Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding

Using low volume eDNA methods to sample pelagic marine animal assemblages

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low-oxygen, high-sulfur sinkholes and springs

High-sulfur, low-oxygen environments formed by underwater sinkholes and springs create unique habitats populated by microbial mat communities. To explore the diversity and biogeography of these mats, samples were collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Our study investigated previously undescribed eukaryotic diversity in these habitats and further explored their bacterial communities. Mat samples and water parameters were collected from sulfur spring sites during the spring, summer, and fall of 2022. Cyanobacteria and diatoms were cultured from mat subsamples to create a culture-based DNA reference library. Remaining mat samples were used for metabarcoding of the 16S and rbcL regions to explore bacterial and diatom diversity, respectively. Analyses of water chemistry, alpha diversity, and beta diversity articulated a range of high-sulfur, low-oxygen habitats, each with distinct microbial communities. Conductivity, pH, dissolved oxygen, temperature, sulfate, and chloride had significant influences on community composition but did not describe the differences between communities well. Chloride concentration had the strongest correlation with microbial community structure. Mantel tests revealed that biogeography contributed to differences between communities as well. Our results provide novel information on microbial mat composition and present evidence that both local conditions and biogeography influence these unique communities.

Life in the Midwater: The Ecology of Deep Pelagic Animals

The water column of the deep ocean is dark, cold, low in food, and under crushing pressures, yet it is full of diverse life. Due to its enormous volume, this mesopelagic zone is home to some of the most abundant animals on the planet. Rather than struggling to survive, they thrive-owing to a broad set of adaptations for feeding, behavior, and physiology. Our understanding of these adaptations is constrained by the tools available for exploring the deep sea, but this tool kit is expanding along with technological advances. Each time we apply a new method to the depths, we gain surprising insights about genetics, ecology, behavior, physiology, diversity, and the dynamics of change. These discoveries show structure within the seemingly uniform habitat, limits to the seemingly inexhaustible resources, and vulnerability in the seemingly impervious environment. To understand midwater ecology, we need to reimagine the rules that govern terrestrial ecosystems. By spending more time at depth-with whatever tools are available-we can fill the knowledge gaps and better link ecology to the environment throughout the water column.

Metabarcoding analysis of marine zooplankton confirms the ecological role of a sheltered bight along an exposed continental shelf

Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.

Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration

The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.

A manager's guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.

Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. "V" stratified by depth, and "A" differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.