Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material.
Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding
Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited.
Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding
Since 2010, considerable efforts have been undertaken to monitor the environmental status of European marine waters and ensuring the development of methodological standards for the evaluation of this status. However, the current routine biomonitoring implicates time-consuming and costly manual sorting and morphological identification of benthic macrofauna.
Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys.
Benthic foraminiferal metabarcoding and morphology-based assessment around three offshore gas platforms: Congruence and complementarity
Since the 1960 s, there has been a rapid expansion of drilling activities in the central and northern Adriatic Sea to meet the increasing global energy demand. The discharges of organic and inorganic pollutants, as well as the alteration of the sediment substrate, are among the main impacts associated with these activities.
Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys.
Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy)
The environmental DNA (eDNA) metabarcoding represents a new promising tool for biomonitoring and environmental impact assessment. One of the main advantages of eDNA metabarcoding, compared to the traditional morphotaxonomy-based methods, is to provide a more holistic biodiversity information that includes inconspicuous morphologically non-identifiable taxa.
Responses of foraminifera communities to aquaculture-derived organic enrichment as revealed by environmental DNA metabarcoding
The diversity of the haemosporidian genera Plasmodium, Haemoproteus and Leucocytozoon in birds from rain forests in Madagascar is characterized combining techniques of PCR and microscopy and based on the examination of 72 host individuals of 23 species in 15 families. High total prevalence of haemosporidians (68%) is detected, with Leucocytozoon infections being predominant (59.7%) and lower comparable prevalence of Plasmodium (18.0%) and Haemoproteus (23.6%) infections.
Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community.
A comparison of different ciliate metabarcode genes as bioindicators for environmental impact assessments of salmon aquaculture
Ciliates are powerful indicators for monitoring the impact of aquaculture and other industrial activities in the marine environment. Here we tested the efficiency of four different genetic markers (V4 and V9 regions of the SSU rRNA gene, D1 and D2 regions of the LSU rRNA gene, obtained from environmental (e)DNA and environmental (e)RNA) of benthic ciliate communities for environmental monitoring.