1
|
Bonacolta AM, Krause-Massaguer J, Smit NJ, Sikkel PC, Del Campo J. A new and widespread group of fish apicomplexan parasites. Curr Biol 2024; 34:2748-2755.e3. [PMID: 38821048 DOI: 10.1016/j.cub.2024.04.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexans are obligate intracellular parasites that have evolved from a free-living, phototrophic ancestor. They have been reported from marine environmental samples in high numbers,1 with several clades of apicomplexan-related lineages (ARLs) having been described from environmental sequencing data (16S rRNA gene metabarcoding).2 The most notable of these are the corallicolids (previously ARL-V), which possess chlorophyll-biosynthesis genes in their relic chloroplast (apicoplast) and are geographically widespread and abundant symbionts of anthozoans.3 Corallicolids are related to the Eimeriorina, a suborder of apicomplexan coccidians that include other notable members such as Toxoplasma gondii.4Ophioblennius macclurei, the redlip blenny, along with other tropical reef fishes, is known to be infected by Haemogregarina-like and Haemohormidium-like parasites5 supposedly belonging to the Adeleorina; however, phylogenetics shows that these parasites are instead related to the Eimeriorina.6,7 Hybrid genomic sequencing of apicomplexan-infected O. macclurei blood recovered the entire rRNA operon of this apicomplexan parasite along with the complete mitochondrion and apicoplast genomes. Phylogenetic analyses using this new genomic information consistently place these fish-infecting apicomplexans, hereby informally named ichthyocolids, sister to the corallicolids within Coccidia. The apicoplast genome did not contain chlorophyll biosynthesis genes, providing evidence for another independent loss of this pathway within Apicomplexa. Based on the 16S rRNA gene found in the apicoplast, this group corresponds to the previously described ARL-VI. Screening of fish microbiome studies using the plastid 16S rRNA gene shows these parasites to be geographically and taxonomically widespread in fish species across the globe with implications for commercial fisheries and oceanic food webs.
Collapse
Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Joana Krause-Massaguer
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Nico J Smit
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Paul C Sikkel
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain.
| |
Collapse
|
2
|
Gruber-Vodicka H, Berndt H, Duarte I. Symbiosis: Aquatic apicomplexans shedding light on disguised associations. Curr Biol 2024; 34:R576-R578. [PMID: 38889680 DOI: 10.1016/j.cub.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Aquatic apicomplexans called Corallicolida have been found in tropical and coral-reef settings, infecting many coral species. New data challenge this tropical distribution and expand the corallicolids' range well into the cold temperate. Surprisingly, the sister clade to corallicolids infects only one group of vertebrates - bony fishes.
Collapse
Affiliation(s)
| | - Henry Berndt
- Marine Symbiosis Group, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Igor Duarte
- Marine Symbiosis Group, Zoological Institute, Kiel University, 24118 Kiel, Germany
| |
Collapse
|
3
|
Vohsen SA, Herrera S. Coral microbiomes are structured by environmental gradients in deep waters. ENVIRONMENTAL MICROBIOME 2024; 19:38. [PMID: 38858739 PMCID: PMC11165896 DOI: 10.1186/s40793-024-00579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/02/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing. RESULTS Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. CONCLUSIONS Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.
Collapse
Affiliation(s)
- Samuel A Vohsen
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
| | - Santiago Herrera
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
| |
Collapse
|
4
|
Trznadel M, Holt CC, Livingston SJ, Kwong WK, Keeling PJ. Coral-infecting parasites in cold marine ecosystems. Curr Biol 2024; 34:1810-1816.e4. [PMID: 38608678 DOI: 10.1016/j.cub.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Coral reefs are a biodiversity hotspot,1,2 and the association between coral and intracellular dinoflagellates is a model for endosymbiosis.3,4 Recently, corals and related anthozoans have also been found to harbor another kind of endosymbiont, apicomplexans called corallicolids.5 Apicomplexans are a diverse lineage of obligate intracellular parasites6 that include human pathogens such as the malaria parasite, Plasmodium.7 Global environmental sequencing shows corallicolids are tightly associated with tropical and subtropical reef environments,5,8,9 where they infect diverse corals across a range of depths in many reef systems, and correlate with host mortality during bleaching events.10 All of this points to corallicolids being ecologically significant to coral reefs, but it is also possible they are even more widely distributed because most environmental sampling is biased against parasites that maintain a tight association with their hosts throughout their life cycle. We tested the global distribution of corallicolids using a more direct approach, by specifically targeting potential anthozoan host animals from cold/temperate marine waters outside the coral reef context. We found that corallicolids are in fact common in such hosts, in some cases at high frequency, and that they infect the same tissue as parasites from topical coral reefs. Parasite phylogeny suggests corallicolids move between hosts and habitats relatively frequently, but that biogeography is more conserved. Overall, these results greatly expand the range of corallicolids beyond coral reefs, suggesting they are globally distributed parasites of marine anthozoans, which also illustrates significant blind spots that result from strategies commonly used to sample microbial biodiversity.
Collapse
Affiliation(s)
- Morelia Trznadel
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Corey C Holt
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samuel J Livingston
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Waldan K Kwong
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
5
|
Bonacolta AM, Miravall J, Gómez-Gras D, Ledoux JB, López-Sendino P, Garrabou J, Massana R, Del Campo J. Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata. Environ Microbiol 2024; 26:e16548. [PMID: 38072822 DOI: 10.1111/1462-2920.16548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/21/2023] [Indexed: 01/30/2024]
Abstract
Paramuricea clavata is an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. The microbiome may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat stress. To investigate this, the prokaryotic and eukaryotic microbiome of P. clavata collected from around the Mediterranean was characterised before experimental heat stress to determine if its microbial composition influences the thermal response of the holobiont. We found that members of P. clavata's microeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from the Dino-Group I Clade 1 were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. We hypothesise that P. clavata mortality following heat stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provide a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.
Collapse
Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
- Programa de Biodiversiat, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Jordi Miravall
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Daniel Gómez-Gras
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawaii, USA
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBIO), Universitat de Barcelona, Barcelona, Spain
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Paula López-Sendino
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Joaquim Garrabou
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Catalonia, Spain
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
- Programa de Biodiversiat, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| |
Collapse
|
6
|
McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
Collapse
Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| |
Collapse
|
7
|
Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
Collapse
Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| |
Collapse
|
8
|
Shimpi GG, Bentlage B. Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes. Bioessays 2023; 45:e2200190. [PMID: 36412071 DOI: 10.1002/bies.202200190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
Collapse
|
9
|
Sivakumar T, Tuvshintulga B, Otgonsuren D, Batmagnai E, Ahedor B, Kothalawala H, Vimalakumar SC, Silva SSP, Yamagishi J, Yokoyama N. Phylogenetic analyses of the mitochondrial, plastid, and nuclear genes of Babesia sp. Mymensingh and its naming as Babesia naoakii n. sp. Parasit Vectors 2022; 15:299. [PMID: 36002908 PMCID: PMC9404586 DOI: 10.1186/s13071-022-05374-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/26/2022] [Indexed: 12/05/2022] Open
Abstract
Background The recently discovered Babesia sp. Mymensingh, which causes clinical bovine babesiosis, has a wide geographical distribution. We investigated the phylogenetic position of Babesia sp. Mymensingh using its mitochondrial, plastid, and nuclear genes. Based on morphological and molecular data, Babesia sp. Mymensingh is a unique species and we named it as Babesia naoakii n. sp. Methods A blood DNA sample from a Babesia sp. Mymensingh-infected cow was subjected to genome sequencing to obtain the sequences of mitochondrial, plastid, and nuclear genes. Six phylogenetic trees were then constructed with (1) concatenated amino acid sequences of cytochrome oxidase subunit I, cytochrome oxidase subunit III, and cytochrome b genes of the mitochondrial genome; (2) 16S rRNA of the plastid genome; (3) nucleotide sequences of the elongation factor Tu gene of the plastid genome; (4) ITS1-5.8S rRNA-ITS2; (5) concatenated nucleotide sequences of 89 nuclear genes; and (6) concatenated amino acid sequences translated from the 89 nuclear genes. Results In all six phylogenetic trees, B. naoakii n. sp. formed a sister clade to the common ancestor of Babesia bigemina and B. ovata. The concatenated nuclear genes of B. naoakii n. sp. and their translated amino acid sequences shared lower identity scores with the sequences from B. bigemina (82.7% and 84.7%, respectively) and B. ovata (83.5% and 85.5%, respectively) compared with the identity scores shared between the B. bigemina and B. ovata sequences (86.3% and 87.9%, respectively). Conclusions Our study showed that B. naoakii n. sp. occupies a unique phylogenetic position distinct from existing Babesia species. Our findings, together with morphological differences, identify B. naoakii n. sp. as a distinct parasite species. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05374-9.
Collapse
Affiliation(s)
- Thillaiampalam Sivakumar
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Bumduuren Tuvshintulga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Davaajav Otgonsuren
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Enkhbaatar Batmagnai
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Believe Ahedor
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | | | | | | | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Naoaki Yokoyama
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan. .,OIE Reference Laboratory for Bovine Babesiosis, National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.
| |
Collapse
|
10
|
Maire J, Buerger P, Chan WY, Deore P, Dungan AM, Nitschke MR, van Oppen MJH. Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome. Integr Comp Biol 2022; 62:1700-1709. [PMID: 35259253 PMCID: PMC9801979 DOI: 10.1093/icb/icac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 01/05/2023] Open
Abstract
The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
Collapse
Affiliation(s)
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pranali Deore
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashley M Dungan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| |
Collapse
|
11
|
Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
12
|
|
13
|
Kwong WK, Irwin NAT, Mathur V, Na I, Okamoto N, Vermeij MJA, Keeling PJ. Taxonomy of the Apicomplexan Symbionts of Coral, including Corallicolida ord. nov., Reassignment of the Genus Gemmocystis, and Description of New Species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov. J Eukaryot Microbiol 2021; 68:e12852. [PMID: 33768669 DOI: 10.1111/jeu.12852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called "corallicolids", are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.
Collapse
Affiliation(s)
- Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ina Na
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Mark J A Vermeij
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, Amsterdam, 1098 XH, The Netherlands
- CARMABI Foundation, PO Box 2090, Piscaderabaai z/n, Willemstad, Curaçao
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| |
Collapse
|
14
|
Peixoto RS, Sweet M, Villela HDM, Cardoso P, Thomas T, Voolstra CR, Høj L, Bourne DG. Coral Probiotics: Premise, Promise, Prospects. Annu Rev Anim Biosci 2020; 9:265-288. [PMID: 33321044 DOI: 10.1146/annurev-animal-090120-115444] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.
Collapse
Affiliation(s)
- Raquel S Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,IMAM-AquaRio, Rio de Janeiro Aquarium Research Center, Rio de Janeiro, 20220-360, Brazil.,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, United Kingdom
| | - Helena D M Villela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Pedro Cardoso
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78457, Germany.,Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| |
Collapse
|
15
|
van de Water JAJM, Coppari M, Enrichetti F, Ferrier-Pagès C, Bo M. Local Conditions Influence the Prokaryotic Communities Associated With the Mesophotic Black Coral Antipathella subpinnata. Front Microbiol 2020; 11:537813. [PMID: 33123099 PMCID: PMC7573217 DOI: 10.3389/fmicb.2020.537813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/09/2020] [Indexed: 12/31/2022] Open
Abstract
Black corals are important habitat-forming species in the mesophotic and deep-sea zones of the world’s oceans because of their arborescent colony structure and tendency to form animal forests. Although we have started unraveling the ecology of mesophotic black corals, the importance of the associated microbes to their health has remained unexplored. Here, we provide in-depth assessments of black coral-microbe symbioses by investigating the spatial and temporal stability of these associations, and make comparisons with a sympatric octocoral with similar colony structure. To this end, we collected samples of Antipathella subpinnata colonies from three mesophotic shoals situated along the Ligurian Coast of the Mediterranean Sea (Bordighera, Portofino, Savona) in the spring of 2017. At the Portofino shoal, samples of A. subpinnata and the gorgonian Eunicella cavolini were collected in November 2016 and May 2017. Bacterial communities were profiled using 16S rRNA gene amplicon sequencing. The bacterial community of E. cavolini was consistently dominated by Endozoicomonas. Contrastingly, the black coral microbiome was more diverse, and was primarily composed of numerous Bacteroidetes, Alpha- and Gammaproteobacterial taxa, putatively involved in all steps of the nitrogen and sulfur cycles. Compositional differences in the A. subpinnata microbiome existed between all locations and both time points, and no phylotypes were consistently associated with A. subpinnata. This highlights that local conditions may influence the bacterial community structure and potentially nutrient cycling within the A. subpinnata holobiont. But it also suggests that this coral holobiont possesses a high degree of microbiome flexibility, which may be a mechanism to acclimate to environmental change.
Collapse
Affiliation(s)
| | - Martina Coppari
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, Genova, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare, Rome, Italy
| | - Francesco Enrichetti
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, Genova, Italy
| | | | - Marzia Bo
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, Genova, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare, Rome, Italy
| |
Collapse
|