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Zhong KX, Chan AM, Collicutt B, Daspe M, Finke JF, Foss M, Green TJ, Harley CDG, Hesketh AV, Miller KM, Otto SP, Rolheiser K, Saunders R, Sutherland BJG, Suttle CA. The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification. Appl Environ Microbiol 2024; 90:e0005224. [PMID: 38466091 PMCID: PMC11022565 DOI: 10.1128/aem.00052-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
Pacific oysters (Magallana gigas, a.k.a. Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and pCO2 levels (800, 1,600, and 2,800 µatm) in a fully crossed design for 3 weeks. Under all conditions, the microbiome changed over time, with a large decrease in the relative abundance of potentially pathogenic ciliates (Uronema marinum) in all treatments with time. The microbiome composition differed significantly with temperature, but not acidification, indicating that Pacific oyster spat microbiomes can be altered by ocean warming but is resilient to ocean acidification in our experiments. Microbial taxa differed in relative abundance with temperature, implying different adaptive strategies and ecological specializations among microorganisms. Additionally, a small proportion (~0.2% of the total taxa) of the relatively abundant microbial taxa were core constituents (>50% occurrence among samples) across different temperatures, pCO2 levels, or time. Some taxa, including A4b bacteria and members of the family Saprospiraceae in the phyla Chloroflexi (syn. Chloroflexota) and Bacteroidetes (syn. Bacteroidota), respectively, as well as protists in the genera Labyrinthula and Aplanochytrium in the class Labyrinthulomycetes, and Pseudoperkinsus tapetis in the class Ichthyosporea were core constituents across temperatures, pCO2 levels, and time, suggesting that they play an important, albeit unknown, role in maintaining the structural and functional stability of the Pacific oyster spat microbiome in response to ocean warming and acidification. These findings highlight the flexibility of the spat microbiome to environmental changes.IMPORTANCEPacific oysters are the most economically important and widely farmed species of oyster, and their production depends on healthy oyster spat. In turn, spat health and productivity are affected by the associated microbiota; yet, studies have not scrutinized the effects of temperature and pCO2 on the prokaryotic and eukaryotic microbiomes of spat. Here, we show that both the prokaryotic and, for the first time, eukaryotic microbiome of Pacific oyster spat are surprisingly resilient to changes in acidification, but sensitive to ocean warming. The findings have potential implications for oyster survival amid climate change and underscore the need to understand temperature and pCO2 effects on the microbiome and the cascading effects on oyster health and productivity.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy M. Chan
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Maxim Daspe
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan F. Finke
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Megan Foss
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Timothy J. Green
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Christopher D. G. Harley
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amelia V. Hesketh
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Sarah P. Otto
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Ben J. G. Sutherland
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada
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Park E, Leander B. Coinfection of slime feather duster worms (Annelida, Myxicola) by different gregarine apicomplexans ( Selenidium) and astome ciliates reflects spatial niche partitioning and host specificity. Parasitology 2024; 151:400-411. [PMID: 38465385 PMCID: PMC11044062 DOI: 10.1017/s0031182024000209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
Individual organisms can host multiple species of parasites (or symbionts), and one species of parasite can infect different host species, creating complex interactions among multiple hosts and parasites. When multiple parasite species coexist in a host, they may compete or use strategies, such as spatial niche partitioning, to reduce competition. Here, we present a host–symbiont system with two species of Selenidium (Apicomplexa, Gregarinida) and one species of astome ciliate co-infecting two different species of slime feather duster worms (Annelida, Sabellidae, Myxicola) living in neighbouring habitats. We examined the morphology of the endosymbionts with light and scanning electron microscopy (SEM) and inferred their phylogenetic interrelationships using small subunit (SSU) rDNA sequences. In the host ‘Myxicola sp. Quadra’, we found two distinct species of Selenidium; S. cf. mesnili exclusively inhabited the foregut, and S. elongatum n. sp. inhabited the mid to hindgut, reflecting spatial niche partitioning. Selenidium elongatum n. sp. was also present in the host M. aesthetica, which harboured the astome ciliate Pennarella elegantia n. gen. et sp. Selenidium cf. mesnili and P. elegantia n. gen. et sp. were absent in the other host species, indicating host specificity. This system offers an intriguing opportunity to explore diverse aspects of host–endosymbiont interactions and competition among endosymbionts.
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Affiliation(s)
- Eunji Park
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Hakai Institute, British Columbia, Canada
| | - Brian Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Hakai Institute, British Columbia, Canada
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3
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Graham OJ, Adamczyk EM, Schenk S, Dawkins P, Burke S, Chei E, Cisz K, Dayal S, Elstner J, Hausner ALP, Hughes T, Manglani O, McDonald M, Mikles C, Poslednik A, Vinton A, Wegener Parfrey L, Harvell CD. Manipulation of the seagrass-associated microbiome reduces disease severity. Environ Microbiol 2024; 26:e16582. [PMID: 38195072 DOI: 10.1111/1462-2920.16582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.
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Affiliation(s)
- Olivia J Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily M Adamczyk
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siobhan Schenk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phoebe Dawkins
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Samantha Burke
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily Chei
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kaitlyn Cisz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Sukanya Dayal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jack Elstner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Taylor Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Omisha Manglani
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Miles McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Chloe Mikles
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Anna Poslednik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Audrey Vinton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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McLaskey AK, Forster I, Hunt BPV. Distinct trophic ecologies of zooplankton size classes are maintained throughout the seasonal cycle. Oecologia 2024; 204:227-239. [PMID: 38219265 DOI: 10.1007/s00442-023-05501-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/10/2023] [Indexed: 01/16/2024]
Abstract
Marine food webs are strongly size-structured and size-based analysis of communities is a useful approach to evaluate food webs in a way that can be compared across systems. Fatty acid analysis is commonly used to identify diet sources of species, offering a powerful complement to stable isotopes, but is rarely applied to size-structured communities. In this study, we used fatty acids and stable isotopes to characterize size-based variation in prey resources and trophic pathways over a nine-month temperate coastal ocean time series of seven plankton size classes, from > 0.7-μm particulate organic matter through > 2000-μm zooplankton. Zooplankton size classes were generally distinguishable by their dietary fatty acids, while stable isotopes revealed more seasonal variability. Fatty acids of zooplankton were correlated with those of their prey (particulate organic matter and smaller zooplankton) and identified trophic pathways, including widespread ties to the microbial food web. Diatom fatty acids also contributed to zooplankton but fall blooms were more important than spring. Concurrent isotope-based trophic position estimates and fatty acid markers of carnivory showed that some indicators (18:1ω9/18:1ω7) are not consistent across size classes, while others (DHA:EPA) are relatively reliable. Both analysis methods provided distinct information to build a more robust understanding of resource use. For example, fatty acid markers showed that trophic position was likely underestimated in 250-μm zooplankton, probably due to their consumption of protists with low isotopic fractionation factors. Applying fatty acid analysis to a size-structured framework provides more insight into trophic pathways than isotopes alone.
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Affiliation(s)
- Anna K McLaskey
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada.
- Hakai Institute, Campbell River, BC, Canada.
| | - Ian Forster
- Pacific Science Enterprise Center, Fisheries and Oceans Canada, West Vancouver, BC, Canada
| | - Brian P V Hunt
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
- Hakai Institute, Campbell River, BC, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
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5
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Beaty F, Gehman ALM, Brownlee G, Harley CDG. Not just range limits: Warming rate and thermal sensitivity shape climate change vulnerability in a species range center. Ecology 2023; 104:e4183. [PMID: 37786322 DOI: 10.1002/ecy.4183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Climate change manifests unevenly across space and time and produces complex patterns of stress for ecological systems. Species can also show substantial among-population variability in response to environmental change across their geographic range due to evolutionary processes. Explanatory factors or their proxies, such as temperature and latitude, help parse these sources of environmental and intraspecific variability; however, overemphasizing latitudinal trends can obscure the role of local environmental conditions in shaping population vulnerability to climate change. Focusing on the geographic center of a species range to disentangle latitude, we test the hypothesis that populations from warmer regions of a species range are more vulnerable to ocean warming. We conducted a mesocosm experiment and field reciprocal transplant with four populations of a marine snail, Nucella lamellosa, from two regions in British Columbia, Canada, that differ in thermal characteristics: the Central Coast, a cool region, and the Strait of Georgia, one of the warmest regions of this species' range and one that is warming faster than the Central Coast. Populations from the Strait of Georgia experienced growth reductions at contemporary summertime seawater temperatures in the laboratory and showed stark reductions in survival and growth under future seawater conditions and when outplanted at their native transplant sites. This indicates a high vulnerability to ocean warming, especially given the faster rate of ocean warming in this region. In contrast, populations from the cooler Central Coast demonstrated high performance at contemporary seawater temperatures and high growth and survival in projected future seawater temperatures and at their native outplant sites. Given their position within the geographic center of N. lamellosa's range, extirpation events in the vulnerable Strait of Georgia populations could compromise connectivity within the metapopulation and lead to gaps across this species' range. Overall, our study supports predictions that populations from warm regions of species ranges are more vulnerable to environmental warming, suggests that the Strait of Georgia and other inland or coastal seas could be focal points for climate change effects and ecological transformation, and emphasizes the importance of analyzing climate change vulnerability in the context of regional environmental data and throughout a species' range.
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Affiliation(s)
- Fiona Beaty
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
- Institute for the Ocean and Fisheries, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
| | - Alyssa-Lois M Gehman
- Institute for the Ocean and Fisheries, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
- Hakai Institute, Quadra Island, British Columbia, Canada
| | - Graham Brownlee
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
| | - Christopher D G Harley
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
- Institute for the Ocean and Fisheries, University of British Columbia, Unceded xwməθkwəy̓əm (Musqueam) Territory, Vancouver, British Columbia, Canada
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Van Steenkiste NWL, Wakeman KC, Söderström B, Leander BS. Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa). Sci Rep 2023; 13:21050. [PMID: 38030717 PMCID: PMC10687266 DOI: 10.1038/s41598-023-48233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
Microturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of "gregarines", "sporozoans", and "apicomplexans" parasitizing microturbellarians in the literature-some of them dating back to the nineteenth century-these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.
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Affiliation(s)
- Niels W L Van Steenkiste
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada.
- Hakai Institute, Heriot Bay, Quadra Island, BC, Canada.
| | - Kevin C Wakeman
- Institute for the Advancement of High Education, Hokkaido University, Sapporo, Japan.
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Brian S Leander
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada
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Loudon AH, Park J, Parfrey LW. Identifying the core microbiome of the sea star Pisaster ochraceus in the context of sea star wasting disease. FEMS Microbiol Ecol 2023; 99:6998556. [PMID: 36690340 DOI: 10.1093/femsec/fiad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
Sea stars are keystone species and their mass die-offs due to sea star wasting disease (SSWD) impact marine communities and have fueled recent interest in the microbiome of sea stars. We assessed the host specificity of the microbiome associated with three body regions of the sea star Pisaster ochraceus using 16S rRNA gene amplicon surveys of the bacterial communities living on and in Pisaster, their environment, and sympatric marine hosts across three populations in British Columbia, Canada. Overall, the bacterial communities on Pisaster are distinct from their environment and differ by both body region and geography. We identified core bacteria specifically associated with Pisaster across populations and nearly absent in other hosts and the environment. We then investigated the distribution of these core bacteria on SSWD-affected Pisaster from one BC site and by reanalyzing a study of SSWD on Pisaster from California. We find no differences in the distribution of core bacteria in early disease at either site and two core taxa differ in relative abundance in advanced disease in California. Using phylogenetic analyses, we find that most core bacteria have close relatives on other sea stars and marine animals, suggesting these clades have evolutionary adaptions to an animal-associated lifestyle.
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Affiliation(s)
- Andrew H Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jungsoo Park
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Hakai Institute, PO Box 25039, Campbell River, BC V9W 0B7, Canada
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Reidy R, Gauthier S, Doniol-Valcroze T, Lemay MA, Clemente-Carvalho RBG, Cowen LLE, Juanes F. Integrating technologies provides insight into the subsurface foraging behaviour of a humpback whale (Megaptera novaeangliae) feeding on walleye pollock (Gadus chalcogrammus) in Juan de Fuca Strait, Canada. PLoS One 2023; 18:e0282651. [PMID: 36877706 PMCID: PMC9987809 DOI: 10.1371/journal.pone.0282651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/19/2023] [Indexed: 03/07/2023] Open
Abstract
Subsurface foraging is an important proportion of the activity budget of rorqual whales, yet information on their behaviour underwater remains challenging to obtain. Rorquals are assumed to feed throughout the water column and to select prey as a function of depth, availability and density, but there remain limitations in the precise identification of targeted prey. Current data on rorqual foraging in western Canadian waters have thus been limited to observations of prey species amenable to surface feeding, such as euphausiids and Pacific herring (Clupea pallasii), with no information on deeper alternative prey sources. We measured the foraging behaviour of a humpback whale (Megaptera novaeangliae) in Juan de Fuca Strait, British Columbia, using three complimentary methods: whale-borne tag data, acoustic prey mapping, and fecal sub-sampling. Acoustically detected prey layers were near the seafloor and consistent with dense schools of walleye pollock (Gadus chalcogrammus) distributed above more diffuse aggregations of pollock. Analysis of a fecal sample from the tagged whale confirmed that it had been feeding on pollock. Integrating the dive profile with the prey data revealed that the whale's foraging effort followed the general pattern of areal prey density, wherein the whale had a higher lunge-feeding rate at the highest prey abundance and stopped feeding when prey became limited. Our findings of a humpback whale feeding on seasonally energy-dense fish like walleye pollock, which are potentially abundant in British Columbia, suggests that pollock may be an important prey source for this rapidly growing whale population. This result is informative when assessing regional fishing activities for semi-pelagic species as well as the whales' vulnerability to fishing gear entanglements and feeding disturbances during a narrow window of prey acquisition.
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Affiliation(s)
- Rhonda Reidy
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
| | - Stéphane Gauthier
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, British Columbia, Canada
| | - Thomas Doniol-Valcroze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Matthew A. Lemay
- Hakai Institute Genomics Laboratory, Quadra Island, British Columbia, Canada
| | | | - Laura L. E. Cowen
- Department of Mathematics and Statistics, University of Victoria, Victoria, British Columbia, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. Microbiome 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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Drever CR, Cook-Patton SC, Akhter F, Badiou PH, Chmura GL, Davidson SJ, Desjardins RL, Dyk A, Fargione JE, Fellows M, Filewod B, Hessing-Lewis M, Jayasundara S, Keeton WS, Kroeger T, Lark TJ, Le E, Leavitt SM, LeClerc ME, Lemprière TC, Metsaranta J, McConkey B, Neilson E, St-Laurent GP, Puric-Mladenovic D, Rodrigue S, Soolanayakanahally RY, Spawn SA, Strack M, Smyth C, Thevathasan N, Voicu M, Williams CA, Woodbury PB, Worth DE, Xu Z, Yeo S, Kurz WA. Natural climate solutions for Canada. Sci Adv 2021; 7:7/23/eabd6034. [PMID: 34088658 PMCID: PMC8177698 DOI: 10.1126/sciadv.abd6034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/20/2021] [Indexed: 05/15/2023]
Abstract
Alongside the steep reductions needed in fossil fuel emissions, natural climate solutions (NCS) represent readily deployable options that can contribute to Canada's goals for emission reductions. We estimate the mitigation potential of 24 NCS related to the protection, management, and restoration of natural systems that can also deliver numerous co-benefits, such as enhanced soil productivity, clean air and water, and biodiversity conservation. NCS can provide up to 78.2 (41.0 to 115.1) Tg CO2e/year (95% CI) of mitigation annually in 2030 and 394.4 (173.2 to 612.4) Tg CO2e cumulatively between 2021 and 2030, with 34% available at ≤CAD 50/Mg CO2e. Avoided conversion of grassland, avoided peatland disturbance, cover crops, and improved forest management offer the largest mitigation opportunities. The mitigation identified here represents an important potential contribution to the Paris Agreement, such that NCS combined with existing mitigation plans could help Canada to meet or exceed its climate goals.
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Affiliation(s)
| | - Susan C Cook-Patton
- The Nature Conservancy, Arlington, VA, USA
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | | | - Pascal H Badiou
- Ducks Unlimited Canada, Institute for Wetland and Waterfowl Research, Stonewall, MB, Canada
| | | | | | | | - Andrew Dyk
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | | | - Max Fellows
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | | | | | | | | | | | - Tyler J Lark
- University of Wisconsin-Madison, Madison, WI, USA
| | - Edward Le
- Canadian Forest Service, Natural Resources Canada, Ottawa, ON, Canada
| | | | - Marie-Eve LeClerc
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Tony C Lemprière
- Canadian Forest Service, Natural Resources Canada, Toronto, ON, Canada
| | - Juha Metsaranta
- Canadian Forest Service, Natural Resources Canada, Edmonton, AB, Canada
| | | | - Eric Neilson
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | | | | | | | | | - Seth A Spawn
- University of Wisconsin-Madison, Madison, WI, USA
| | | | - Carolyn Smyth
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | | | - Mihai Voicu
- Canadian Forest Service, Natural Resources Canada, Edmonton, AB, Canada
| | | | | | - Devon E Worth
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Zhen Xu
- Canadian Forest Service, Natural Resources Canada, Ottawa, ON, Canada
| | | | - Werner A Kurz
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
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11
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Angel P, Herranz M, Leander BS. Insights into the Morphology of Haplozoan Parasites (Dinoflagellata) using Confocal Laser Scanning Microscopy. J Eukaryot Microbiol 2021; 68:e12855. [PMID: 33894083 DOI: 10.1111/jeu.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/26/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022]
Abstract
We describe new insights into the morphology and life history of the bizarre parasite Haplozoon axiothellae (Dinoflagellata) using light microscopy (LM), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). Trophonts were isolated from the intestines of host maldanid polychaetes, Axiothella rubrocincta, collected from San Juan Island, Washington, USA. LM and SEM confirmed features previously observed, such as amphiesmal projections, mature and immature junctions between the nucleated compartments of the vermiform syncytium and visible polygonal alveoli. CLSM of adult trophonts fluorescently stained for DNA, tubulin, centrin, and plasma membrane demonstrated several new ultrastructural traits: (1) an extensive basket of parallel microtubules within the trophomere used for host attachment, (2) two physically separated MTOCs (i.e. putative pairs of basal bodies) beneath pores on the ventral side of each compartment, (3) robust mitotic and/or meiotic spindles associated with one to four nuclei in each compartment, (4) spindles with polar bodies that are disconnected from the MTOCs, (5) a centrin-stained fibril within the trophomeres that potentially functions to retract the motile stylet, and (6) cytokinesis in the posterior-most compartments. This study renames haplozoan compartments using the suffix "-mere" rather than "-cyte" (i.e. trophomere, gonomere, sporomere) to reflect their status within a single syncytium.
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Affiliation(s)
- Phil Angel
- The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Maria Herranz
- The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Brian S Leander
- The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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12
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Friele P, Millard TH, Mitchell A, Allstadt KE, Menounos B, Geertsema M, Clague JJ. Observations on the May 2019 Joffre Peak landslides, British Columbia. Landslides 2020; 17:913-930. [PMID: 32355468 PMCID: PMC7175743 DOI: 10.1007/s10346-019-01332-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/26/2019] [Indexed: 06/11/2023]
Abstract
Two catastrophic landslides occurred in quick succession on 13 and 16 May 2019, from the north face of Joffre Peak, Cerise Creek, southern Coast Mountains, British Columbia. With headscarps at 2560 m and 2690 m elevation, both began as rock avalanches, rapidly transforming into debris flows along middle Cerise Creek, and finally into debris floods affecting the fan. Beyond the fan margin, a flood surge on Cayoosh Creek reached bankfull and attenuated rapidly downstream; only fine sediment reached Duffey Lake. The toe of the main debris flow deposit reached 4 km from the headscarp, with a travel angle of 0.28, while the debris flood phase reached the fan margin 5.9 km downstream, with a travel angle of 0.22. Photogrammetry indicates the source volume of each event is 2-3 Mm3, with combined volume of 5 Mm3. Lidar differencing, used to assess deposit volume, yielded a similar total result, although error in the depth estimate introduced large volume error masking the expected increase due to dilation and entrainment. The average velocity of the rock avalanche-debris flow phases, from seismic analysis, was ~ 25-30 m/s, and the velocity of the 16 May debris flood on the upper fan, from super-elevation and boulder sizes, was 5-10 m/s. The volume of debris deposited on the fan was ~ 104 m3, 2 orders of magnitude less than the avalanche/debris flow phases. Progressive glacier retreat and permafrost degradation were likely the conditioning factors; precursor rockfall activity was noted at least ~6 months previous; thus, the mountain was primed to fail. The 13 May landslide was apparently triggered by rapid snowmelt, with debuttressing triggering the 16 May event.
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Affiliation(s)
- Pierre Friele
- Cordilleran Geoscience, PO Box 612, Squamish, BC V8B 0A5 Canada
| | - Tom H. Millard
- BC Ministry of Forests Lands Natural Resource Operations and Rural Development (BC FLNRORD), 2100 Labieux Rd #103, Nanaimo, BC V9T 6E9 Canada
| | - Andrew Mitchell
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2207 Main Mall #2020, Vancouver, BC V6T 1Z4 Canada
| | - Kate E. Allstadt
- U.S. Geological Survey, Geologic Hazards Science Center, Box 25046, DFC, MS 966, Denver, CO 80225 USA
| | - Brian Menounos
- Geography Program and Natural Resources and Environmental Studies Institute, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9 Canada
| | - Marten Geertsema
- BC Ministry of Forests Lands Natural Resource Operations and Rural Development, 2000 Ospika Blvd S, Prince George, BC V2N 4W5 Canada
| | - John J. Clague
- Department of Earth Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6 Canada
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13
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Smith NF, Lepofsky D, Toniello G, Holmes K, Wilson L, Neudorf CM, Roberts C. 3500 years of shellfish mariculture on the Northwest Coast of North America. PLoS One 2019; 14:e0211194. [PMID: 30811412 PMCID: PMC6392220 DOI: 10.1371/journal.pone.0211194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 11/24/2022] Open
Abstract
Ancient systems of mariculture were foundations of social-ecological systems of many coastal Indigenous Peoples. However, since such systems either do not leave tangible remains in the archaeological record, and/or are hard to date, we know little about their development and use. Clam gardens, traditional mariculture features located within the intertidal zone along the Northwest Coast of North America, are composed of a rock wall positioned at the low tide mark and a flattened terrace on the landward side of the wall. Because these features are largely composed of rock and sediment, and have complex formation histories, they can be difficult to age. On northern Quadra Island, British Columbia, we identify three variations in clam garden form, constructed in different geomorphological settings, each of which require different sampling approaches to obtain ages on construction and ongoing use. To age the clam gardens, we consider radiocarbon dating of invertebrates that inhabit beach deposits (both pre- and post-garden construction), and the relationship of the gardens and clam samples to the local sea level history and taphonomic processes. Within our study area, we find clam gardens have been in use for 3500 years, likely corresponding to other social and ecological changes of the time. These data allow us to formulate guidelines on samples most suitable to constrain the age of initial and on-going wall construction and use of clam gardens, which can be extrapolated to dating other ancient mariculture features in other regions. Such dating programs are the foundation for understanding the long-term development of traditional marine management practices and how they are situated in broader social-ecological systems.
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Affiliation(s)
- Nicole F. Smith
- Hakai Institute, Heriot Bay, BC, Canada
- Independent Archaeologist, Victoria, BC, Canada
| | - Dana Lepofsky
- Hakai Institute, Heriot Bay, BC, Canada
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
- * E-mail:
| | - Ginevra Toniello
- Hakai Institute, Heriot Bay, BC, Canada
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
| | | | - Louie Wilson
- Hakai Institute, Heriot Bay, BC, Canada
- We Wai Kai Nation, Quathiaski Cove, BC, Canada
| | - Christina M. Neudorf
- Hakai Institute, Heriot Bay, BC, Canada
- Department of Geography and the Environment, University of the Fraser Valley, Abbotsford, BC, Canada
| | - Christine Roberts
- Hakai Institute, Heriot Bay, BC, Canada
- Wei Wai Kum First Nation, Campbell River, BC, Canada
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14
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Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. R Soc Open Sci 2018; 5:171707. [PMID: 29765641 PMCID: PMC5936906 DOI: 10.1098/rsos.171707] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/06/2018] [Indexed: 05/16/2023]
Abstract
Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of 'typical excavates', including flagellar vanes (as an opposed pair, unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of '-FS/LB' datasets instead suggested a relationship between malawimonads and metamonads. The 'malawimonad+metamonad signal' in morphological and molecular data argues against a strict Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes.
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Affiliation(s)
- Aaron A. Heiss
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Martin Kolisko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Fleming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Matthew W. Brown
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Andrew J. Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alastair G. B. Simpson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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15
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Artelle KA, Reynolds JD, Treves A, Walsh JC, Paquet PC, Darimont CT. Hallmarks of science missing from North American wildlife management. Sci Adv 2018; 4:eaao0167. [PMID: 29532032 PMCID: PMC5842039 DOI: 10.1126/sciadv.aao0167] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
Resource management agencies commonly defend controversial policy by claiming adherence to science-based approaches. For example, proponents and practitioners of the "North American Model of Wildlife Conservation," which guides hunting policy across much of the United States and Canada, assert that science plays a central role in shaping policy. However, what that means is rarely defined. We propose a framework that identifies four fundamental hallmarks of science relevant to natural resource management (measurable objectives, evidence, transparency, and independent review) and test for their presence in hunt management plans created by 62 U.S. state and Canadian provincial and territorial agencies across 667 management systems (species-jurisdictions). We found that most (60%) systems contained fewer than half of the indicator criteria assessed, with more criteria detected in systems that were peer-reviewed, that pertained to "big game," and in jurisdictions at increasing latitudes. These results raise doubt about the purported scientific basis of hunt management across the United States and Canada. Our framework provides guidance for adopting a science-based approach to safeguard not only wildlife but also agencies from potential social, legal, and political conflict.
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Affiliation(s)
- Kyle A. Artelle
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- Raincoast Conservation Foundation, P.O. Box 2429, Sidney, British Columbia V8L 3Y3, Canada
- Hakai Institute, P.O. Box 309, Heriot Bay, British Columbia V0P 1H0, Canada
| | - John D. Reynolds
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Adrian Treves
- Nelson Institute for Environmental Studies, University of Wisconsin–Madison, 30A Science Hall, 550 North Park Street, Madison, WI 53706, USA
| | - Jessica C. Walsh
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Paul C. Paquet
- Raincoast Conservation Foundation, P.O. Box 2429, Sidney, British Columbia V8L 3Y3, Canada
- Department of Geography, University of Victoria, P.O. Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2, Canada
| | - Chris T. Darimont
- Raincoast Conservation Foundation, P.O. Box 2429, Sidney, British Columbia V8L 3Y3, Canada
- Hakai Institute, P.O. Box 309, Heriot Bay, British Columbia V0P 1H0, Canada
- Department of Geography, University of Victoria, P.O. Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2, Canada
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16
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Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife 2014; 3:e03125. [PMID: 25171894 PMCID: PMC4164917 DOI: 10.7554/elife.03125] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus-host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.
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Affiliation(s)
- Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Monica Torres Beltran
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Patrick Schwientek
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | | | - Tanja Woyke
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
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