Biology subjects

Rodriguez Barreto, D.

Publications and source records attributed to Rodriguez Barreto, D..

2 recordsLinked to original sources

bioRxiv2020

Rapid quantitative assessment of fish larvae community composition using metabarcoding

Climate change stressors greatly impact the early life-stages of many organisms but their cryptic morphology often renders them difficult to monitor using morphological identification. High-throughput sequencing of DNA amplicons (metabarcoding) is potentially a rapid and cost-effective method to monitor early life-stages for management and environmental impact assessment purposes. Yet, there is conflicting information about the quantitative capability of metabarcoding. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve relative abundance estimates, the amount of tissue for each specimen was standardised and mitochondrial primers with conserved binding sites were used. Family level correction factors for amplification bias and back-calculations were applied to estimate numbers of individuals of a given taxon in a sample. Estimates from metabarcoding reads and morphological assessment were positively correlated for relative family abundances as well as taxon richness (Rs=0.81, P=0.007) and diversity (Rs=0.88, P=0.003). After applying family level correction, back-estimates of the number of individuals per family within a sample were accurate to {+/-} 2 individuals. Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient and faster alternative to morphological identification that can be applied to terrestrial and aquatic habitats.

ecology↗

bioRxiv2019

Environmental plasticity and colonisation history in the Atlantic salmon microbiome: a translocation experiment

Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for non-mammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between captive and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for six weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterised the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive plasticity in both gut and skin microbiota, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable historical effects of fish origin. Microbiome structure was also strongly influenced by current environmental conditions but, for the first time in fish, we also found evidence of colonisation history, including a number of OTUs characteristic of captive rearing. These results may have important implications for host adaptation to local selective pressures, and also highlight how conditions during early life can have a long-term influence on the microbiome and, potentially, host health.

microbiology↗