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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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2
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O'Mahony ÉN, Sremba AL, Keen EM, Robinson N, Dundas A, Steel D, Wray J, Baker CS, Gaggiotti OE. Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics. Mol Ecol Resour 2024:e13957. [PMID: 38576153 DOI: 10.1111/1755-0998.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.
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Affiliation(s)
- Éadin N O'Mahony
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - Angela L Sremba
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
- Cooperative Institute for Marine Ecosystem Resources, Oregon State University, Newport, Oregon, USA
| | - Eric M Keen
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
- Sewanee: The University of the South, Sewanee, Tennessee, USA
| | - Nicole Robinson
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Archie Dundas
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Janie Wray
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Oscar E Gaggiotti
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
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3
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Zhang X, Ying C, Jiang M, Lin D, You L, Yin D, Zhang J, Liu K, Xu P. The bacteria of Yangtze finless porpoise ( Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment. Front Microbiol 2022; 13:1006251. [PMID: 36605503 PMCID: PMC9808046 DOI: 10.3389/fmicb.2022.1006251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.
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Affiliation(s)
- Xizhao Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Congping Ying
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Min Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Lei You
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,*Correspondence: Kai Liu,
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,Pao Xu,
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5
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Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu. Appl Environ Microbiol 2022; 88:e0232821. [PMID: 35285714 DOI: 10.1128/aem.02328-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.
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6
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Atkinson S, Rogan A, Baker CS, Dagdag R, Redlinger M, Polinski J, Urban J, Sremba A, Branson M, Mashburn K, Pallin L, Klink A, Steel D, Bortz E, Kerr I. Genetic, Endocrine, and Microbiological Assessments of Blue, Humpback and Killer Whale Health using Unoccupied Aerial Systems. WILDLIFE SOC B 2021. [DOI: 10.1002/wsb.1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shannon Atkinson
- University of Alaska Fairbanks, College of Fisheries and Ocean Sciences 17101 Pt Lena Loop Rd. Juneau AK 99801 USA
| | | | - C. Scott Baker
- Marine Mammal Institute Oregon State University, Hatfield Marine Science Center 2030 SE Marine Science Dr. Newport OR 97365 USA
| | - Ralf Dagdag
- University of Alaska Anchorage, Department of Biological Sciences 3211 Providence Dr. Anchorage AK 99508 USA
| | - Matthew Redlinger
- University of Alaska Anchorage, Department of Biological Sciences 3211 Providence Dr. Anchorage AK 99508 USA
| | - Jennifer Polinski
- Gloucester Marine Genomics Institute, 417 Main St Gloucester MA 01930 USA
| | - Jorge Urban
- Universidad Autónoma de Baja California Sur, Departamento Académico de Ciencias Marinas y Costeras, La Paz Baja California Sur México
| | - Angie Sremba
- Marine Mammal Institute Oregon State University, Hatfield Marine Science Center 2030 SE Marine Science Dr. Newport OR 97365 USA
| | - Maile Branson
- University of Alaska Fairbanks, Department of Biology and Wildlife 2090 Koyukuk Dr. Fairbanks AK 99775 USA
| | - Kendall Mashburn
- University of Alaska Fairbanks, College of Fisheries and Ocean Sciences 17101 Pt Lena Loop Rd. Juneau AK 99801 USA
| | - Logan Pallin
- Marine Mammal Institute Oregon State University, Hatfield Marine Science Center 2030 SE Marine Science Dr. Newport OR 97365 USA
| | - Amy Klink
- University of Alaska Anchorage, Department of Biological Sciences 3211 Providence Dr. Anchorage AK 99508 USA
| | - Debbie Steel
- Marine Mammal Institute Oregon State University, Hatfield Marine Science Center 2030 SE Marine Science Dr. Newport OR 97365 USA
| | - Eric Bortz
- University of Alaska Anchorage, Department of Biological Sciences 3211 Providence Dr. Anchorage AK 99508 USA
| | - Iain Kerr
- Ocean Alliance Gloucester MA 01930 USA
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7
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M. Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J. Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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Ding J, Sun H, Liang A, Liu J, Song L, Lv M, Zhu D. Testosterone amendment alters metabolite profiles of the soil microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:115928. [PMID: 33139098 DOI: 10.1016/j.envpol.2020.115928] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/23/2020] [Accepted: 10/24/2020] [Indexed: 05/24/2023]
Abstract
Steroid hormones are prevalent in the environment and have become emerging pollutants, but little is known about their effects on soil microbial community composition and function. In the present study, three representative soils in China were amended with environmentally relevant concentrations of testosterone and responses of soil bacterial community composition and soil function were assessed using high-throughput sequencing and nontargeted metabolomics. Our results showed that testosterone exposure significantly shifted bacterial community structure and metabolic profiles in soils at Ningbo (NB) and Kunming (KM), which may reflect high bioavailability of the hormone. Abundances of several bacterial taxa associated with nutrient cycling were reduced by testosterone and metabolites related to amino acid metabolism were downregulated. A close connection between bacterial taxa and specific metabolites was observed and confirmed by Procrustes tests and a co-occurrence network. These results provide an insight into the effects of steroid hormones on soil microbial community and highlight that nontargeted metabolomics is an effective tool for investigating the impacts of pollutants.
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Affiliation(s)
- Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Aiping Liang
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Jin Liu
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Lehui Song
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| | - Min Lv
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
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9
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Van Cise AM, Wade PR, Goertz CEC, Burek-Huntington K, Parsons KM, Clauss T, Hobbs RC, Apprill A. Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics. Anim Microbiome 2020; 2:39. [PMID: 33499987 PMCID: PMC7807513 DOI: 10.1186/s42523-020-00057-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/08/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Host-specific microbiomes play an important role in individual health and ecology; in marine mammals, epidermal microbiomes may be a protective barrier between the host and its aqueous environment. Understanding these epidermal-associated microbial communities, and their ecological- or health-driven variability, is the first step toward developing health indices for rapid assessment of individual or population health. In Cook Inlet, Alaska, an endangered population of beluga whales (Delphinapterus leucas) numbers fewer than 300 animals and continues to decline, despite more than a decade of conservation effort. Characterizing the epidermal microbiome of this species could provide insight into the ecology and health of this endangered population and allow the development of minimally invasive health indicators based on tissue samples. RESULTS We sequenced the hypervariable IV region of bacterial and archaeal SSU rRNA genes from epidermal tissue samples collected from endangered Cook Inlet beluga whales (n = 33) and the nearest neighboring population in Bristol Bay (n = 39) between 2012 and 2018. We examined the sequences using amplicon sequence variant (ASV)-based analyses, and no ASVs were associated with all individuals, indicating a greater degree of epidermal microbiome variability among beluga whales than in previously studied cetacean species and suggesting the absence of a species-specific core microbiome. Epidermal microbiome composition differed significantly between populations and across sampling years. Comparing the microbiomes of Bristol Bay individuals of known health status revealed 11 ASVs associated with potential pathogens that differed in abundance between healthy individuals and those with skin lesions or dermatitis. Molting and non-molting individuals also differed significantly in microbial diversity and the abundance of potential pathogen-associated ASVs, indicating the importance of molting in maintaining skin health. CONCLUSIONS We provide novel insights into the dynamics of Alaskan beluga whale epidermal microbial communities. A core epidermal microbiome was not identified across all animals. We characterize microbial dynamics related to population, sampling year and health state including level of skin molting. The results of this study provide a basis for future work to understand the role of the skin microbiome in beluga whale health and to develop health indices for management of the endangered Cook Inlet beluga whales, and cetaceans more broadly.
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Affiliation(s)
- Amy M Van Cise
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- North Gulf Oceanic Society, Visiting Scientist at Northwest Fisheries Science Center, NOAA National Marine Fisheries Service, Seattle, WA, USA.
| | - Paul R Wade
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Seattle, WA, USA
| | | | | | - Kim M Parsons
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Seattle, WA, USA
- Conservation Biology Division, Northwest Fisheries Science Center, NOAA National Marine Fisheries Service, Seattle, WA, USA
| | - Tonya Clauss
- Animal & Environmental Heath, Georgia Aquarium, Atlanta, GA, USA
| | - Roderick C Hobbs
- Marine Mammal Laboratory (retired), Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Seattle, WA, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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10
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Vendl C, Slavich E, Nelson T, Acevedo-Whitehouse K, Montgomery K, Ferrari B, Thomas T, Rogers T. Does sociality drive diversity and composition of airway microbiota in cetaceans? ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:324-333. [PMID: 32162479 DOI: 10.1111/1758-2229.12835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/25/2020] [Accepted: 03/09/2020] [Indexed: 05/23/2023]
Abstract
The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.
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Affiliation(s)
- Catharina Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Eve Slavich
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, UNSW, 2052, Australia
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Building G40, Level 9, Gold Coast Campus, Griffith University, Southport, QLD, 4215, Australia
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, 76230, Mexico
| | - Kate Montgomery
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Belinda Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
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Ozkan J, Coroneo M, Sandbach J, Subedi D, Willcox M, Thomas T. Bacterial contamination of intravitreal needles by the ocular surface microbiome. Ocul Surf 2020; 19:169-175. [PMID: 32497656 DOI: 10.1016/j.jtos.2020.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 12/28/2022]
Abstract
PURPOSE The ocular surface microbiota are recognised as one of causative microorganisms in post-procedural endophthalmitis but in many cases the vitreous tap is culture negative. This study investigated bacterial contamination of intravitreal (IVT) needles using multiple approaches covering culturing, 16S rRNA gene sequencing, fluorescent in situ hybridisation (FISH) and scanning electron microscopy (SEM). METHODS IVT needles were obtained immediately after injection from patients undergoing treatment for predominantly age-related macular degeneration. Eighteen needles were analysed by culturing on chocolate blood agar. In addition, 40 needles were analysed by extracting DNA and paired-end sequencing of the 16S rRNA gene. Sequences were quality filtered (USEARCH), taxonomically classified (SILVA) and contaminant filtered (DECONTAM). Nine needles were analysed by either FISH using the bacterial probe EUB338 or SEM. RESULTS Using culturing, three bacteria were identified from 5 of 18 needles (28%) - Kocuria kristinae, Staphylococcus hominis and Sphingomonas paucimobilis. The negative control needles showed no growth. Following rigorous data filtering, bacterial community analysis using 16S rRNA gene sequencing showed the presence of predominantly Corynebacterium but also Pseudomonas, Acinetobacter, Sphingomonas, Staphylococcus and Bacillus on the needles. Cocci-shaped cells in a tetrad formation were observed using FISH, while SEM images showed cocci-shaped bacteria in pairs and irregular tetrads. CONCLUSIONS The study showed evidence for a large diversity of bacteria on IVT needles and visually confirmed their adherence. The diversity was similar to that found on the ocular surface and in conjunctival tissue. This suggests the risk of exogenous endophthalmitis remains even with sterilization of the conjunctival surface.
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Affiliation(s)
- Jerome Ozkan
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.
| | - Minas Coroneo
- Department of Ophthalmology, Prince of Wales Hospital, University of New South Wales, Sydney, Australia
| | - Jennifer Sandbach
- Department of Ophthalmology, Prince of Wales Hospital, University of New South Wales, Sydney, Australia
| | - Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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12
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Palmer R, Fleming GTA, Glaeser S, Semmler T, Flamm A, Ewers C, Kämpfer P, Budich O, Berrow S, O'Brien J, Siebert U, Collins E, Ruttledge M, Eisenberg T. Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon. DISEASES OF AQUATIC ORGANISMS 2020; 139:161-174. [PMID: 32406871 DOI: 10.3354/dao03478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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Affiliation(s)
- Roy Palmer
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland
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