Michael P. Doane

Sydney Institute of Marine Science

The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbi...

Background: Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Bi...

Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated micro...

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiom...

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiom...

Chondrichthyes, an ancient and diverse class of vertebrates, are crucial to the health of marine ecosystems. Excessive demand for chondrichthyan products has increased fishing pressure, threatening ∼30% of species with extinction in recent decades. India is the second-largest shark landing nation globally and the province of Gujarat, is the largest...

In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An assoc...

Microbiomes share an intimate relationship with the organisms they colonize, even across evolutionary timescales. That’s the basis of a theory called phylosymbiosis. Phylosymbiosis holds that microbial communities evolve as their host evolves and has been confirmed to exist for certain insects and mammals. Researchers recently tested whether that r...

Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing th...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes...

We present the complete mitochondrial genome of the Sharpnose/Granulated Guitarfish Glaucostegus granulatus, obtained with whole genome shotgun sequencing of genomic DNA. The 16,547 bp long circular genome consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. A few protein-coding genes ended with incomp...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes a...

Background Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. Ho...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes a...

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that...

The Sharpnose Guitarfish (Glaucostegus granulatus) is one of fifteen critically endangered Rhino Rays which has been exploited as incidental catch, leading to severe population depletions and localized disappearances. Like many chondrichthyan species, there are no species-specific time-series data available for the Sharpnose Guitarfish that can be...

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficien...

Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments...

Background: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent i...

Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (...

Microbial taxa associated with the water column and kelp surface at the genera level from a six month in situ sampling in the Point Loma kelp forest. (TIF)

The proportion of reads that went into each bin for genus and function. (DOCX)

Setting an appropriate cutoff based on variability of rare features. The coefficient of variance as a function of relative abundances of (a) genera and (b) gene function Level 3 categories in three biological replicates across four environmental conditions (present-day ○, elevated temperature □, elevated pCO2 △, and future ◇) indicates a minimum cu...

Microbial taxa associated with the water column and kelp surface at the order level from a six month in situ sampling in the Point Loma kelp forest. (TIF)

Sequencing summary of water column and kelp surface microbiomes. (DOCX)

Background Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to...

The common thresher shark (Alopias vulpinus) is an important fisheries species in the northeastern Pacific Ocean along California, USA and Mexico; yet genetic understanding of this species is incomplete. Using IonTorrent PGM generated metagenomic libraries constructed from the skin surface, we recovered the complete mitogenome of the common threshe...

The percent cover of each replicate benthic organism

Phyla within the domain bacteria The average abundances of sequences at the phyla level within the domain Bacteria were compared between macro-organism aura-biomes. Asterisks above a domain designate a significance difference, while color delineates which samples varied.

Variation between the samples at the domain level The average abundances of sequences at the domain level were compared between macro-organism aura-biomes. Asterisks above a domain designate a significance difference, while color delineates which samples varied.

The summary statistics of the 16 metagenomes sequenced for the aura-biome analysis One standard error is provided for reads and GC content.

The top 100 genera between treatments The proportion of sequences in the top 100 genera found in each family in each metagenome, Mb, Mussismilia braziliensis; Fma, fleshy macroalgae; TA, turf algae; Pc, Palythoa caribaeorum and WC, water column.

Water physio-chemistry Water conditions were recorded for each dive with the Manta2 Series Multiprobe TM.

As coral reef habitats decline worldwide, some reefs are transitioning from coral-to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef orga...

The health of sharks is linked with emergent properties of its microbiome. Most marine organisms have mucus overlying the skin, but shark have dermal denticles that protrude above the mucus. We characterized the microbiome from the skin of the common thresher shark (Alopias vulpinus) to investigate the structure and composition of the skin microbio...