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.
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.
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.
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.
Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture
The backbone of benthic marine monitoring programs is the biological component, traditionally the macrofauna inventory. Such macrofauna-based environmental impact assessments (EIA), however, are very time consuming and expensive. To overcome these shortcomings, we used environmental metabarcoding to test the potential of protists as bioindicators in EIAs.
Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture
We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n=72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference data from standard macrofauna biomonitoring surveys of the same samples.
The rapid growth of the salmon industry necessitates the development of fast and accurate tools to assess its environmental impact. Macrobenthic monitoring is commonly used to measure the impact of organic enrichment associated with salmon farm activities. However, classical benthic monitoring can hardly answer the rapidly growing demand because the morphological identification of macro-invertebrates is time-consuming, expensive and requires taxonomic expertise.
Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding
Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats.
Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demand highly trained specialists and are extremely time-consuming and costly, making it unsuitable for large-scale biomonitoring efforts involving numerous samples.