Aimee van der Reis

University of Auckland · Institute of Marine Science

Plankton are central to planetary ecology, generating 50% of Earth's atmospheric oxygen and forming the largest system of interconnected life at the base of the marine food chain. Yet, current oceanographic models aimed at predicting global climate change lack high-resolution biological data, emphasizing the need for innovative approaches to collec...

Deep-sea benthic ecosystems are difficult to study, particularly when trying to clarify diet and trophic relationships. New Zealand scampi Metanephrops challengeri are endemic, commercially prized deep-sea lobsters that are bottom trawled. These lobsters are typically the dominant mobile megafaunal species in the deep-sea benthic habitat, and their...

Background: Probiotics are effective to rectify the imbalanced gut microbiota in the diseased cohorts. Two Bifidobacterium strains (LI09 and LI10) were found to alleviate D-galactosamine-induced liver damage (LD) in rats in our previous work. A series of bioinformatic and statistical analyses were performed to determine the vital bacteria in the g...

DNA metabarcoding is now a well-established method that uses DNA sequencing techniques and bioinformatics to identify a wide variety of species from mixed samples, such as gut content and sea water samples. A major benefit of this method is its sensitivity, which allows the detection of the presence of animals in the sampled environment, without ha...

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary i...

PCR profile designed for the optimum DNA amplification using either the COI or 18S primers (A) Initial denaturation at 95 °C for 60 s. (B) 20 “touch-up” cycles, with each cycle having a denaturation step at 95 °C for 30 s, an annealing step starting at 45 °C for 30 s (each annealing cycle increases 1 °C every cycle) and a final extension step at 72...

The DNA concentration and purity ratios per individual for each digesta source Nucleic acids have strong absorbance at 260 nm, which is also the wavelength where purines and pyrimidines peak. At 280 nm, proteins and phenolic compounds have a strong absorbance. Pure DNA should ideally be 1.8 for A260/A280 (Watts, 2014).

18S diet reads 18S genus reads were filtered from the 18S cleaned reads and then categorized into DNA negative reads, lobster and/or terrestrial reads and diet reads.

Taxa identified as diet taxa (genus and/or species level) from the COI databases The taxa are separated into their OTUs with their assigned taxonomic identity, hit counts, Midori RDP confidence levels, NCBI e-values and grouping.

COI diet sequences COI OTUs, assigned sequences (genus and/or species level) and their GC percentage.

The DNA concentration and purity ratios per individual per DNA extraction kit Nucleic acids have strong absorbance at 260 nm, which is also the wavelength where purines and pyrimidines peak. At 280 nm, proteins and phenolic compounds have a strong absorbance. Pure DNA should ideally be 1.8 for A260/A280 (Watts, 2014).

Bioline reaction Reagent volumes and concentrations used in a 25 µl Bioline reaction.

Processed reads for COI and 18S Resulting totals for paired, merged and cleaned reads for COI and 18S.

18S diet sequences 18S OTUs, assigned sequences (genus and/or species level) and their GC percentage.

Platinum Taq reaction Reagent volumes and concentrations used in a 25 µl Platinum Taq reaction.

Taxa identified as diet taxa (genus and/or species level) from the 18S databases The taxa are separated into their OTUs with their assigned taxonomic identity, hit counts, SILVA RDP confidence levels, PR2 RDP confidence levels, NCBI e-values and grouping.