The marine mammal microbiome: current knowledge and future directions

Nelson, Tiffanie M.; Apprill, Amy; Mann, Janet; Rogers, Tracey L.; Brown, Mark V.

doi:10.1071/ma15004

Cited by 62 publications

(60 citation statements)

References 56 publications

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“…The collection of bacterial microbiota is as an indicator of cetacean health is growing (Hogg et al, 2009;Schroeder et al, 2009;Acevedo-Whitehouse et al, 2010;Lima et al, 2012;Hunt et al, 2013;Nelson et al, 2015;Raverty et al, 2017). We were able to sample a number of individuals from a single population over a very short time frame.…”

Section: Discussionmentioning

confidence: 93%

An Economical Custom-Built Drone for Assessing Whale Health

Pirotta

Smith²,

Ostrowski

et al. 2017

Front. Mar. Sci.

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Drones or Unmanned Aerial Vehicles (UAVs) have huge potential to improve the safety and efficiency of sample collection from wild animals under logistically challenging circumstances. Here we present a method for surveying population health that uses UAVs to sample respiratory vapor, 'whale blow,' exhaled by free-swimming humpback whales (Megaptera novaeangliae), and coupled this with amplification and sequencing of respiratory tract microbiota. We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated 'blow' to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and dronecaptured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa. Whale-specific taxa included species and genera previously associated with the respiratory tracts or oral cavities of mammals (e.g., Pseudomonas, Clostridia, Cardiobacterium), as well as species previously isolated from dolphin or killer whale blowholes (Corynebacteria, others). Many examples of exogenous marine species were identified, including Tenacibaculum and Psychrobacter spp. that have been associated with the skin microbiota of marine mammals and fish and may include pathogens. This information provides a baseline of respiratory tract microbiota profiles of contemporary whale health. Customized UAVs are a promising new tool for marine megafauna research and may have broad application in cost-effective monitoring and management of whale populations worldwide.

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Section: Discussionmentioning

confidence: 93%

An Economical Custom-Built Drone for Assessing Whale Health

Pirotta

Smith²,

Ostrowski

et al. 2017

Front. Mar. Sci.

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“…Social and geographical factors have been found to influence microbial diversity in terrestrial and semiterrestrial animals (Koskella et al., ). However, there is less understanding of how these factors interplay in a wide‐ranging social marine mammalian system (Nelson, Apprill, Mann, Rogers, & Brown, ). We found that beta diversity of the killer whale skin microbiome was significantly influenced by ecotype and latitude.…”

Section: Discussionmentioning

confidence: 99%

“…Concordant with our results, a study of the microbiome of four captive killer whales and the sea water from their pool found that the skin microbiota were more diverse and phylogenetically distinct from the sea water microbial community (Chiarello et al., ). Killer whales are highly social mammals (Baird, ; Ford, ), and thus, they are likely to have a high potential for horizontal transfer of microbes between individuals during contact (Nelson et al., ). Ecotype‐specific social behaviour, organization and population structure, as well as other variables related to ecotype ecology, such as range size and diet (due to transmission of bacteria from different prey species; Wasimuddin et al., ), are all likely to affect the diversity of microbial species that individuals are exposed to and also influence the level of horizontal transfer of microbes between whales.…”

Section: Discussionmentioning

confidence: 99%

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

et al. 2018

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Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

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“…The microbiomes of marine mammals (phylum Chordata) ( Figure 3G) have recently been investigated and offer a comparative study system to terrestrial mammals (reviewed within Nelson et al, 2015). Marine mammals are often viewed as sentinel species of the ocean, because they appear to rapidly respond to ocean conditions, disturbances, and pathogens similarly to humans (Bossart, 2011).…”

Section: Overview Of Diverse and Emerging Animal-microbiome Study Sysmentioning

confidence: 99%

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

2017

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All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal-microbial relationships were historically explored in single host-symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment. This review explores the nature of marine animal-microbiome relationships and interactions, and possible factors that may shift associations from symbiotic to dissociated states. I present a brief review of current microbiome research and opportunities, using examples of select marine animals that span diverse phyla within the Animalia, including systems that are more and less developed for symbiosis research, including two represented in my own research program. Lastly, I consider challenges and emerging solutions for moving these and other study systems into a more detailed understanding of host-microbiome interactions within a changing ocean.

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The marine mammal microbiome: current knowledge and future directions

Cited by 62 publications

References 56 publications

An Economical Custom-Built Drone for Assessing Whale Health

An Economical Custom-Built Drone for Assessing Whale Health

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

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