoding results. Differential abundance analysis, used to compare representation of operational taxonomic units between copepod and seston samples, showed that two filamentous taxa (a streptophyte and a cyanobacterium) were most overrepresented in copepod samples, whereas cryptophytes and most ochropytes (diatoms and related taxa) were underrepresented in copepod samples. These findings could reflect unexpected feeding patterns or trophic upgrading. Understanding the capabilities and limitations of DNA metabarcoding is key to its use in diet analysis and integration with traditional approaches.

    

   more » « less