Dataset Information

Quantification of marine benthic communities with metabarcoding.

ABSTRACT: DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.

SUBMITTER: Klunder L

PROVIDER: S-EPMC9298412 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Quantification of marine benthic communities with metabarcoding.

Klunder Lise L van Bleijswijk Judith D L JDL Kleine Schaars Loran L van der Veer Henk W HW Luttikhuizen Pieternella C PC Bijleveld Allert I AI

Molecular ecology resources 20211101 3

DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomas ...[more]

PMID: 34687591

Similar Datasets

Project description:BackgroundFreshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use and recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally. Aquatic insects and other macroinvertebrates are often used as indicators of ecological condition in freshwater biomonitoring programs; however, these diverse groups can present challenges to morphological identification and coarse-level taxonomic resolution can mask patterns in community composition. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. While individual stream reaches can be very heterogenous, most community ecology studies focus on larger, landscape-level patterns of community composition. A high degree of community variability at the local scale has important implications for both biomonitoring and ecological research, and the incorporation of DNA metabarcoding into local biodiversity assessments will inform future sampling protocols.ResultsWe sampled twenty streams in southern Ontario, Canada, for aquatic macroinvertebrates across multiple time points and assessed local community variability by comparing field replicates taken ten meters apart within the same stream. Using bulk-tissue DNA metabarcoding, we revealed that aquatic macroinvertebrate communities are highly diverse at small spatial scales with unprecedented levels of local taxonomic turnover. We detected over 1600 Operational Taxonomic Units (OTUs) from 149 families, and a single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Benthic communities were largely comprised of rare taxa detected only once per stream despite multiple biological replicates (24-94% rare taxa per site). In addition to numerous rare taxa, our species pool estimates indicated that there was a large proportion of taxa that remained undetected by our sampling regime (14-94% per site). Our sites were located across a gradient of agricultural activity, and while we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use. Within-stream dissimilarity estimates were consistently high for all levels of taxonomic resolution (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales.

Project description:As marine ecosystems are influenced by global and regional processes, standardized information on community structure has become crucial for assessing broad-scale responses to natural and anthropogenic disturbances. Extensive biogeographic provinces, such as the Brazilian Province in the southwest Atlantic, present numerous theoretical and methodological challenges for understanding community patterns on a macroecological scale. In particular, the Brazilian Province is composed of a complex system of heterogeneous reefs and a few offshore islands, with contrasting histories and geophysical-chemical environments. Despite the large extent of the Brazilian Province (almost 8,000 kilometers), most studies of shallow benthic communities are qualitative surveys and/or have been geographically restricted. We quantified community structure of shallow reef habitats from 0° to 27°S latitude using a standard photographic quadrat technique. Percent cover data indicated that benthic communities of Brazilian reefs were dominated by algal turfs and frondose macroalgae, with low percent cover of reef-building corals. Community composition differed significantly among localities, mostly because of their macroalgal abundance, despite reef type or geographic region, with no evident latitudinal pattern. Benthic diversity was lower in the tropics, contrary to the general latitudinal diversity gradient pattern. Richness peaked at mid-latitudes, between 20°S to 23°S, where it was ~3.5-fold higher than localities with the lowest richness. This study provides the first large-scale description of benthic communities along the southwestern Atlantic, providing a baseline for macroecological comparisons and evaluation of future impacts. Moreover, the new understanding of richness distribution along Brazilian reefs will contribute to conservation planning efforts, such as management strategies and the spatial prioritization for the creation of new marine protected areas.

Dataset Information

Quantification of marine benthic communities with metabarcoding.

Publications

Quantification of marine benthic communities with metabarcoding.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets